More stories

  • in

    Comparison of soil and corn residue cutting performance of different discs used for vertical tillage

    The results of ANOVA tests were summarised in Table 1. None of the interaction effect was significant. Therefore, the main effects of disc type and working depth were presented in the following sections.
    Table 1 Summary of ANOVA test results.
    Full size table

    Soil cutting forces
    The rippled disc required an average draft force of 675 N, which was numerically the highest among the discs (Fig. 1a). The notched disc had a minimal draft force demand of 579 N. Increasing the working depth from the shallow (63.5 mm) to deep (127 mm) resulted in the draft force increasing from 291 to 965 N. This more-than-tripled increase was significant and can be explained by the soil dynamics theory that draft force varies with the contact area between soil and tool22. The rippled edge slightly increased the surface area as compared to the smooth edge, while the notched edge slightly decreased the contact area due to the notches. As for the depth effect, a deeper operation significantly increased the portion of the disc in contact with soil regardless of the disc type.
    Figure 1

    Soil cutting forces of different discs at different working depths: (a) draft force, (b) vertical force, and (c) lateral force; means followed by different lower case letters or upper case letters are significantly different according to Tukey’s test at the significance level of 0.05; error bars are standard deviations.

    Full size image

    All the vertical forces measured were positive, which indicated that they were acting on the disc in the downward direction (Fig. 1b) that favored the disc penetration into the soil. The rippled disc had the maximal vertical force of 289 N, which will help to maintain its working depth as compared to the other two discs. As was expected, the notched disc experienced the minimal vertical force of 164 N, which was lower than that of the rippled disc. The plain disc had a medium vertical force, which was not different from the other two discs. The lower vertical force of the notched disc may not necessarily affect its superior ability of soil penetration. The deep working depth created a 65.9% higher vertical force as compared to the shallow depth. The vertical forces of similar magnitudes were also observed in previous studies, such as approximately 200 N in Nalavade et al.23.
    There were no significant differences among the discs in terms of the lateral force (Fig. 1c). The notched disc had the minimal lateral force of 215 N. The lateral force increased roughly twofold from 171 to 347 N as the disc was operated from the shallow to deep depths, which was significant. The insignificant difference in the lateral force among the discs was partially attributed to their identical disc angles and similar concavity. Lower lateral forces are usually desired in terms of the frame stability of the implement. The increase of the lateral force as the depth increased indicated a great deal of attention must be paid on the frame strength when designing the disc for deep tillage application.
    The soil cutting forces were resultant forces of passive cutting reaction on the concave face and the scrubbing reaction on the convex face for a concave disc24. Both the cutting force and scrubbing force acted at some angle between the horizontal and vertical directions. The projected soil cutting force was against the travel direction in the horizontal direction and downward in the vertical direction; on the other hand, the projected scrubbing force is along the travel direction and upward. The resultant draft force was against the travel direction and the resultant vertical force was downward, which was the same as that of the cutting force. This agreed with the literature that the scrubbing force on the trailing convex side of the disc tends to be minor compared to the cutting force on the leading concave side of the disc22. However, the soil cutting forces were smaller than those reported in Godwin et al.25. The combination of shallow concavity and small disc angle used in this study possibly helped in reducing the soil cutting forces in all three directions. The results agreed with that in Choi and Erback20, where the notched disc had the least forces and the forces were more dependent on the working depth than the disc shape.
    Soil displacements
    The soil forward displacement was maximized with the rippled disc and was minimized with the notched disc (Fig. 2a). The plain disc resulted in a medium soil forward displacement of 264 mm. During the operation of the notched disc, some soil particles might not be pushed forward, but being passed over by the notches. This could explain the small soil displacements observed for the notched disc. However, statistical analysis did not show any significant differences among the three discs with regard to soil forward displacement. The soil tracers were dislodged 184 mm on average when the discs were used at the shallow depth, which was increased by 73.4% at the deep depth.
    Figure 2

    Soil displacements of different discs at different working depths in three directions: (a) forward, (b) lateral, and (c) upward; means followed by different lower case letters or upper case letters are significantly different according to Tukey’s test at the significance level of 0.05; error bars are standard deviations.

    Full size image

    The rippled disc moved the soil tracers the furthest in the lateral direction at 197 mm (Fig. 2b). The notched disc created the minimal soil lateral displacement of 109 mm, which was less than that of the other two discs. The soil lateral displacement was increased by 42.0% as the working depth changed from the shallow to deep depth. The soil lateral displacement was the average displacement of all the tracers in the lateral direction and a positive value denoted the direction pointing toward the concave face of the disc. It was worth noting that soil tracers on the convex side tended to be pushed away in the opposite direction as compared to other tracers as observed in the experiment. This was related to the scrubbing action as described above.
    No significant difference was found in the soil vertical displacement among the treatments (Fig. 2c). All the soil vertical displacements were less than 20 mm with an average of 10.6 mm. Similar to the lateral displacement, not all tracers were dislodged in the same direction. However, the majority of them were in an upward direction including the average value. The small upward displacements indicated moderate soil swelling and elevating movements and minimal soil overturning effect of the discs. This was supported by the soil failure pattern study in Nalavade et al.23, which observed that the dominating compressive shear failure pattern of the free-rolling disc discouraged soil inversion actions.
    Residue mixing
    The rippled disc had the highest residue mixing rate of 23.1%, which was higher than that of the notched disc, being the lowest at 14.7% (Fig. 3). The residue mixing of the plain disc was medium among the three discs. As for the working depth, the shallow depth created a residue mixing of 16.7%, which was lower than that of the deep depth.
    Figure 3

    Residue mixing of different discs at different working depths; means followed by different lower case letters or upper case letters are significantly different according to Tukey’s test at the significance level of 0.05; error bars are standard deviations.

    Full size image

    The residue mixing could be used to estimate the amount of residue being incorporated into the soil, given the surface residue before tillage was 7500 kg/ha. Therefore, the rippled disc was the most effective in terms of the residue incorporation at a rate of 2746 kg/ha. The residue incorporation increased by 606 kg/ha as the working depth increased from shallow to deep. Also, deducting the residue mixing from the original residue cover of 63.1% would be the residue cover remaining. None of the treatments resulted in a residue cover less than 30%, which suggested that all treatments would satisfy the requirement of conservation tillage.
    Residue cutting
    The residue cutting effectiveness of the discs varied from the highest to the lowest as the rippled, notched, and plain with no significant differences were found (Fig. 4). The total residue cutting of the notched disc consisted of one-third of partially cut while no partially cut was observed for the rippled disc. As for the plain disc, roughly a quarter of the total residue cutting was partially cut. The shallow working depth had a numerically higher residue cutting rate than the deep depth: 32.8% versus 22.2%. One in every four residue tracers being cut was partially cut when the discs were operated at the shallow depth. As a comparison, less than one residue was partially cut for every ten residue tracers being cut at the deep depth. The results suggested that the most effective treatment in cutting residues was the rippled disc at the shallow depth. On average, only 27.5% of the residue tracers were being cut, either partially or completely, by the discs. Partial cuts tended to be pushed into the soil and damaged by the discs. The majority of the remaining residue was pushed aside by the discs through disturbed soil.
    Figure 4

    Residue cutting including completely cut and partially cut of different discs at different working depths; means followed by different lower case letters or upper case letters are significantly different according to Tukey’s test at the significance level of 0.05; error bars are standard deviations.

    Full size image

    The effects of disc type and working depth on the residue cutting efficiency of the discs differed from the previous studies of disc openers. For example, the plain disc was found to have a much higher residue cutting efficiency than the notched and serrated discs and the efficiency increased as the working depth increased17. The primary cause of the difference was due to the difference in residue cutting mechanism between the angled tillage discs and relatively straight disc openers. The concaved discs disturbed a fair amount of soil ahead of the disc and relied on the edge to “hook” lying residues in order to cut them. Therefore, the rippled and notched discs had numerically higher residue cutting rates than the plain disc thanks to their hooking edges. The shallower the working depth, the less the soil disturbance and the higher the residue cutting efficiency is. On the other hand, a straight disc opener would ride over all possible residues on the path and penetrate the soil without causing significant disturbance to the seedbed. The difference in residue cutting effectiveness can also be accounted for in part by the difference in residue characteristics such as type, percent cover, and moisture content. For instance, wet rice residue with a moisture content of 41.4% at 2000 kg/ha15 versus dry corn stalk with a moisture content of 4.5% at 7500 kg/ha in this study. Previous studies have shown that the cutting performance of the disc openers was significantly affected by the mechanical properties of the residue26 and residue density17.
    The numerically higher portion of surface residue being cut at the shallow depth was attributed to a smaller cutting angle. This cutting angle was the angle of absolute velocity vector acting on the residue with the vertical axis in Kushwaha et al.16, whose analytical model showed that the angle of absolute velocity vector for a disc is smaller at a shallower depth. The disc tended to cut or bend the residues at a smaller cutting angle, while the disc tended to push the residue ahead at a larger cutting angle. The notched disc had the numerically highest portion of partially cut among the three discs, which agreed with the results in Bianchini and Magalhaes21. Kushwaha et al.17 also observed that residue pieces were held into the notches and serrations of the discs instead of being cut, being thrown backward as the disc exited from the soil. More

