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Tracing the symptomology of predation through macroscopic plaquesA culture bioassay (Expanded Microcoleus Mortality Assay, or EMMA) (Fig. 1 and see Materials and Methods) based on the capacity of a soil to induce complete mortality in the foundational biocrust cyanobacterium Microcoleus vaginatus helped us trace the pathogen detected in biocrust production facilities to the development of cm-sized plaques, or zones of cyanobacterial clearing, in natural biocrusts. These plaques were revealed to the naked eye (Fig. 2) when the soil was wet (i.e., after a rain event), as impacted areas would fail to green up by the migration of cyanobacteria to the surface21, enabling us to detect and quantify them with relative ease. Soil samples obtained from such plaques (n = 30) from different sites (n = 6; Table S1) in the US Southwest were invariably EMMA + , and the pathogens always filterable with pore sizes 0.45–1 µm but not larger, and always insensitive to the eukaryotic inhibitor cycloheximide, indicating the agent’s prokaryotic nature and small size, while paired samples from asymptomatic areas just outside the plaques were always EMMA- (Table S2). These end-point EMMA solutions never gave rise to cyanobacterial re-growth upon further incubation and maintained its infectivity of fresh cyanobacterial cultures for up to 6 months. A one-time, small-scale sampling across a plaque at intervals of 2 mm using microcoring22 showed that the boundary of the visible plaque demarcated exactly the end of infectivity, samples 0–2 mm outside the plaque proving non-infective. Further, inoculation of healthy, natural biocrusts with EMMA + suspensions resulted in the local development of biocrust plaques, and soil from these plaques was itself EMMA + , in partial fulfillment of Koch’s postulates. Yet, standard microbiological plating failed to yield any isolates that were EMMA + (we tested 30 unique isolates), even though standard plating with similar isolation efforts can successfully cultivate a large portion of heterotrophs from biocrusts23.Fig. 1: EMMA bioassay (Expanded Microcoleus Mortality Assay), used to study biocrust pathogens.a Typical visual progression of a positive EMMA inoculated with soil or culture to be tested, as used to test for pathogenicity to Microcoleus vaginatus PPC 9802 in the field and in enrichments. b Typical degradation of cyanobacterial biomass during an EMMA displayed through electron microscopy: healthy Microcoleus vaginatus PPC 9802 filaments (top) display abundant photosynthetic membranes (white arrows), peptidoglycan cross-walls (yellow arrows) and carboxysomes (green arrow). As infection proceeds (downwards), patent degradation of intracellular structures follows, leaving only cellular ghosts in the form of peptidoglycan wall remnants (yellow arrows), including the characteristically enlarged peptidoglycan “bumper” of terminal cells (red arrow). Intracellular bacilloid bacteria can sometimes be observed (blue arrow). Cyanobacterial cultures lose all viability. Scale bars = 1 µm. n = 250 images from 4 independent experiments. c Assay modification used in flow cytometry/cell sorting, showing enrichments positive for predation in the top two rows and those negative for predation below. d Test and controls in EMMA to ensure prokaryotic nature of the disease agent.Full size imageFig. 2: Symptomology in nature: biocrust plaques.Main: Macroscopic view of a soil surface colonized by cyanobacterial biocrusts and impacted by multiple plaques as taken after a rain in a quadrat used for field surveys. Insert: Close-up of a single plaque, showing well-demarcated boundaries and a typical central area of new cyanobacterial colonization.Full size imageCultivation, identification, and salient genomic traits of the cyanobacterial pathogenTo study these organisms, we turned to enrichment of pathogen/prey co-cultures based on repeated passages through EMMA and differential size filtration combined with dilution-to-extinction approaches, followed by purification with flow cytometry/cell sorting. The process was monitored by 16S rRNA gene amplicon sequencing, and eventually yielded a highly enriched co-culture of the cyanobacterium with a genetically homogenous (one single Amplicon Sequence Variant) population that made up more than 80% of reads (Fig. 3 a, b). We name the organism represented by this ASV Candidatus Cyanoraptor togatus. That it corresponds indeed to the predator is supported by the fact that of the 17 ASV’s detected in the final enrichment, only 10 were consistently detected at all infectious stages in the process and, among these, only our candidate ASV steadily increased in relative abundance through the enrichment process (Fig. 3 a, b). This final enrichment of C. togatus, LGM-1, constitutes the basis for downstream biological and molecular analyses. Its ASV was most similar to little-known members of the family Chitinophagaceae in the phylum Bacteroidetes. LGM-1’s genome was sequenced and assembled into a single 3.3 Mb contig with 1,781 putative and 1,328 hypothetical genes (Table S3), though most proteins had low identity (Fig. 4: Compiled paired ratios of functional parameters and compositional (relative) abundance in biocrusts across plaque boundaries (circles), red bars denoting the medians for each group of ratios, and bar background color denoting the p-values that the median is significantly different from unity (Wilcoxon paired ratio two-sided tests), where gray is non-significant (p  >  0.1), light orange is 0.05   > p   p  More