  • in

    Comparative models disentangle drivers of fruit production variability of an economically and ecologically important long-lived Amazonian tree

    We set out to disentangle the manifold and interacting drivers of fruit production of large, long-lived tropical canopy trees. We used two B. excelsa populations as models given the critical importance of this single species to ecosystem processes, Amazonian livelihoods, and tropical biodiversity conservation. Our findings uncovered that over 10 years, one site (Cachoeira) consistently generated production levels that were threefold higher than that of the other site (Filipinas). Fruit production variation at Cachoeira was also relatively constant at both individual and population levels compared to Filipinas. Yet as anticipated in the tropics (versus temperate regions) where low climate variability minimizes resource variation18, neither population exhibited masting behavior as indicated by synchrony (S).
    Given that we hypothesized that fruit production would show similar patterns over time, and common driving variables, we expected weather and weather cues to play important roles in fruit production. Because our research sites are only ~ 30 km apart, we assumed that each population and individual tree experienced approximately the same weather and climatic cues. Our climate model indicated that more wet days during the narrow 3-month dry season prior to flowering resulted in increased fruit production. Furthermore, the model also indicated that when drier atmospheric conditions (represented by VAP) were present and extended beyond the dry season into the flowering period, fruit production tended to be reduced. Still, models that used the simple “year” variable to explain fruit production variation (versus multiple specific, albeit remote climate variables) had better statistical fit. This leads us to question what overall weather conditions might have caused the extremely low and highly variable production levels of 2017; in Filipinas, more than half of the trees did not produce any fruits (Fig. 1). Local Brazil nut harvesters also characterized 2017 as an exceptional nadir in production – a sentiment echoed in popular media across the Amazon basin19.
    The year 2015 was a “Very Strong” El Niño year, which followed immediately on a “Weak” one (2014)20. These years relate to our 2017 production because of  > 15-month fruit maturation lag times. Such El Niño events yield sunny, dry conditions in our study region. Over the 10-year study, VAP for 2017 production was the lowest ranked (26.27 hPa), and 2016 was the second lowest (25.37 hPa) (SI Table S2), signaling back-to-back years of persistent low atmospheric moisture. While increases in solar radiation can boost forest productivity21,22, persistent dry conditions and higher accompanying temperatures induce tree stress23, and ultimately higher mortality24. As a canopy emergent, B. excelsa crowns are exposed to greater radiation levels and higher evaporative demand. Hence, they are predicted to be particularly sensitive to drought due to hydraulic stress25, potentially exacerbated by increased water column tension in such exceptionally tall trees23. Still, such large trees access stored groundwater via deep roots more than previously assumed26, and fluctuations in water supply can be moderated by internal storage in stems, roots and leaves27. It is unknown, however, the extent to which two successive El Niño years may have impacted groundwater recharge and storage, and aggravated overall tree stress. There is evidence that canopy trees are resilient to normal Amazonian dry seasons due to deep roots that access water stored from wet season precipitation3,28; yet they are more vulnerable to extended tropical droughts, as demonstrated by the higher rates of large tree, drought-related mortality29. Corlett23 suggested that this tall tree vulnerability can be attributed to the physiological challenges of transporting water from drying soil through lengthy water conduits to exposed leaves. B. excelsa demonstrates drought avoidance by losing leaves during the dry period, but only for a few days in our study region30, where deciduousness is unexceptional and average rainfall falls short of ~ 2000 mm expected for evergreen tropical forests31. Finally, drought inducement experiments have demonstrated that lower rainfall levels over time negatively affect tropical tree fruit production. Throughfall exclusion over a 4-year period had a cumulative negative effect on fruit production (− 12%) of a sub-canopy tropical Rubiaceae, but differences were only significant in 1 year32.
    Delayed rainy season onset also may have influenced the extremely low 2017 fruit production. In our region, the rainy season typically begins in September, yet the key 6-month rainfall (DTF; June through November) period that influenced 2017 production was the lowest in our 10-year data set. Moreover, of the entire 117-year CRU data set, the 2017 DTF period was the 16th lowest on record (SI Table S2), indicating that rainy season onset was delayed beyond norms. Since 1979, there has been a delay in dry season end dates (or rainy season onset) and an increase in dry season length for southern Amazonia33. Grogan and Schulze34 reported that delayed rainy season onset had a negative effect on tropical canopy tree growth, but they did not track fecundity. Finally, negative correlations between fruit production and minimum temperatures during both DPF and DTF (dry season prior to, and through flowering, respectively), particularly in Cachoeira, are consistent with other tropical studies that have showed clear negative effects of high nighttime temperatures on tropical tree growth22. In sum, evidence suggests that dry, and perhaps warming, conditions may have produced cascading effects that compromised 2017 fruit production at both sites (Table S2). Still, Cachoeira responded better than Filipinas not only in 2017, but across all years, as indicated by highly significant site effects across models.
    Given these results, we explored the role that site differences might play in fruit production. Previous studies have detected subtle differences in demographic structures at our sites, indicating the presence of smaller B. excelsa individuals in the Filipinas population, but without a clear attribution to ecological or socioeconomic factors9. While Cachoeira has a longer history of disturbance (i.e., low-intensity timber harvest), which could influence the dominance of B. excelsa, we lack evidence that this disturbance influences production. Despite close proximity, our sites are located in different watersheds, and are characterized by slightly different forest types and soil characteristics. Specifically, Cachoeira’s significantly higher levels of P and K (Table 1) are informative, as soil P has been positively linked to higher levels of B. excelsa production11,17. Costa35 showed that B. excelsa can be productive in acidic, less fertile soils, while suggesting that Ca is a key macronutrient for this species.
    Site quality has been used extensively to explain and predict productivity across diverse forest types for decades36, and inclusion of more site variables (such as depth to water table) would likely yield improved explanations for Cachoeira’s comparatively superior production. Notwithstanding, individual tree differences, regardless of site, offer further fruit production insights. As with almost all trees, B. excelsa reproductive status and fruit production levels are explained by DBH12,16,37,38,39, with the most productive trees in the 100–150 cm DBH range11. Moreover, DBH for these trees is correlated with crown size17, which was a significant and positive explanatory variable for all our production models, although less so for large trees (≥ 100 cm DBH) in Cachoeira versus Filipinas (Table 2, Models 4a & b). Large crowns of individual trees imply greater photosynthetic capacity and sturdy physical structures that support carbohydrate and nutrient demands of the large B. excelsa fruits. Large-diameter trees with big crowns produce more fruits. Furthermore, these trees are tall; all exhibit dominant or co-dominant canopy positions, suggesting fairly unlimited access to light. Notably, while basal area growth was a significant predictor of fruit production in trees More

  • in

    Dental microwear texture analysis as a tool for dietary discrimination in elasmobranchs

    Given that elasmobranchs are well known for the rate at which they replace their teeth, it is perhaps surprising that anterior teeth are retained long enough for dietarily informative microwear textures to develop. Yet our results demonstrate that tooth microwear textures vary with diet in C. taurus, and show that DMTA can provide an additional, potentially powerful tool for dietary discrimination in elasmobranchs. Furthermore, recent analysis indicates that C. taurus mostly consume prey in one piece30, implying less interaction of teeth with prey than would the case in animals that process their food before swallowing. We predict that for elasmobranchs that bite their prey the relationship between diet and microwear texture will be even stronger than that reported here.
    Sampling individuals with different diets reveals increases in PC 1 values that in turn correspond to changes in a number of different ISO texture parameters. In general terms, as noted above, there is a trend towards ‘rougher’ surfaces with increases in the proportion of elasmobranchs in C. taurus diets, and with increasing consumption of benthic elasmobranchs30,31,32 (which may be associated with an increase in the amount of sediment consumed with prey). The increase in variance of PC1 values may also reflect increased diversity of prey types30,31,32 in larger individuals. To a degree, the greater variance might reflect the greater difference between maximum development of ‘rough’ microwear texture in a tooth near the end of its functional life compared to a smooth, recently erupted tooth. Either way, our results indicate that microwear texture tracks diet, but more work will be required to tease apart these additional factors.
    Our analyses indicate that the tooth microwear textures of Specimen 5, from a different geographic area to other specimens, and for which we have no dietary data, are closely comparable to those of samples 1, 2 and 3, in terms of both values and variances. On this basis we interpret specimen 5 to have had a diet dominated by fish. The larger size of this specimen (at ca. 335 cm, larger than any other specimens analysed) lends further support to the hypothesis that microwear texture is tracking diet, and not size. Our dietary predictions regarding C. taurus from this area could be tested using traditional stomach contents, or stable isotope analyses, but this is outside the scope of the present study.
    Our results also suggest that application of DMTA to analysis of the diet of individual sharks will produce more reliable results if multiple teeth are sampled rather than a single tooth. Comparing the six teeth of the aquarium individuals (fed only fish) with six teeth sampled randomly from the wild individuals (which had more varied diets) revealed significant differences in every sub-sampling (Supplementary Table S5). However the number of parameters displaying a significant difference between wild and aquarium teeth varied, and fewer significant differences than were found than analyses comparing the aquarium teeth to multiple teeth from each wild individual. This suggests that analyses based on single isolated teeth rather than those from jaws, a situation that would commonly arise in analyses of fossil teeth, have the potential to detect differences between populations and species with different diets, but will be less sensitive than analyses based on multiple teeth per individual. To a certain extent, this will be offset in collections of isolated fossil teeth because the vast majority are teeth that were shed at the end of the functional cycle, so there will be much less sampling of recently erupted teeth with less well-developed microwear textures. (Due to the rate of tooth replacement in elasmobranchs, the number of teeth shed by an individual in its lifetime outnumber the number of teeth in the individuals jaw at time of death by several orders of magnitude).
    Drawing wider comparisons with microwear texture analyses in other groups of vertebrates, of the relationship between diet and 3D microwear texture based on ISO parameters, the number of parameters that differ between samples of C. taurus is larger than most previous studies, probably due to greater differences in material properties of food between the samples compared. Wild C. taurus consume a wider variety of prey than aquarium fed C. taurus. Wild individuals consume ‘harder’ prey items, whilst interacting with the natural environment. A wild individual consuming a benthic elasmobranch will have to bite through dermal denticles, a larger cartilage skeleton and inevitably will ingest some sediment during the process. In contrast aquarium individuals are largely fed whole and partial fish within the water column, a much ‘softer’ diet. Comparison of this study to others analysing vertebrate diet, repeatedly display significant differences in certain parameters when comparing groups with harder/softer diets. Purnell and Darras23 found that Sdq, Sdr, Vmc, Vvv, Sk and Sa discriminated best between the specialist durophagous and more opportunist durophagous fish in their study (based on ANOVA and PCA), with these parameters also differing between populations of the opportunist durophage Archosargus probatocephalus with different proportions of hard prey in their diets. Of these parameters, Sk, Sa, Vmc, and Vvv produce pairwise differences between C. taurus samples (between 1 and 4). These parameters capture aspects of surface heights and the volumes of material within the core and voids in valleys, respectively (Supplementary Table S1 online). All increase in value as the proportion of elasmobranchs in the diet increases, the same as the pattern of increase with durophagy seen in Archosargus probatocephalus and Anarhichas lupus23. Vmc, Vvv, and Sk were also found to increase with the amount of hard-shelled prey in the diet of cichlids24. This means that ‘harder’ diets produce tooth surface textures with greater core depth and an increase in the volumes of core material and valleys. In short ‘harder’ diets produce rougher tooth surfaces.
    This conclusion is also supported by a recent DMTA study on reptiles29, which exhibit significant overlap with sharks in the parameter trends correlating with ‘harder’ diets. Of the parameters correlating with increasing PC 1 values in sharks, parameters correlated with increasing dietary ‘hardness’ in reptiles include those capturing aspects of texture height (Sa, Sq, S5z), the number of peaks (Spk), and the depth, void volume and material volume of the core (Sk, Vvc, Vmc). Once again ‘harder’ diets produce rougher tooth surfaces.
    Other studies, although focussed on terrestrial rather than aquatic vertebrates, have found similar patterns. Vmc, Vvc, Vvv, and Sa increase with more abrasive diets in grazing ungulate mammals34; Vmc, Vvv and Sk increase with increasingly ‘hard’ prey in insectivorous bats21. Unlike other studies, the latter found Sa (the average surface height) to decrease with harder diets26. A recent study of bats and moles35 found that, like sharks, increasing the ‘hardness’ of the prey creates rougher tooth surfaces that can be defined by increases in Sa, Vmc, VVc values (amongst others) and a decrease in Sds values (amongst others). More

  • in

    Automated design of synthetic microbial communities

    1.
    Pantoja-Hernández, L. & Martínez-García, J. C. Retroactivity in the context of modularly structured biomolecular systems. Front. Bioeng. Biotechnol. 3, 85 (2015).
    PubMed  PubMed Central  Article  Google Scholar 
    2.
    Jayanthi, S. & Del Vecchio, D. Retroactivity attenuation in bio-molecular systems based on timescale separation. IEEE Trans. Autom. Control 56, 748–761 (2011).
    MathSciNet  Article  Google Scholar 

    3.
    Gyorgy, A. et al. Isocost lines describe the cellular economy of genetic circuits. Biophys. J. 109, 639–646 (2015).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    4.
    Summers, D. The kinetics of plasmid loss. Trends Biotechnol 9, 273–278 (1991).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    5.
    Mishra, D., Rivera, P. M., Lin, A., Del Vecchio, D. & Weiss, R. A load driver device for engineering modularity in biological networks. Nat. Biotechnol. 32, 1268–1275 (2014).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    6.
    Weiße, A. Y., Oyarzún, D. A., Danos, V. & Swain, P. S. Mechanistic links between cellular trade-offs, gene expression, and growth. Proc. Natl. Acad. Sci. USA 112, E1038–E1047 (2015).
    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

    7.
    Brenner, K., You, L. & Arnold, F. H. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 26, 483–489 (2008).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    8.
    Kennedy, T. A. et al. Biodiversity as a barrier to ecological invasion. Nature 417, 636–638 (2002).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    9.
    Beyter, D. et al. Diversity, productivity, and stability of an industrial microbial ecosystem. Appl. Environ. Microbiol. 82, 2494–2505 (2016).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    10.
    Butler, G. J. & Wolkowicz, G. S. K. A mathematical model of the chemostat with a general class of functions describing nutrient uptake. SIAM J. Appl. Math. 45, 138–151 (1985).
    MathSciNet  Article  Google Scholar 

    11.
    Foster, K. R. & Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845–1850 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    12.
    Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microb. 8, 15–25 (2010).
    CAS  Article  Google Scholar 

    13.
    Freilich, S. et al. Competitive and cooperative metabolic interactions in bacterial communities. Nat. Commun. 2, 589 (2011).
    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

    14.
    Zelezniak, A. et al. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl. Acad. Sci. USA 112, 6449–6454 (2015).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    15.
    May, A. et al. Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 7, e7565 (2019).
    PubMed  PubMed Central  Article  Google Scholar 

    16.
    Czaran, T. L., Hoekstra, R. F. & Pagie, L. Chemical warfare between microbes promotes biodiversity. Proc. Natl. Acad. Sci. USA 99, 786–790 (2002).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    17.
    Dinh, C. V., Chen, X. & Prather, K. L. J. Development of a quorum-sensing based circuit for control of coculture population composition in a naringenin production system. ACS Synth. Biol. 9, 590–597 (2020).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    18.
    Stephens, K., Pozo, M., Tsao, C.-Y., Hauk, P. & Bentley, W. E. Bacterial coculture with cell signaling translator and growth controller modules for autonomously regulated culture composition. Nat. Commun. 10, 4129 (2019).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    19.
    Liu, F., Mao, J., Lu, T. & Hua, Q. Synthetic, context-dependent microbial consortium of predator and prey. ACS Synth. Biol. 8, 1713–1722 (2019).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    20.
    Gupta, A., Reizman, I. M. B., Reisch, C. R. & Prather, K. L. J. Dynamic regulation of metabolic flux in engineered bacteria using a pathwayindependent quorum-sensing circuit. Nat. Biotechnol. 35, 273–279 (2017).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    21.
    Scott, S. R. & Hasty, J. Quorum sensing communication modules for microbial consortia. ACS Synth. Biol. 5, 969–977 (2016).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    22.
    Balagaddé, F. K. et al. A synthetic Escherichia coli predator–prey ecosystem. Mol. Syst. Biol. 4, 187 (2008).
    PubMed  PubMed Central  Article  Google Scholar 

    23.
    Kong, W., Meldgin, D. R., Collins, J. J. & Lu, T. Designing microbial consortia with defined social interactions. Nat. Chem. Biol. 14, 821–829 (2018).
    CAS  PubMed  Article  Google Scholar 

    24.
    Rebuffat S. M. (ed. Kastin, A. J.) In Handbook of Biologically Active Peptides 129–137 (Elsevier, 2013).

    25.
    Geldart, K., Forkus, B., McChesney, E., McCue, M. & Kaznessis, Y. pMPES: a modular peptide expression system for the delivery of antimicrobial peptides to the site of gastrointestinal infections using probiotics. Pharmaceuticals 9, 60 (2016).
    PubMed Central  Article  CAS  PubMed  Google Scholar 

    26.
    Fedorec, A. J. H. et al. Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in Escherichia coli. iScience 14, 323–334 (2019).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    27.
    MacDonald, J. T., Barnes, C., Kitney, R. I., Freemont, P. S. & Stan, G.-B. V. Computational design approaches and tools for synthetic biology. Integr. Biol. 3, 97 (2011).
    Article  Google Scholar 

    28.
    Kirk, P., Thorne, T. & Stumpf, M. P. H. Model selection in systems and synthetic biology. Curr. Opin. Biotechnol. 24, 767–774 (2013).
    CAS  PubMed  Article  Google Scholar 

    29.
    Barnes, C. P., Silk, D., Sheng, X. & Stumpf, M. P. H. Bayesian design of synthetic biological systems. Proc. Natl. Acad. Sci. USA 108, 15190–15195 (2011).
    ADS  CAS  PubMed  Article  Google Scholar 