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Genetic structure of the parental populationBased on the lnPD and ΔK values obtained using STRUCTURE, we identified two genetic groups within the DHS Acer population (Supplementary Fig. S1). The q value from STRUCTURE analysis represents the proportion of ancestral origin28 (Fig. 2a). Among the 70 individual trees, 72.9% were assigned a q value smaller than 0.1 or larger than 0.9, thereby signifying a typical bimodal distribution (Fig. 2b). Individuals with q value greater than 0.9 and consistent genetic origin from the NEA region were defined as the NEA lineage (hereafter “NEA-DHS”), whereas those with values less than 0.1 and with consistent genetic origin from the SEA region were defined as the SEA lineage (hereafter “SEA-DHS”). Individuals with intermediate q value between 0.1 and 0.9 were defined as hybrid genetic types (hereafter “Hybrid-DHS”). Accordingly, we identified 27 SEA-DHS (38.6%), 24 NEA-DHS (34.3%), and 19 Hybrid-DHS (27.1%) (Fig. 2b).Figure 2Genetic structure of the parental and offspring population. (a) Bar plots illustrating the genetic composition of the adult (leaf) and offspring (fruit) populations in the Daheishan National Nature Reserve (DHS). Each individual is represented by a line partitioned into color segments corresponding to its ancestral proportion. Red color represents the ancestral proportion of Southern East Asia lineage. Green color represents the ancestral proportion of Northern East Asia lineage. Black lines in bar plots of leaf population separate individuals with ancestral proportion (q value) bigger than 0.9 or smaller than 0.1 from hybrids (0.1  0.5) produced by the SEA-DHS were obtained from a single tree, which was identified as SEA-DHS based on the DHS-only dataset, although it was indicated to be Hybrid-DHS based on the whole-range dataset. The Hybrid-DHS maternal trees produced 17.6% pure SEA-DHS seeds, 57.6% pure NEA-DHS seeds, and 24.7% hybrid seeds.Flowering phenologyThe sexual system of Acer has four phenotypes: duodichogamous, protogynous, protandrous, and male31. Hence, there are three functional sex types: (1) “Male I” flowers open earlier than “Female” flowers, with mature stamens, no style, and ovary; (2) “Female” flowers have mature pistils, short filaments, and indehiscence anthers; (3) “Male II” flowers open later than “Female” flowers, with mature stamens, ovaries, and separated stigmas. Duodichogamy is characterized by “Male I,” “Female,” and “Male II” types; protandry by “Male I” and “Female” types; and protogyny by “Female” and “Male II” types31.During the flowering season, we monitored a total of 10,074 flowers produced by 29 trees (Fig. 2d), among which one tree (SEA-DHS) was protandrous, four trees (three Hybrid-DHS and one NEA-DHS) were protogynous, and the remaining 24 trees were duodichogamous. We observed that the blooming phenology of SEA-DHS and NEA-DHS differed significantly to most assessed phenological indices, with a single exception being a marginally significant difference in the peak blooming time of Male I (Table 1). Compared with NEA-DHS, SEA-DHS were characterized by significantly later flowering phenology, with Male I commencement and cessation of blooming being on average two and three days later, respectively. Similarly, the commencement, peak, and cessation of Female occurred later by averages of 4, 4, and 5 days, respectively, whereas those of Male II occurred later by 5, 4, and 5 days, respectively. Furthermore, the duration of blooming was significantly longer in the SEA-DHS group than in the NEA-DHS group by three days. In the case of Hybrid-DHS, the values obtained for all assessed phenological indices were intermediate between those of the two parental types. Among these, the values of the six indices differed significantly from one or the other parental types, with the majority (5/6) differing from those of the SEA-DHS. Thus, phenologically, Hybrid-DHS appeared to be closer to NEA-DHS.Table 1 Flowering phenology of SEA-DHS, Hybrid-DHS, and NEA-DHS.Full size tableHowever, despite the differing phenology of the SEA-DHS and NEA-DHS, we observed instances of overlap in the blooming periods of male or female flowers in one genetic type with those of flowers of the opposite sex in another genetic type. For example, the peak of Female among NEA-DHS (11.67 ± 0.67) was found to coincide with the peak of Male I (11.44 ± 1.06; p = 0.879) in SEA-DHS. Similarly, Female blooming in the SEA-DHS peaked (16.11 ± 1.09) just 1 d after the peak of Male II (15.50 ± 0.43) in the NEA-DHS (p = 0.667), which at this time still retained an abundance of male flowers in bloom. In contrast, we detected no overlapping phenology with respect to the blooming of Male I of NEA-DHS or Male II of SEA-DHS with the Female in another genetic type.Morphological variation of leaves and fruitLeaves Among the eight leaf indices, all except InfectionRatio were significantly different between lineages. Generally, the leaves of NEA-DHS were found to have seven lobes, whereas those of SEA-DHS were typically five lobed (Lobes#), thereby contributing to significantly larger leaves in NEA-DHS than in SEA-DHS (TotalArea). Furthermore, NEA-DHS leaves had shorter and wider central lobes (CentralLength and CentralWidth), as well as an earlier and narrower inflection of the central lobes (InflectionLength and InflectionWidth), compared with those of