    30.
    Woods, M. L., Leon, M., Perez-Carrasco, R. & Barnes, C. P. A Statistical approach reveals designs for the most robust stochastic gene oscillators. ACS Synth. Biol. 5, 459–470 (2016).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    31.
    Leon, M., Woods, M. L., Fedorec, A. J. H. & Barnes, C. P. A computational method for the investigation of multistable systems and its application to genetic switches. BMC Syst. Biol. 10, 130 (2016).
    PubMed  PubMed Central  Article  Google Scholar 

    32.
    Yeoh, J. W. et al. An automated biomodel selection system (BMSS) for gene circuit designs. ACS Synth. Biol. 8, 1484–1497 (2019).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    33.
    Beal, J. et al. An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth. Biol. 1, 317–331 (2012).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    34.
    Rodrigo, G. & Jaramillo, A. AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth. Biol. 2, 230–236 (2013).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    35.
    Friedman, J. & Gore, J. Ecological systems biology: the dynamics of interacting populations. Current Opinion in Systems Biology 1, 114–121 (2017).
    Article  Google Scholar 

    36.
    Toni, T., Welch, D., Strelkowa, N., Ipsen, A. & Stumpf, M. P. H. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. R. Soc. Interface 6, 187–202 (2009).
    PubMed  Article  PubMed Central  Google Scholar 

    37.
    Kass, R. E. & Raftery, A. E. Bayes factors. J. Am. Stat. Assoc. 90, 773–795 (1995).
    MathSciNet  Article  Google Scholar 

    38.
    Salis, H. M., Mirsky, E. A. & Christopher, C. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946–950 (2009).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    39.
    Marisch, K. et al. A Comparative analysis of industrial Escherichia coli K-12 and B strains in high-glucose batch cultivations on process-, transcriptomeand proteome level. PLoS ONE 8, e70516 (2013).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    40.
    Treloar, N. J., Fedorec, A. J. H., Ingalls, B. & Barnes, C. P. Deep reinforcement learning for the control of microbial co-cultures in bioreactors. PLOS Comput. Biol. 16, e1007783 (2020).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    41.
    Lee, D. D. & Seung, H. S. Learning the parts of objects by non-negative matrix factorization. Nature 401, 788–791 (1999).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    42.
    Kerner, A., Park, J., Williams, A. & Lin, X. N. A programmable Escherichia coli consortium via tunable symbiosis. PLoS ONE 7, e34032 (2012).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    43.
    Zhou, K., Qiao, K., Edgar, S. & Stephanopoulos, G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol. 33, 377–383 (2015).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    44.
    Shou, W., Ram, S. & Vilar, J. M. G. Synthetic cooperation in engineered yeast populations. Proc. Natl. Acad. Sci. USA 104, 1877–1882 (2007).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    45.
    Pande, S. et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J 8, 953–962 (2014).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    46.
    Yurtsev, E. A., Conwill, A. & Gore, J. Oscillatory dynamics in a bacterial crossprotection mutualism. Proc. Natl. Acad. Sci. USA 113, 6236–6241 (2016).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    47.
    Hosoda, K. et al. Cooperative adaptation to establishment of a synthetic bacterial mutualism. PLoS ONE 6, e17105 (2011).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    48.
    Zhang, X. & Reed, J. L. Adaptive evolution of synthetic cooperating communities improves growth performance. PLoS ONE 9, e108297 (2014).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    49.
    Chen, Y., Kim, J. K., Hirning, A. J., Josi, K. & Bennett, M. R. Emergent genetic oscillations in a synthetic microbial consortium. Science 349, 986–989 (2015).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    50.
    Bernstein, H. C., Paulson, S. D. & Carlson, R. P. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. J. Biotechnol. 157, 159–166 (2012).
    CAS  PubMed  Article  Google Scholar 

    51.
    Scott, S. R. et al. A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis. Nat. Microbiol. 2, 17083 (2017).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    52.
    Ziesack, M. et al. Engineered Interspecies amino acid cross-feeding increases population evenness in a synthetic bacterial consortium. mSystems 4, e00352–19 (2019).
    PubMed  PubMed Central  Article  Google Scholar 

    53.
    Liao, M. J., Din, M. O., Tsimring, L. & Hasty, J. Rock-paper-scissors: engineered population dynamics increase genetic stability. Science 365, 1045–1049 (2019).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    54.
    Ahn, J. et al. Human gut microbiome and risk for colorectal cancer. J. Natl Cancer Inst 105, 1907–1911 (2013).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    55.
    Stokell, J. R. et al. Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period. J. Clin. Microbiol. 53, 237–247 (2015).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    56.
    Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).
    PubMed  Article  PubMed Central  Google Scholar 

    57.
    Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).
    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

    58.
    Wang, X., Policarpio, L., Prajapati, D., Li, Z. & Zhang, H. Developing E. coli– E. coli co-cultures to overcome barriers of heterologous tryptamine biosynthesis. Metab. Eng. Commun. 10, e00110 (2020).
    PubMed  Article  PubMed Central  Google Scholar 

    59.
    Yuan, S. F., Yi, X., Johnston, T. G. & Alper, H. S. De novo resveratrol production through modular engineering of an Escherichia coli–Saccharomyces cerevisiae co-culture. Microb. Cell Factor 19, 143 (2020).
    CAS  Article  Google Scholar 

    60.
    Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol 1, 109 (2017).
    PubMed  Article  Google Scholar 

    61.
    Carmona-Fontaine, C. & Xavier, J. B. Altruistic cell death and collective drug resistance. Molecular Systems Biology 8, 627 (2012).
    PubMed  PubMed Central  Article  Google Scholar 

    62.
    Tanouchi, Y., Pai, A., Buchler, N. E. & You, L. Programming stress-induced altruistic death in engineered bacteria. Mol. Syst. Biol. 8, 626 (2012).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    63.
    Ackermann, M. et al. Self-destructive cooperation mediated by phenotypic noise. Nature 454, 987–990 (2008).
    ADS  CAS  PubMed  Article  Google Scholar 

    64.
    Williams, G. T. Programmed cell death: a fundamental protective response to pathogens. Trends Microbiol 2, 463–464 (1994).
    CAS  PubMed  Article  Google Scholar 

    65.
    Calles, B., Goñi-Moreno, Á. & Lorenzo, V. Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module. Mol. Syst. Biol. 15, e8777 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    66.
    Fedorec, A., Karkaria, B., Sulu, M. & Barnes, C. Single strain control of microbial consortia. bioRxiv, https://doi.org/10.1101/2019.12.23.887331 (2019).

    67.
    Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & Lilley, A. K. The contribution of species richness and composition to bacterial services. Nature 436, 1157–1160 (2005).
    ADS  CAS  PubMed  Article  Google Scholar 

    68.
    Hsu, R. H. et al. Venturelli. Microbial interaction network inference in microfluidic droplets. Cell Syst 9, 229–242.e4 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    69.
    Doekes, H. M., De Boer, R. J. & Hermsen, R. Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations. PLoS Comput. Biol. 15, e1007333 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    70.
    McNaughton, S. J. Stability and diversity of ecological communities. Nature 274, 251–253 (1978).
    ADS  Article  Google Scholar 

    71.
    Sterner, R. W., Bajpai, A. & Adams, T. The enigma of food chain length: absence of theoretical evidence for dynamic constraints. Ecology 78, 2258–2262 (1997).
    Article  Google Scholar 

    72.
    Barabás, G., Michalska-Smith, M. J. & Allesina, S. Self-regulation and the stability of large ecological networks. Nat. Ecol. Evol. 1, 1870–1875 (2017).
    PubMed  Article  PubMed Central  Google Scholar 

    73.
    Thébault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).
    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

    74.
    Tang, S., Pawar, S. & Allesina, S. Correlation between interaction strengths drives stability in large ecological networks. Ecol. Lett. 17, 1094–1100 (2014).
    PubMed  Article  PubMed Central  Google Scholar 

    75.
    Harris, C. R. et al. Array programming with NumPy. Nature 585, 357–362 (2020).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    76.
    Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    77.
    Siek, J. G., Lee, L.-Q., Lumsdaine, A. The Boost Graph Library, 243 (Addison-Wesley, 2002).

    78.
    Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
    MathSciNet  Google Scholar 

    79.
    Harper, M., et al. python-ternary: ternary plots in python. Zenodo https://doi.org/10.5281/zenodo.594435 (2019).

    80.
    Wickham, H. ggplot2-Positioning Elegant Graphics for Data Analysis (Springer-Verlag New York, 2016).

    81.
    Kylilis, N., Tuza, Z. A., Stan, G. B. & Polizzi, K. M. Tools for engineering coordinated system behaviour in synthetic microbial consortia. Nat. Commun. 9, 2677 (2018).
    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

    82.
    Senn, H., Lendenmann, U., Snozzi, M., Hamer, G. & Egli, T. The growth of Escherichia coli in glucose-limited chemostat cultures: a re-examination of the kinetics. BBA—Gen. Subj. 1201, 424–436 (1994).
    Article  Google Scholar 

    83.
    Destoumieux-Garzón, D. The iron-siderophore transporter FhuA is the receptor for the antimicrobial peptide microcin J25: role of the microcin Val11-Pro16 β-hairpin region in the recognition mechanism. Biochem. J. 389, 869–876 (2005).
    PubMed  PubMed Central  Article  Google Scholar 

    84.
    Kaur, K. et al. Characterization of a highly potent antimicrobial peptide microcin N from uropathogenic Escherichia coli. FEMS Microbiology Letters 363, fnw095 (2016).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    85.
    Andersen, K. B. & Meyenburg, K. V. Are growth rates of Escherichia coli in batch cultures limited by respiration? J. Bacteriol. 144, 114–123 (1980).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    86.
    Marenda, M., Zanardo, M., Trovato, A., Seno, F. & Squartini, A. Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries. Sci. Rep. 6, 39142 (2016).
    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

    87.
    Destoumieux-Garzón, D. et al. Microcin E492 antibacterial activity: evidence for a TonB-dependent inner membrane permeabilization on Escherichia coli. Mol. Microbiol. 49, 1031–1041 (2003).
    PubMed  Article  CAS  PubMed Central  Google Scholar 

    88.
    Karkaria, B. D., Fedorec, A. J. H. & Barnes, C. P. Automated design of synthetic microbial communities. Zenodo https://doi.org/10.5281/zenodo.4266261 (2020). More

  • in

    3D morphology of nematode encapsulation in snail shells, revealed by micro-CT imaging

    1.
    Frank, S. A. Immunology and Evolution of Infectious Diseases (Princeton, Princeton University Press, 2002).
    Google Scholar 
    2.
    Barker, G. M. Natural Enemies of Terrestrial Molluscs (CABI Publishing, Wallingford, 2004).
    Google Scholar 

    3.
    Grewal, P. S., Grewal, S. K., Tan, L. & Adams, B. J. Parasitism of molluscs by nematodes: types of associations and evolutionary trends. J. Nematol. 35, 146–156 (2003).
    CAS  PubMed  PubMed Central  Google Scholar 

    4.
    Blaxter, M. L. et al. A molecular evolutionary framework for the phylum Nematoda. Nature 392, 71–75 (1998).
    ADS  CAS  Article  Google Scholar 

    5.
    Pieterse, A., Malan, A. P. & Ross, J. L. Nematodes that associate with terrestrial molluscs as definitive hosts, including Phasmarhabditis hermaphrodita (Rhabditida: Rhabditidae) and its development as a biological molluscicide. J. Helminthol. 91, 517–527 (2017).
    CAS  Article  Google Scholar 

    6.
    Tillier, S., Masselot, M. & Tillier, A. Phylogenic relationships of the pulmonate gastropods from rRNA sequences, and tempo and age of the Stylommatophoran radiation. In Origin and Evolutionary Radiation of the Mollusca (ed. Taylor, J.D.) 267–284 (Oxford, Oxford University Press, 1996).

    7.
    Félix, M-A. & Braendle, C. The natural history of Caenorhabditis elegans. Curr. Biol. 20, R965-R969 (2010).

    8.
    Bolt, G., Monrad, J., Koch, J. & Jensen, A. L. Canine angiostrongylosis: a review. Vet. Rec. 135, 447–452 (1994).
    CAS  Article  Google Scholar 

    9.
    Loker E.S. Gastropod immunobiology in Invertebrate Immunity (ed. Soderhall, K.) 17–43 (Springer, 2010).

    10.
    South, A. Terrestrial Slugs: Biology, Ecology and Control (Chapman & Hall, London, 1992).
    Google Scholar 

    11.
    Wilson, M. J., Glen, D. M. & George, S. K. The rhabditid nematode Phasmarhabditis hermaphrodita as a potential biological control agent for slugs. Biocontrol Sci. Technol. 3, 503–511 (1993).
    Article  Google Scholar 

    12.
    Williams, A. J. & Rae, R. Susceptibility of the Giant African Snail (Achatina fulica) exposed to the gastropod parasitic nematode Phasmarhabditis hermaphrodita. J. Invertebr. Pathol. 127, 122–126 (2015).
    CAS  Article  Google Scholar 

    13.
    Williams, A. & Rae, R. Cepaea nemoralis uses its shell as a defence mechanism to trap and kill parasitic nematodes. J. Mollus. Stud. 12, 1–2 (2016).
    Google Scholar 

    14.
    Rae, R. The gastropod shell has been co-opted to kill parasitic nematodes. Sci. Rep. 7, 4745. https://doi.org/10.1038/s41598-017-04695-5 (2017).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    15.
    Rae, R., 2018. Shell encapsulation of parasitic nematodes by Arianta arbustorum (Linnaeus, 1758) in the laboratory and in field collections. J. Molluscan Stud. 84, 92–95 (2018).

    16.
    Cowlishaw, R. M., Andrus, P. & Rae, R. An investigation into nematodes encapsulated in shells of wild, farmed and museum specimens of Cornu aspersum and Helix pomatia. J. Conchol. 43, 1–8 (2020).
    Google Scholar 

    17.
    Lowenstam, H. A. & Weiner, S. On Biomineralization (Oxford University Press, Oxford, 1989).
    Google Scholar 

    18.
    Rae, R. G., Robertson, J. F. & Wilson, M. J. Susceptibility and immune response of Deroceras reticulatum, Milax gagates and Limax pseudoflavus exposed to the slug parasitic nematode Phasmarhabditis hermaphrodita. J. Invertebr. Pathol. 97, 61–69 (2008).
    Article  Google Scholar 

    19.
    Littlewood, D. T. J. & Donovan, S. K. Fossil parasites: a case of identity. Geol. Today. 19, 136–142 (2003).
    Article  Google Scholar 

    20.
    Poinar, G. O. Jr. The geological record of parasitic nematode evolution. Adv. Parasitol. 90, 53–92 (2015).
    Article  Google Scholar 

    21.
    Garwood, R., Dunlop, J.A. & Sutton, M.D. High-fidelity X-ray micro-tomography reconstruction of siderite-hosted Carboniferous arachnids. Biol. Lett. 5, 6 https://doi.org/10.1098/rsbl.2009.0464 (2009).

    22.
    Inoue, S. & Kondo, S. Structure pattern formation in ammonites and the unknown rear mantle structure. Sci. Rep. 6, 33689; https://doi.org/10.1038/srep33689 (2016).

    23.
    Shapiro, B. Ancient DNA. In Princeton Guide to Evolution (ed. Losos, J.) 475–481 (Princeton, Princeton University Press, 2013).

    24.
    Slon, V. et al. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature 561, 113–116 (2018).
    ADS  CAS  Article  Google Scholar 

    25.
    Swarts, K. et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357, 512–515 (2017).
    ADS  CAS  Article  Google Scholar 

    26.
    Spyrou, M. A. et al. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat. Commun. 9, 2234. https://doi.org/10.1038/s41467-018-04550-9 (2018).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    27.
    Loreille, O., Roumat, E., Verneau, O., Bouchet, F. & Hänni, C. Ancient DNA from Ascaris: extraction amplification and sequences from eggs collected from coprolites. Int. J. Parasitol. 31, 1101–1106 (2001).
    CAS  Article  Google Scholar 

    28.
    Søe, M. J., Nejsum, P., Fredensborg, B. L. & Kapel, C. M. O. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement. J. Parasitol. 101, 57–63 (2015).
    Article  Google Scholar 

    29.
    Lubell, D. Prehistoric edible land snails in the cicum-Mediterranean: the archaeological evidence. In Petits Animaux et Societes Humaines. Du Complement Alimentaire Aux Resources Utiliaires. XXIVe rencontres internationals d’archeologie et d’histoire d’Antibes (eds. Brugal, J-J & Dess, J.) 77–98 (Editions APDCA, 2004).