SEA-DHS (Table 2). Six indices had correlation coefficients of less than 0.7, which were used for principal component analysis (PCA) analysis (Supplementary Table S2). The first two axes of the PCA were found to explain 63.7% of the variation in leaf morphology (Fig. 3a), with InflectionLength, CentralLength, and CentralRatio contributing the most to the first axis (38.2%), whereas TotalArea contributed the most to the second axis (25.5%) (Supplementary Table S3). The leaves of SEA-DHS and NEA-DHS plants were largely clustered in separate groups (Fig. 3a). However, all indices were continuous variables with large overlaps between the lineages (Table 2). For example, NEA-DHS had a significantly larger leaf area (21.06–88.70 cm2) than SEA-DHS (11.34–70.09 cm2). The shape of the central lobe is another major leaf trait that distinguishes between the two species. NEA-DHS had a shorter and wider central lobe (CentralRatio:0.67–2.49), while SEA-DHS had a longer and narrower central lobe (CentralRatio:0.9–3.46).Table 2 Morphological variation in the leaves and fruits of Acer trees in the Daheishan National Nature Reserve.Full size tableFigure 3Morphological variation in the leaves (a) and fruits (b) of southern and northern East Asia lineages of the Acer species complex in the Daheishan National Nature Reserve based on principal component analysis. SEA-DHS: Southern East Asia lineage of the Acer species complex in the DHS; NEA-DHS: Northern East Asia lineage of the Acer species complex in the DHS; Hybrid-DHS: hybrids between SEA-DHS and NEA-DHS lineages.Full size imageWith regard to Hybrid-DHS, the leaves were morphologically intermediate between those of the two parental types (Fig. 3a), as were the values of the assessed morphological trait indices (Table 2).Fruits 11 indices of fruits were significantly different between lineages. NEA-DHS tend to be characterized by smaller fruits (FruitLength and FruitWidth), seeds (SeedLength, SeedWidth and JunctionWidth), and fruit wings (WingLength and WingWidth). Moreover, the seed wings of NEA-DHS fruits are typically oriented at an obtuse angle, whereas those of SEA-DHS fruits tend to be aligned at a right angle (FruitAngle). The length ratio of the wing and seed (Wing:Seed) was larger in NEA-DHS than in SEA-DHS (1.24 vs 1.06, respectively, Table 2). Eight indices had correlation coefficients of less than 0.7, which were retained for PCA analysis (Supplementary Table S4). The first two axes of the PCA explained 58.4% of the variation in fruit morphology (Fig. 3b), with JunctionWidth and SeedLength contributing the most to the first axis (35.1%), whereas SeedRatio and WingRatio contributed the most to the second axis (23.3%) (Supplementary Table S3). The fruits of SEA-DHS and NEA-DHS plants were largely clustered in separate groups, with most fruits of SEA-DHS having negative values in Axis 1, while most fruits of NEA-DHS having positive values (Fig. 3b). Both JunctionWidth and SeedLength in Axis 1 reflect the size of the seed. NEA-DHS had smaller seed (SeedLength: 0.63–1.21 cm, SeedWidth:0.43–0.75 cm), while larger seed in SEA-DHS (SeedLength:0.79–1.49 cm, SeedWidth:0.49–0.93 cm). All indices were continuous variables with large overlaps between the lineages (Table 2).The morphology of Hybrid-DHS fruits was generally intermediate between that of the two parental types (Fig. 3b), as reflected in the values of the different morphological traits. The exceptions in this regard were FruitLength, WingLength, as well as two ratio indices (SeedRatio and WingRatio), with hybrid trees typically producing longer fruit with longer fruit wings (Table 2).Ecological niche divergence between NEA and SEAWe found a positive correlation between q value from Structure analysis and altitude (Pearson’s r = 0.83, p  670 m), whereas SEA-DHS was clustered at the foothill ( More

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Climate models need to capture a full spectrum of data from forests such as the Brazilian Amazon.Credit: Florence Goisnard/AFP/Getty

Humanity’s understanding of how forests are responding to climate change is disconcertingly fragile. Take carbon fertilization, for example — the phenomenon by which plants absorb more carbon dioxide as its concentration in the atmosphere increases. This is one of the principal mechanisms by which nature has so far saved us from the worst of climate change, but there’s little understanding of its future trajectory. In fact, researchers don’t fully understand how climate change interacts with a multitude of forest processes. Complex, unsolved questions include how climate warming affects forest health; how it affects the performance of forests as a carbon sink; and whether it alters the ecosystem services that forests provide. Forests are our life-support system, and we should be more serious about taking their pulse.Six papers in this week’s Nature provide important insights into those questions. They also underline some of the challenges that must be overcome if we are to fully understand forests’ potential in the fight against climate change. These challenges are not only in the science itself, but also relate to how forest scientists collaborate, how they are funded (especially where data collection is concerned) and how they are trained.Forest science is an amalgam of disciplines. Ecologists and plant scientists measure tree growth, soil nutrients and other parameters in thousands of forest plots around the world. Physical scientists monitor