    30.
    Eamsobhana, P. Eosinophilic meningitis caused by Angiostrongylus cantonenses – a neglected disease with escalating importance. Trop. Biomed. 31, 569–578 (2014).
    CAS  PubMed  Google Scholar  More

  • in

    Utilization of the zebrafish model to unravel the harmful effects of biomass burning during Amazonian wildfires

    In vivo study: embryotoxicity test
    Zebrafish embryos exposed to tested compounds developed lethal and sub-lethal alterations including different abnormalities and unhatching events. LC50 (for mortality rate) and EC50 (for abnormality and unhatching rate) values were extrapolated from concentration–response curves shown in Fig. 1. The rate of dead, abnormal, and/or unhatched specimens was concentration-dependent for all tested compounds (Fig. 1a–c). The lethality of the negative control group was less than 5%. Compounds 4NC and CAT showed the highest toxicity with LC50 values of 8.16 and 10.95 mg/L, respectively, followed by 4,6DNG  > 5NG  > GUA. Experimental LC50/EC50 values and the predicted ones obtained by ECOlogical Structure Activity Relationship (ECOSAR) v2.0 software (https://www.epa.gov/tsca-screening-tools/ecological-structure-activity-relationships-ecosar-predictive-model) based on Quantitative Structure Activity Relationships (QSAR) models showed 4NC and CAT as the most toxic chemicals (Table 2). However, it is important to notice that experimental values for both compounds were approximately two times lower than the predicted ones. This led to the classification of 4NC into the group of molecules toxic to fish (1  GUA).
    Figure 3

    Recorded sublethal morphological effects in D. rerio embryos/larvae after 48, 72, and 96 h of exposure to CAT, 4NC, GUA, 5NG, and 4,6DNG. Negative control: normally developed embryo at (a) 48, (b) 72, and (c) 96 hpf. During exposure period alterations were manifested as: (d) yolk sac edema (arrow); (e) pericardial edema (asterisk), undeveloped tail region (arrow); (f) hatched fish with malformed spine (arrow); (g) underdeveloped tail and necrosis of its apical part (dashed arrow), rare pigments; (h) pericardial edema (asterisk), scoliosis (arrow), necrosis of the apical part of the tail (dashed arrow), rare pigments, not hatched; (i) scoliosis (arrows), blood accumulation in the brain region (dashed arrow); (j) pericardial edema (asterisk), yolk sac edema (arrow), scoliosis (dashed arrow); (k, l) pericardial edema (asterisk); (m) underdeveloped embryo: underdeveloped head (arrow), tail not detached (asterisk), delay or anomaly in the absorption of the yolk sac; (n) pericardial edema (asterisk), blood accumulation (arrow), not hatched; (o) pericardial edema (asterisk), blood clotting (arrow), not hatched; (p) blood accumulation at the yolk sac (arrow); (r) hatched fish with malformed spine; (s) pericardial edema (black asterisk), blood accumulation above the yolk sac (arrow), swelling of the yolk sac (white asterisk), yolk sac edema (dashed arrow), mild scoliosis. Developmental abnormalities were recorded using LAS EZ 3.2.0 digitizing software (https://www.leica-microsystems.com/products/microscope-software/p/leica-las-ez/).

    Full size image

    The morphometric measurements (Fig. 4) showed that all tested samples significantly affected sensorial (eye area), skeletal (head height), and physiological (yolk and pericardial sac area) parameters in zebrafish. Significant differences among all treatments with exact p values are presented in Table S2.
    Figure 4

    Morphometric measurements of D. rerio larvae after 96-h exposure to tested compounds (CAT, 4NC, GUA, 5NG, and 4,6DNG) and control (C). (a) Lateral view showing eye area (EA), head height (HH), yolk sac area (YSA), and pericardial sac area (PSA). Scale bar = 1000 µm. Morphometric parameters are presented by their mean value (b–e; n = 15). The symbol * indicates a significant difference between tested samples and negative control (*p  More

  • in

    Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession

    1.
    Battin, T. J. et al. Biophysical controls on organic carbon fluxes in fluvial networks. Nat. Geosci. 1, 95–100 (2008).
    CAS  Article  Google Scholar 
    2.
    Tranvik, L. J. et al. Lakes and reservoirs as regulators of carbon cycling and climate. Limnol. Oceanogr. 54, 2298–2314 (2009).
    CAS  Article  Google Scholar 

    3.
    Raymond, P. A. et al. Global carbon dioxide emissions from inland waters. Nature 503, 355–359 (2013).
    CAS  PubMed  Article  Google Scholar 

    4.
    Downing, J. A. Emerging global role of small lakes and ponds: little things mean a lot. Limnetica 29, 9–24 (2010).
    Google Scholar 

    5.
    Bastviken, D., Tranvik, L. J., Downing, J. A., Crill, P. M. & Enrich-Prast, A. Freshwater methane emissions offset the continental carbon sink. Science 331, 50–50 (2011).
    CAS  PubMed  Article  Google Scholar 

    6.
    Fairchild, G. W. & Velinsky, D. J. Effects of small ponds on stream water chemistry. Lake Reserv. Manag. 22, 321–330 (2006).
    CAS  Article  Google Scholar 

    7.
    Yin, C. & Shan, B. Multipond systems: a sustainable way to control diffuse phosphorus pollution. AMBIO 30, 369–375 (2001).
    CAS  PubMed  Article  Google Scholar 

    8.
    Stanley, E. H. & Doyle, M. W. A geomorphic perspective on nutrient retention following dam removal: geomorphic models provide a means of predicting ecosystem responses to dam removal. BioScience 52, 693–701 (2002).
    Article  Google Scholar 

    9.
    Downing, J. A., Cherrier, C. T. & Fulweiler, R. W. Low ratios of silica to dissolved nitrogen supplied to rivers arise from agriculture not reservoirs. Ecol. Lett. 19, 1414–1418 (2016).
    PubMed  Article  Google Scholar 

    10.
    Dickman, M. Some effects of lake renewal on phytoplankton productivity and species composition. Limnol. Oceanogr. 14, 660–666 (1969).
    Article  Google Scholar 

    11.
    Madsen, H., Lawrence, D., Lang, M., Martinkova, M. & Kjeldsen, T. R. Review of trend analysis and climate change projections of extreme precipitation and floods in Europe. J. Hydrol. 519, 3634–3650 (2014).
    Article  Google Scholar 

    12.
    Clark, J. M. et al. The importance of the relationship between scale and process in understanding long-term DOC dynamics. Sci. Total Environ. 408, 2768–2775 (2010).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    13.
    Vystavna, Y., Hejzlar, J. & Kopáček, J. Long-term trends of phosphorus concentrations in an artificial lake: socio-economic and climate drivers. PLoS ONE 12, e0186917 (2017).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    14.
    Reynolds, C. S. Phytoplankton assemblages and their periodicity in stratifying lake systems. Ecography 3, 141–159 (1980).
    Article  Google Scholar 

    15.
    Sommer, U., Gliwicz, Z. M., Lampert, W. & Duncan, A. The PEG-model of seasonal succession of planktonic events in fresh waters. Arch. Hydrobiol. 106, 433–471 (1986).
    Google Scholar 

    16.
    Kundzewicz, Z. W. et al. Differences in flood hazard projections in Europe—their causes and consequences for decision making. Hydrol. Sci. J. 62, 1–14 (2017).
    Google Scholar 

    17.
    Arnell, N. W. & Gosling, S. N. The impacts of climate change on river flood risk at the global scale. Clim. Change 134, 387–401 (2016).
    Article  Google Scholar 

    18.
    Hirabayashi, Y. et al. Global flood risk under climate change. Nat. Clim. Change 3, 816–821 (2013).
    Article  Google Scholar 

    19.
    Lynch, L. M. et al. River channel connectivity shifts metabolite composition and dissolved organic matter chemistry. Nat. Commun. 10, 459 (2019).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    20.
    Pimm, S. L. The complexity and stability of ecosystems. Nature 307, 321–326 (1984).
    Article  Google Scholar 

    21.
    Shade, A. et al. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J. 6, 2153–2167 (2012).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    22.
    Holling, C. S. Resilience and stability of ecological systems. Annu. Rev. Ecol. Evol. Syst. 4, 1–23 (1973).
    Article  Google Scholar 

    23.
    Holling, C. S. & Gunderson, L. H. in Panarchy Synopsis: Understanding Transformations in Human and Natural Systems (eds Gunderson, L. H. & Holling, C. S.) 25–62 (Island Press, 2002).

    24.
    Gabaldón, C. et al. Repeated flood disturbance enhances rotifer dominance and diversity in a zooplankton community of a small dammed mountain pond. J. Limnol. 76, 13 (2016).
    Google Scholar 

    25.
    Porcal, P. & Kopáček, J. Photochemical degradation of dissolved organic matter reduces the availability of phosphorus for aquatic primary producers. Chemosphere 193, 1018–1026 (2018).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    26.
    Macarthur, R. & Levins, R. The limiting similarity, convergence, and divergence of coexisting species. Am. Nat. 101, 377–385 (1967).
    Article  Google Scholar 

    27.
    Newton, R. J., Kent, A. D., Triplett, E. W. & McMahon, K. D. Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes. Environ. Microbiol. 8, 956–970 (2006).
    PubMed  Article  PubMed Central  Google Scholar 

    28.
    Neuenschwander, S. M., Ghai, R., Pernthaler, J. & Salcher, M. M. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME J. 12, 185–198 (2018).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    29.
    Cabello-Yeves, P. J. et al. Reconstruction of diverse verrucomicrobial genomes from metagenome datasets of freshwater reservoirs. Front. Microbiol. 8, 2131 (2017).
    PubMed  PubMed Central  Article  Google Scholar 

    30.
    Reznick, D., Bryant, M. J. & Bashey, F. r- and K-selection revisited: the role of population regulation in life-history evolution. Ecology 83, 1509–1520 (2002).
    Article  Google Scholar 

    31.
    Mac Arthur, R. H. & Wilson, E. O. The Theory of Island Biogeography (Princeton Univ. Press, 1967).

    32.
    Šimek, K. et al. A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol. Oceanogr. 59, 1477–1492 (2014).
    Article  CAS  Google Scholar 

    33.
    Logue, J. B., Mouquet, N., Peter, H. & Hillebrand, H. Empirical approaches to metacommunities: a review and comparison with theory. Trends Ecol. Evol. 26, 482–491 (2011).
    PubMed  Article  Google Scholar 

    34.
    Shabarova, T. et al. Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools. FEMS Microbiol. Ecol. 89, 111–126 (2014).
    CAS  PubMed  Article  Google Scholar 

    35.
    Shabarova, T., Widmer, F. & Pernthaler, J. Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools. Environ. Microbiol. 15, 2476–2488 (2013).
    CAS  PubMed  Article  Google Scholar 

    36.
    Jones, S. E. et al. Typhoons initiate predictable change in aquatic bacterial communities. Limnol. Oceanogr. 53, 1319–1326 (2008).
    Article  Google Scholar 

    37.
    Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 417 (2012).
    PubMed  PubMed Central  Article  Google Scholar 

    38.
    Hahn, M. W. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl. Environ. Microb. 69, 5248–5254 (2003).
    CAS  Article  Google Scholar 

    39.
    Salcher, M. M., Neuenschwander, S. M., Posch, T. & Pernthaler, J. The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. ISME J. 9, 2442–2453 (2015).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    40.
    Vuono, D. C. et al. Disturbance and temporal partitioning of the activated sludge metacommunity. ISME J. 9, 425–435 (2014).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    41.
    Shabarova, T. et al. Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach. Environ. Microbiol. 19, 1296–1309 (2017).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    42.
    Hahn, M. W., Lang, E., Tarao, M. & Brandt, U. Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. Int. J. Syst. Evol. Microbiol. 61, 781–787 (2011).
    CAS  PubMed  Article  PubMed Central  Google Scholar 

    43.
    Hahn, M. W. et al. The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living Polynucleobacter population. PLoS ONE 7, e32772 (2012).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    44.
    Pernthaler, J. Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Microbiol. 3, 537–546 (2005).
    CAS  PubMed  Article  Google Scholar 

    45.
    Sommer, U. et al. Beyond the plankton ecology group (Peg) model: mechanisms driving plankton succession. Annu. Rev. Ecol. Evol. Syst. 43, 429–448 (2012).
    Article  Google Scholar 

    46.
    Šimek, K. et al. Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates. Limnol. Oceanogr. 63, 484–502 (2018).
    Article  Google Scholar 

    47.
    Posch, T. et al. Network of interactions between ciliates and phytoplankton during spring. Front. Microbiol. 6, 1289 (2015).
    PubMed  PubMed Central  Article  Google Scholar 

    48.
    Geraldes, A. M. & Boavida, M.-J. Zooplankton assemblages in two reservoirs: one subjected to accentuated water level fluctuations, the other with more stable water levels. Aquat. Ecol. 41, 273–284 (2007).
    CAS  Article  Google Scholar 

    49.
    Nilssen, J. P. & Wærvågen, S. B. Superficial ecosystem similarities vs autecological stripping: the ‘twin species’ Mesocyclops leuckarti (Claus) and Thermocyclops oithonoides (Sars)—seasonal habitat utilisation and life history traits. J. Limnol. 59, 79–102 (2000).
    Article  Google Scholar 

    50.
    Cole, T. M. & Wells, S. A. CE-QUAL-W2: A Two-Dimensional, Laterally Averaged, Hydrodynamic and Water Quality Model, Version 4.1 (Department of Civil and Environmental Engineering, 2018).

    51.
    Brussaard, C. P. D. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microb. 70, 1506–1513 (2004).
    CAS  Article  Google Scholar 

    52.
    Porter, K. G. & Feig, Y. S. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943–948 (1980).
    Article  Google Scholar 

    53.
    Sherr, E. B. & Sherr, B. F. in Handbook of Methods in Aquatic Microbial Ecology (eds Kemp, P. F. et al.) 207–212 (Lewis Publishers, 1993).

    54.
    Sherr, E. B. & Sherr, B. F. in Handbook of Methods in Aquatic Microbial Ecology (eds Kemp, P. F. et al.) 695–701 (Lewis Publishers, 1993).

    55.
    Kasalický, V., Jezbera, J., Hahn, M. W. & Šimek, K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS ONE 8, e58209 (2013).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    56.
    Šimek, K. et al. Microbial food webs in hypertrophic fishponds: omnivorous ciliate taxa are major protistan bacterivores. Limnol. Oceanogr. 64, 2295–2309 (2019).
    Article  CAS  Google Scholar 

    57.
    Lund, J. W. G., Kipling, C. & Le Cren, E. D. The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia 11, 143–170 (1958).
    Article  Google Scholar 

    58.
    Hillebrand, H., Dürselen, C. D., Kirschtel, D., Pollingher, U. & Zohary, T. Biovolume calculation for pelagic and benthic microalgae. J. Phycol. 35, 403–424 (1999).
    Article  Google Scholar 

    59.
    Straškraba, M. & Hrbáček, J. Net-plankton cycle in slapy reservoir during 1958–1960. Hydrobiol. Stud. 1, 113–153 (1966).
    Google Scholar 

    60.
    Nercessian, O., Noyes, E., Kalyuzhnaya, M. G., Lidstrom, M. E. & Chistoserdova, L. Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl. Environ. Microb. 71, 6885–6899 (2005).
    CAS  Article  Google Scholar 

    61.
    Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    62.
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).

    63.
    Yilmaz, P. et al. The SILVA and ‘all-species living tree project (LTP)’ taxonomic frameworks. Nucleic Acids Res. 42, D643–D648 (2014).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    64.
    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    65.
    Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).
    CAS  PubMed  PubMed Central  Google Scholar 

    66.
    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    67.
    Schöfl, G. reutils: talk to the NCBI EUtils. R version 0.2.3 https://CRAN.R-project.org/package=reutils (2016).

    68.
    Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    69.
    Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    70.
    Fuchs, B. M., Glöckner, F. O., Wulf, J. & Amann, R. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microb. 66, 3603–3607 (2000).
    CAS  Article  Google Scholar 

    71.
    Buckley, D. H. & Schmidt, T. M. Environmental factors influencing the distribution of rRNA from verrucomicrobia in soil. FEMS Microbiol. Ecol. 35, 105–112 (2001).
    CAS  PubMed  Article  Google Scholar 

    72.
    Yilmaz, L. S., Parnerkar, S. & Noguera, D. R. mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl. Environ. Microb. 77, 1118–1122 (2011).
    CAS  Article  Google Scholar 

    73.
    Sekar, R. et al. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microb. 69, 2928–2935 (2003).
    CAS  Article  Google Scholar 

    74.
    Lorenzen, C. J. Determination of chlorophyll and pheo-pigments: spectrophotometric equations 1. Limnol. Oceanogr. 12, 343–346 (1967).
    CAS  Article  Google Scholar 

    75.
    Golterman, H. L. Methods for Chemical Analysis of Fresh Waters (F. A. Davis Company, 1969).

    76.
    Murphy, J. & Riley, J. P. A modified single solution method for the determination of phosphate in natural waters. Anal. Chim. Acta 27, 31–36 (1962).
    CAS  Article  Google Scholar 

    77.
    Kopáček, J. & Hejzlar, J. Semi-micro determination of total phosphorus in fresh waters with perchloric acid digestion. Int. J. Environ. Anal. Chem. 53, 173–183 (1993).
    Article  Google Scholar 

    78.
    Oksanen, J. et al. vegan: community ecology package. R version 2.5–6 (2019); https://CRAN.R-project.org/package=vegan More

  • in

    Phenological shifts of abiotic events, producers and consumers across a continent

    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Tomas Roslin

    University of Helsinki, Helsinki, Finland
    Tomas Roslin, Laura Antão, Maria Hällfors, Coong Lo, Juri Kurhinen & Otso Ovaskainen

    EarthCape OY, Helsinki, Finland
    Evgeniy Meyke

    Department of Computer Science, Aalto University, Espoo, Finland
    Gleb Tikhonov

    Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, Mieres, Spain
    Maria del Mar Delgado

    3237 Biology-Psychology Building, University of Maryland, College Park, MD, USA
    Eliezer Gurarie

    National Park Orlovskoe Polesie, Oryol, Russian Federation
    Marina Abadonova

    Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
    Ozodbek Abduraimov, Azizbek Mahmudov & Mirabdulla Turgunov

    Kostomuksha Nature Reserve, Kostomuksha, Russian Federation
    Olga Adrianova, Irina Gaydysh & Natalia Sikkila

    Altai State Nature Biosphere Reserve, Gorno-Altaysk, Russian Federation
    Tatiana Akimova, Svetlana Chuhontseva, Elena Gorbunova, Yury Kalinkin, Helen Korolyova, Oleg Mitrofanov, Miroslava Sahnevich, Vladimir Yakovlev & Tatyana Zubina

    Kabardino-Balkarski Nature Reserve, Kashkhatau, Russian Federation
    Muzhigit Akkiev

    FSE Zapovednoe Podlemorye, Ust-Bargizin, Russian Federation
    Aleksandr Ananin, Evgeniya Bukharova & Natalia Luzhkova

    Institute of General and Experimental Biology, Siberian Branch, Russian Academy of Sciences, Ulan-Ude, Russian Federation
    Aleksandr Ananin