factors such as forest height and above-ground forest biomass using remote-sensing data from drones or satellites. Experimental scientists investigate how forests might behave in a warming world by artificially altering factors such as temperature or carbon dioxide levels in experimental plots. Some of the data they generate are absorbed by yet another community: the modellers, who have created dynamic global vegetation models (DGVMs). These simulate how carbon and water cycles change with climate and, in turn, inform broader earth-system and climate models of the type that feed into policymaking.Different DGVMs make different predictions about how long forests will continue to absorb anthropogenic CO2. One reason for these differences is that models are sensitive to assumptions made about the processes in forests. There are many influences — including temperature, moisture, fire and nutrients — that are generally studied in isolation. Yet they interact with each other.Not all DGVMs account for the dampening effect that a lack of soil phosphorus can have on carbon fertilization, for example. Much of central and eastern Amazonia is poor in phosphorus, and research has shown that introducing phosphorus limitation into DGVMs can cut the carbon-fertilization effect1. This week, Hellen Fernanda Viana Cunha at the National Institute for Amazonian Research in Manaus, Brazil, and her colleagues report2 a powerful experimental demonstration of how the soil’s poor phosphorus content limits carbon absorption in an old-growth Amazonian forest.Models simulating the northward spread of boreal forest as temperatures rise are also missing key drivers3, according to Roman Dial at Alaska Pacific University in Anchorage and his colleagues. They report today that a white-spruce population has migrated surprisingly far north into the Arctic tundra. To explain this, it is necessary to take into account winter winds (which facilitate long-distance dispersal) along with the availability of deep snow and soil nutrients (which promote plant growth).Models are often based on a small number of ‘functional tree types’ — for example, ‘evergreen broadleaf’ or ‘evergreen needle leaf’. These are chosen as a proxy for the behaviour of the planet’s more than 60,000 known tree species. Yet ecologists are discovering that the biology of individual species matters when it comes to a tree’s response to climate change.David Bauman at the Environmental Change Institute at the University of Oxford, UK, and his co-workers reported in May that tree mortality on 24 moist tropical plots in northern Australia has doubled in the past 35 years (and life expectancy has halved), apparently owing to the increasing dryness of the air4. But that was an average of the 81 dominant tree species: mortality rates varied substantially between species, a variation that seemed to be related to the density of their wood.Peter Reich at the Institute for Global Change Biology at the University of Michigan in Ann Arbor and his colleagues now report that modest alterations in temperature and rainfall led to varying rates of growth and survival5 for different species in southern boreal-forest trees. The species that prospered were rare.Failure to examine multiple factors simultaneously means that scientists are making findings that challenge the assumptions in models. Spring is coming earlier for temperate forests and most models assume that, by prolonging the growing season, this increases woody-stem biomass. However, observational work carried out in temperate deciduous forests by Kristina Anderson-Teixeira at the Smithsonian Conservation Biology Institute in Front Royal, Virginia, and her colleagues found no sign of this happening6.Modellers are all too aware of the need to incorporate more complexity into their models, and of the potential that increasing amounts of computing power have to assist them in this endeavour. But they need more data.Continuity problemTo obtain comprehensive, valuable data for the models, continuous, long-term observations need to be made, and that depends on the availability of long-term funding. Achieving such continuity is a problem for both remote-sensing and ground-based operations. The former can cost hundreds of millions of dollars, but the value of its long-term data sets is immense, as demonstrated by a team led by Giovanni Forzieri at the University of Florence in Italy. The authors used 20 years of satellite data to show that nearly one-quarter of the world’s intact forests have already reached their critical threshold for abrupt decline7. But even field-based data collection, which costs a pittance by comparison, struggles to achieve financial security.Important ground-based operations include the Forest Global Earth Observatory (ForestGEO), part of the Smithsonian Tropical Research Institute, which is headquartered in Washington DC. This monitors 7.5 million individual trees in plots around the world. The amount of work that goes into this monitoring is formidable. For example, at present, ForestGEO is conducting the eighth five-yearly census of a plot in Peninsular Malaysia. This involves determining the species for each of the 350,000 trees (there are some 800 species growing there) and measuring the circumference of each trunk. It will take 16 skilled people a year to measure all the trees. Delays in the provision of funding to ForestGEO have held up similar censuses at plots in countries including Papua New Guinea, Vietnam, Brunei and Ecuador.

A ForestGEO researcher making tree measurements at a forest plot in Barro Colorado Island, Panama.Credit: Jorge Aleman, STRI

The future of the plots in North Queensland, which supplied Bauman with a rare 49 years’ worth of continuous data, is uncertain. They have been monitored since the mid-1970s by the Australian public research-funding agency CSIRO — initially every two years, then, more recently, every five years. In 2019, monitoring of the plots was switched to every 50 years because of funding shortages at CSIRO, leaving scientists searching for new sources of funding.Without continuity of funding, organizations such as ForestGEO can’t equip researchers with the requisite skills or collect data over periods longer than an individual’s time in a specific post or a funder’s cycle. “We have trained people and then lost them due to job insecurity,” says Stuart Davies, who leads ForestGEO.Different groups of forest researchers are trying to address these problems. ForestGEO is coordinating the Alliance for Tropical Forest Science in an effort to make it easier to share data, and to bolster the morale and careers of the skilled technicians and scientists — many of whom live in low- and middle-income countries — who do the bulk of the data collection.But we also need more-imaginative funding mechanisms that lift long-term observational plots out of three- to five-year funding cycles. Space agencies that fund remote-sensing satellites could collaborate with other funding agencies, for example, so that earth-observation missions include a fully funded component for ground-based data collection — which is, after all, crucial for calibrating their results. Journals, too, could do more to value and incentivise the production of long-term data sets.And there is a need for more interdisciplinarity. The US Department of Energy is funding a project called NGEE–Tropics (Next-Generation Ecosystem Experiments–Tropics) in which modellers will work with empirical researchers, both observational and experimental, who study tropical forests to create a full, process-rich model of such forests. This is encouraging, and the idea could be pushed further. What is needed is an initiative that pulls the disciplines together towards a goal of building a better understanding of forest processes. Among other things, such an initiative would encourage researchers in different disciplines to take each other’s data needs into account when planning their projects.For this to work, we need to remember that the edifice of forest science relies on the long-term data that scientists wring from forests over decades. Our chances of overcoming climate change are small, but they will diminish further if we forget the basics of monitoring our home planet. More

Shotgun sequencing and generation of metagenome-assembled genomesIn our previous study, 78 Holstein Friesian dairy cows were sampled for rumen content, metagenomic shotgun sequencing was carried out, and raw Illumina sequencing reads were assembled into contigs using megahit assembler using default settings [7]. We used a pooled assembly of the original 78 samples to increase the quality of the metagenome-assembled genomes (MAGs) with the syntax: megahit [14] -t 60 -m 0.5 −1 [Illumina R1 files] −2 [Illumina R2 files]. Next, the assembled contigs were indexed using BBMap [15]: bbmap.sh threads = 60 ref = [contigs filename]. Thereafter, reads from each sample were mapped to the assembled contigs using BBTools’ bbwrap.sh script. In order to determine the depth (coverage) of each contig within each sample, the gi_summarize_bam_contig_depths tool was applied with the parameters: gi_summarize_bam_contig_depths –outputDepth depth.txt –pairedContigs paired.txt *.bam –outputDepth depth.txt –pairedContigs paired.txt.Using the depth information, metabat2 [16] was executed to bind genes together into reconstructed genomes, with parameters: metabat2 -t40 -a depth.txt.To evaluate genomic bin quality, we used the CheckM [17] tool, with parameters: checkm lineage_wf [in directory] [out directory] -x faa –genes -t10.Preparing proteomic search libraryWe generated 93 unique high-quality MAGs, and further increased our MAG database by including phyla that were not represented in our set of MAGs. In order to do so, we used the published compendium of 4,941 rumen metagenome-assembled genomes [18] and dereplicated those MAGs using dRep [19]. We then selected MAGs from phylum Spirochaetes, Actinomycetota, Proteobacteria, Firmicutes, Elusimicrobia, Bacillota, Fibrobacteres and Fusobacteria, which had the highest mean coverage in our samples as calculated using BBMap and gi_summarize_bam_contig_depths as described above [15]. This strategy minimized the false discovery rate (FDR), that would have been obtained if larger and unspecific databases would have been employed [20] and allowed the addition of 14 MAGs to our database.In order to create the proteomic search library, genes were identified along the 107 MAGs using the Prodigal tool [21], with parameters: prodigal meta and translated in silico into proteins, using the same tool. Replicates sequences were removed. Protein sequences from the hosting animal (Bos taurus) and common contaminant protein sequences (64,701 in total) were added to the proteomic search library in order to avoid erroneous target protein identification originating from the host or common contaminants. Finally, in order to subsequently assess the percentage of false-positive identifications within the proteomic search [22], the proteomic search library sequences were reversed in order and served as a decoy database.Proteomic analysisThe bacterial fraction from rumen fluid of the 12 selected animals selected from extreme feed efficiency phenotypes, were obtained at the same time as the samples analyzed for metagenomics and stored at −20 °C until extraction. To extract total proteins, a modified protocol from Deusch and Seifert was used [23]. Briefly, cell pellets were resuspended in 100 µl in 50 mM Tris-HCl (pH 7.5; 0.1 mg/ml chloramphenicol; 1 mM phenylmethylsulfonyl fluoride (PMSF)) and incubated for 10 min at 60 °C and 1200 rpm in a thermo-mixer after addition of 150 µl 20 mM Tris-HCl (pH 7.5; 2% sodium dodecyl sulfate (SDS)). After the addition of 500 µl DNAse buffer (20 mM Tris-HCl pH 7.5; 0.1 mg/ml MgCl2, 1 mM PMSF, 1 μg/ml DNAse I), the cells were lysed by ultra-sonication (amplitude 51–60%; cycle 0.5; 4 × 2 min) on ice, incubated in the thermo-mixer (10 min at 37 °C and 1,200 rpm) and centrifuged at 10,000 × g for 10 min at 4 °C. The supernatant was collected and centrifuged again. The proteins in the supernatant were precipitated by adding 20% pre-cooled trichloroacetic acid (TCA; 20% v/v). After centrifugation (12,000 × g; 30 min; 4 °C), the protein pellets were washed twice in pre-cooled (−20 °C) acetone (2 × 10 min; 12,000 × g; 4 °C) and dried by vacuum centrifugation. The protein pellet was resuspended in 2× SDS sample buffer (4% SDS (w/v); 20% glycerin (w/v); 100 mM Tris-HCl pH 6.8; a pinch of bromophenol blue, 3.6% 2‑mercaptoethanol (v/v)) by 5 min sonication bath and vortexing. Samples were incubated for 5 min at 95 °C and separated by 1D SDS-PAGE (Criterion TG 4-20% Precast Midi Gel, BIO-RAD Laboratories, Inc., USA).As previously described, after fixation and staining, each gel line was cut into 10 pieces, destained, desiccated, and rehydrated in trypsin [24]. The in-gel digest was performed by incubation overnight at 37 °C. Peptides were eluted with Aq. dest. by sonication for 15 min The sample volume was reduced in a vacuum centrifuge.Before MS analysis, the tryptic peptide mixture was loaded on an Easy-nLC II or Easy-nLC 1000 (Thermo Fisher Scientific, USA) system equipped with an in-house built 20 cm column (inner diameter 100 µm; outer diameter 360 µm) filled with ReproSil-Pur 120 C18-AQ reversed-phase material (3 µm particles, Dr. Maisch GmbH, Germany). Peptides were eluted with a nonlinear 156 min gradient from 1 to 99% solvent B (95% acetonitrile (v/v); 0.1% acetic acid (v/v)) in solvent A (0.1% acetic acid (v/v)) with a flow rate of 300 ml/min and injected online into an LTQ Orbitrap Velos or Orbitrap Velos Pro (Thermo Fisher Scientific, USA). Overview scan at a resolution of 30,000 in the Orbitrap in a range of 300-2,000 m/z was followed by 20 MS/MS fragment scans of the 20 most abundant precursor ions. Ions without detected charge state as well as singly charged ions were excluded from MS/MS analysis. Original raw spectra files were converted into the common mzXML format, in order to further process it in downstream analysis. The spectra file from each proteomic run of a given sample was searched against the protein search library, using the Comet [25] search engine with default settings.The TPP pipeline (Trans Proteomic Pipeline) [26] was used to further process the Comet [25, 27] search results and produce a protein abundance table for each sample. In detail, PeptideProphet [28] was applied to validate peptide assignments, with filtering criteria set to probability of 0.001, accurate mass binning, non-parametric errors model (decoy model) and decoy hits reporting. In addition, iProphet [28, 29] was applied to refine peptide identifications coming from PeptideProphet. Finally, ProteinProphet [28,29,30] was applied to statistically validate peptide identifications at the protein level. This was carried out using the command: xinteract -N[my_sample_nick].pep.xml -THREADS = 40 -p0.001 -l6 -PPM -OAPd -dREVERSE_ -ip [file1].pep.xml [file2].pep.xml.. [fileN].pep.xml  > xinteract.out 2  > xinteract.err. Then, TPP GUI was used in order to produce a protein table from the resulting ProtXML files (extension ipro.prot.xml).Subsequently, proteins that had an identification probability < 0.9 were also removed as well as proteins supported with less than 2 unique peptides (see Supplementary Table 1).Quantifying metagenomic presence of MAGsA reference database containing all 107 MAGs’ contigs was created (bbmap.sh command, default settings). Then, the paired-end short reads from each sample (FASTQ files) were mapped into the reference database (bbwrap.sh, default settings), producing alignment (SAM) files, which were converted into BAM format. Subsequently, a contig depth (coverage) table was produced using the command jgi_summarize_bam_contig_depths --outputDepth depth.txt --pairedContigs paired.txt *.bam. As each of the MAGs span on more than one contig, MAG depth in each sample was calculated as contig length weighted by the average depth. Finally, to account for unequal sequencing depth, each MAG depth was normalized to the number of short sequencing reads within the given sample.Correlating metagenomic and proteomic structuresIn order to compare metagenomic and proteomic structures, we first calculated the mean coding gene abundance and mean production levels of each of the 1629 detected core proteins over all 12 cows. Both mean gene abundance and mean production level were translated into ranks using the R rank function. The produced proteins were ranked in descending order and the coding genes in the gene abundance vector were reordered accordingly. The two reordered ranked vectors then plotted using the R pheatmap function, and colored using the same color scale.Selection of proteins for downstream analysisAs our goal was to analyze plasticity in microbial protein production in varying environments, e.g., as a function of host state, only MAGs that were identified in all of the 12 proteomic samples were kept for further analysis. Consequently, only proteins that were identified in at least half of the proteomic samples (e.g., in at least six samples) were selected. This last step aimed to reduce spurious correlation results. These filtering steps retained 79 MAGs coding for a total of 1,629 measurable proteins.Feed efficiency state prediction and ordinationIn order to calculate the accuracy in predicting host feed efficiency state based on the different data layers available (16S rRNA (Supplementary Table 2), metagenomics, metaproteomics), the principal component analysis (PCA) axes for all the samples based on the microbial protein production profiles were calculated. Then, twelve cycles of model building and prediction were made. Each time, the two first PCs of each of five cows along with their phenotype (efficiency state) were used to build a Support Vector Machine (SVM) [R caret package] prediction model and one sample was left out. The model was then used to perform subsequent prediction of the left-out animal phenotype (feed efficiency) by feeding the model with that animal’s first two PCs. This leave-one-out methodology was then repeated over all the samples. Finally, the prediction accuracy was determined as the percent of the cases where the correct label was assigned to the left-out sample. For the proteomics data, this procedure was applied on both the raw protein counts, and the protein production normalized based on MAG abundance, which enabled us to compare the prediction accuracies of the microbial protein production to that of the raw protein counts.Identification proteins associated with a specific host stateIn order to split the proteomics dataset into microbial proteins that tend to be produced differently as a function of the host feed efficiency states, each microbial protein profile was correlated to the sample’s host feed efficiency measure (as calculated by RFI) using the Spearman correlation (R function cor), disregarding the p value. Proteins that had a positive correlation to RFI were grouped as inefficiency associated proteins. In contrast, proteins that presented a negative correlation to RFI were grouped as efficiency associated proteins. To test for equal sizes of these two protein groups, a binomial test was performed (R function binom.test) to examine the probability to get a low number of feed efficient proteins from the overall proteins under examination, when the expected probability was set to 0.5.Functional assignment of proteinsProtein functions were assigned based on the KEGG (Kegg Encyclopedia of Genes and Genomes) [31] database. The entire KEGG genes database was compiled into a Diamond [32] search library. Then, the selected microbial proteins were searched against the database using the Diamond search tool. Significant hits (evalue < 5e-5) were further analyzed to identify the corresponding KO (KEGG Ortholog number). Annotations of glycoside hydrolases were performed using dbcan2 [33].Protein level checkerboard distribution across the feed efficiency groupsThe checkerboard distribution in protein production profiles was estimated separately within the feed efficient and inefficient animal groups. To enable the comparison between the two groups’ checkerboardness level, we chose a standardized C-score estimate (Standardized Effect Size C-score - S.E.S C-Score), based on the comparison of the observed C-score to a null-model distribution derived from simulations. The S.E.S C-score was estimated using the oecosimu function from R vegan package with 100,000 simulated null-model communities.Calculating functional redundancyThe functional redundancy within a given group of proteins was measured as the mean number of times a given KO occurred within a given group, while neglecting proteins that have not been assigned a KO level functional annotation.In order to test whether a given group of proteins exhibits more or less functional redundancy than would have been expected, a null distribution for functional redundancy was created, based on the number of proteins in the given group. A random group of proteins was drawn from the entire set, keeping the same sample size as in the tested group, and the process was repeated 100 times. Then, the functional redundancy for each random protein group was calculated. Thereafter, the null distribution was used to obtain a p value to measure the likelihood of obtaining such a value under the null.Examining functional divergenceExamining the functional divergence between the two groups of proteins, e.g. the feed efficiency and inefficiency associated proteins, was done by first counting the amount of shared functional annotations, in terms of KOs between the two groups. Thereafter, a null distribution for the expected count of KOs was built by randomly splitting in an iterative manner the proteins into groups of the same sizes and calculating the number of shared KOs. A p value for the actual count of shared proteins was obtained by ranking the actual count over the null distribution.Calculating average nearest neighbor ratio (ANN ratio)ANN Ratio analysis was carried out independently for each protein function (KO), containing more than 14 proteins with at least 5 proteins within each feed efficiency group. Initially, all proteins assigned to a given KO were split into two sets, in accordance to their feed efficiency affiliation group. Thereafter, proteins within each set were independently projected into two-dimensional space by PCA applied directly to Sequence Matrix [34]. Average nearest neighbor ratio within each set was then calculated within the minimum enclosing rectangle defined by principal component axes PC1 and PC2, as defined by Clark and Evans [35].MAG feed efficiency score calculationMicroorganism feed efficiency score was calculated for each MAG individually by first ranking each protein being produced by the given microbe along the 12 animals, based on the normalized protein production levels. Thereafter, a representative production value for the microbe in each animal was calculated as the average of the ranked (normalized) protein production levels in that animal (using R rank function). This ranking allowed us to alleviate the potential skewing effect of highly expressed proteins. The microorganism’s Feed Efficiency Score was calculated as the difference between its mean representative production value within feed efficient animals to that within feed inefficient animals. Values close to zero will reflect similar distribution between the two animal groups, positive values will indicate higher expression among efficient animals, and negative values will indicate higher expression among inefficient animals. To calculate significance, the actual feed efficiency score was compared to values in a distribution derived from a permutation based null model. Each of the permuted Feed Efficiency Scores (10,000 for each microbe) was obtained by independently shuffling each of the proteins produced by the MAG between the animals, prior to calculating the actual microorganism feed efficiency score. By positioning the absolute score value over its distribution under permuted assumptions (absolute values), we obtained a significance p value.MAG phylogenetic tree construction and phylogenetic signal estimationIn order to assess the link between phylogenetic similarity between the MAGs and their association with feed efficiency, phylogenetic tree estimating evolutionary relationships between the MAGs was constructed using the PhyloPhlAn pipeline [36]. The phylogenetic signal for Microorganism Feed Efficiency Score was estimated by providing the phylogSignal function from R phylosignal [37] package with MAGs phylogenetic tree and respective values. Pagel’s Lambda statistics was chosen for the analysis, owing to its robustness [38].Plot generationAll bar plots, scatter plots and other point plots were generated with R package ggplot2. Heatmaps were produced by either ggplot2 [39] or pheatmap [https://cran.r-project.org/web/packages/pheatmap/index.html] R packages. KEGG map was produced using the online KEGG Mapper tool [40]. Phylocorrelogram was produced with phyloCorrelogram function from R package phylosignal [37].MAG differential production analysisMAGs that contain a minimal number of proteins (50 functions) were selected for differential protein production analysis, in order to have sufficient data to perform statistical tests. For each MAG, the relative production was used in order to calculate the Jaccard pairwise dissimilarity for core protein production between feed efficient and inefficient cows using the R vegan package. Analysis of similarity between efficiency and inefficiency associated proteins for each MAG (ANOSIM) values and p values were then calculated using the same package.Predicting animal feed efficiency state according to GH family countsUsing all GH annotated proteins, a feature table that sums the count of each GH family within each sample was produced. Thereafter a leave-one-out cross-validation (LOOCV) [R caret package] was performed, each time building a Random Forest (RF) prediction model from the GH family counts and efficiency state of 11 samples, leaving one sample outside. Each one of the RF models, in its turn, was applied on the left-out animal to predict its efficiency state. Model accuracy and AUC curve were calculated based on the LOOCV performance. More