    State Nature Reserve Stolby, Krasnoyarsk, Russian Federation
    Elena Andreeva, Nadezhda Goncharova, Alexander Hritankov, Anastasia Knorre, Vladimir Kozsheechkin & Vladislav Timoshkin

    Carpathian Biosphere Reserve, Rakhiv, Ukraine
    Natalia Andriychuk, Alla Kozurak & Anatoliy Vekliuk

    Nizhne-Svirsky State Nature Reserve, Lodeinoe Pole, Russian Federation
    Maxim Antipin

    State Nature Reserve Prisursky, Cheboksary, Russian Federation
    Konstantin Arzamascev

    Zapovednoe Pribajkalje (Bajkalo-Lensky State Nature Reserve, Pribajkalsky National Park), Irkutsk, Russian Federation
    Svetlana Babina

    Darwin Nature Biosphere Reserve, Borok, Russian Federation
    Miroslav Babushkin, Andrey Kuznetsov, Natalia Nemtseva, Irina Rybnikova & Nicolay Zelenetskiy

    Volzhsko-Kamsky National Nature Biosphere Rezerve, Sadovy, Russian Federation
    Oleg Bakin, Elena Chakhireva & Alexey Pavlov

    FGBU National Park Shushenskiy Bor, Shushenskoe, Russian Federation
    Anna Barabancova & Andrej Tolmachev

    Voronezhsky Nature Biosphere Reserve, Voronezh, Russian Federation
    Inna Basilskaja & Inna Sapelnikova

    Baikalsky State Nature Biosphere Reserve, Tankhoy, Russian Federation
    Nina Belova, Olga Ermakova, Irina Kozyr, Aleksandra Krasnopevtseva & Nikolay Volodchenkov

    Visimsky Nature Biosphere Reserve, Kirovgrad, Russian Federation
    Natalia Belyaeva & Rustam Sibgatullin

    Kondinskie Lakes National Park named after L. F. Stashkevich, Sovietsky, Russian Federation
    Tatjana Bespalova, Alena Butunina, Aleksandra Esengeldenova, Natalia Korotkikh & Evgeniy Larin

    FSBI United Administration of the Kedrovaya Pad’ State Biosphere Nature Reserve and Leopard’s Land National Park, Vladivostok, Russian Federation
    Evgeniya Bisikalova

    Pechoro-Ilych State Nature Reserve, Yaksha, Russian Federation
    Anatoly Bobretsov, Murad Kurbanbagamaev, Irina Megalinskaja, Viktor Teplov, Valentina Teplova & Tatiana Tertitsa

    A. N. Severtsov Institute of Ecology and Evolution, Moscow, Russian Federation
    Vladimir Bobrov & Igor Pospelov

    Komsomolskiy Department, FGBU Zapovednoye Priamurye, Komsomolsk-on-Amur, Russian Federation
    Vadim Bobrovskyi, Olga Kuberskaya, Polina Van & Vladimir Van

    Tigirek State Nature Reserve, Barnaul, Russian Federation
    Elena Bochkareva & Evgeniy A. Davydov

    Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russian Federation
    Elena Bochkareva

    State Nature Reserve Bolshaya Kokshaga, Yoshkar-Ola, Russian Federation
    Gennady Bogdanov

    Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, Russian Federation
    Vladimir Bolshakov

    Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov, Terney, Russian Federation
    Svetlana Bondarchuk, Sergey Elsukov, Ludmila Gromyko, Irina Nesterova & Elena Smirnova

    FSBI Prioksko-Terrasniy State Reserve, Danky, Russian Federation
    Yuri Buyvolov & Galina Sokolova

    Lomonosov Moscow State University, Moscow, Russian Federation
    Anna Buyvolova & Ilya Prokhorov

    National Park Meshchera, Gus-Hrustalnyi, Russian Federation
    Yuri Bykov, Zoya Drozdova & Svetlana Mayorova

    South Urals Federal Research Center of Mineralogy and Geoecology, Ilmeny State Reserve, Ural Branch, Russian Academy of Sciences, Miass, Russian Federation
    Olga Chashchina, Nadezhda Kuyantseva & Valery Zakharov

    FGBU National Park Kenozersky, Arkhangelsk, Russian Federation
    Nadezhda Cherenkova, Svetlana Drovnina & Alexander Samoylov

    FGBU GPZ Kologrivskij les im. M.G. Sinicina, Kologriv, Russian Federation
    Sergej Chistjakov

    Altai State University, Barnaul, Russian Federation
    Evgeniy A. Davydov

    Pryazovskyi National Nature Park, Melitopol’, Ukraine
    Viktor Demchenko, Elena Diadicheva & Valeri Sanko

    State Nature Reserve Privolzhskaya Lesostep, Penza, Russian Federation
    Aleksandr Dobrolyubov & Aleksey Kudryavtsev

    Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
    Ludmila Dostoyevskaya, Violetta Fedotova & Pavel Lebedev

    Sary-Chelek State Nature Reserve, Aksu, Kyrgyzstan
    Akynaly Dubanaev

    Institute for Evolutionary Ecology NAS Ukraine, Kiev, Ukraine
    Yuriy Dubrovsky

    FGBU State Nature Reserve Kuznetsk Alatau, Mezhdurechensk, Russian Federation
    Lidia Epova

    Kerzhenskiy State Nature Biosphere Reserve, Nizhny Novgorod, Russian Federation
    Olga S. Ermakova

    FSBI United Administration of the Mordovia State Nature Reserve and National Park Smolny, Republic of Mordovia, Saransk, Russian Federation
    Elena Ershkova

    Ogarev Mordovia State University, Saransk, Russian Federation
    Elena Ershkova

    Bryansk Forest Nature Reserve, Nerussa, Russian Federation
    Oleg Evstigneev, Evgeniya Kaygorodova, Sergey Kossenko, Sergey Kruglikov & Elena Sitnikova

    Pinezhsky State Nature Reserve, Pinega, Russian Federation
    Irina Fedchenko, Lyudmila Puchnina, Svetlana Rykova & Andrei Sivkov

    The Central Chernozem State Biosphere Nature Reserve named after Professor V.V. Alyokhin, Kurskiy, Russian Federation
    Tatiana Filatova

    Tyumen State University, Tyumen, Russian Federation
    Sergey Gashev

    Reserves of Taimyr, Norilsk, Russian Federation
    Anatoliy Gavrilov, Leonid Kolpashikov, Elena Pospelova & Violetta Strekalovskaya

    Chatkalski National Park, Toshkent, Uzbekistan
    Dmitrij Golovcov

    National Park Ugra, Kaluga, Russian Federation
    Tatyana Gordeeva & Viktorija Teleganova

    Kaniv Nature Reserve, Kaniv, Ukraine
    Vitaly Grishchenko, Yuliia Kulsha, Vasyl Shevchyk & Eugenia Yablonovska-Grishchenko

    Smolenskoe Poozerje National Park, Przhevalskoe, Russian Federation
    Vladimir Hohryakov, Gennadiy Kosenkov & Ksenia Shalaeva

    FSBI Zeya State Nature Reserve, Zeya, Russian Federation
    Elena Ignatenko, Klara Pavlova & Sergei Podolski

    Polistovsky State Nature Reserve, Pskov, Russian Federation
    Svetlana Igosheva & Tatiana Novikova

    Ural State Pedagogical University, Yekaterinburg, Russian Federation
    Uliya Ivanova, Margarita Kupriyanova, Tamara Nezdoliy, Nataliya Skok & Oksana Yantser

    Institute of Mathematical Problems of Biology RAS—the Branch of the Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Russian Federation
    Natalya Ivanova & Maksim Shashkov

    Kronotsky Federal Nature Biosphere Reserve, Yelizovo, Russian Federation
    Fedor Kazansky & Darya Panicheva

    Zhiguli Nature Reserve, P. Bakhilova Polyana, Russian Federation
    Darya Kiseleva

    Institute for Ecology and Geography, Siberian Federal University, Krasnoyarsk, Russian Federation
    Anastasia Knorre

    Central Forest State Nature Biosphere Reserve, Tver, Russian Federation
    Evgenii Korobov, Elena Shujskaja, Sergei Stepanov & Anatolii Zheltukhin

    National Park Bashkirija, Nurgush, Russian Federation
    Elvira Kotlugalyamova & Lilija Sultangareeva

    State Nature Reserve Kurilsky, Juzhno-Kurilsk, Russian Federation
    Evgeny Kozlovsky

    Vodlozersky National Park, Karelia, Petrozavodsk, Russian Federation
    Elena Kulebyakina & Viktor Mamontov

    State Nature Reserve Kivach, Kondopoga, Russian Federation
    Anatoliy Kutenkov, Nadezhda Kutenkova, Anatoliy Shcherbakov, Svetlana Skorokhodova, Alexander Sukhov & Marina Yakovleva

    South-Ural Federal University, Miass, Russian Federation
    Nadezhda Kuyantseva

    Saint-Petersburg State Forest Technical University, St. Petersburg, Russian Federation
    Pavel Lebedev

    Astrakhan Biosphere Reserve, Astrakhan, Russian Federation
    Kirill Litvinov

    FSBI United Administration of the Lazovsky State Reserve and National Park Zov Tigra, Lazo, Russian Federation
    Lidiya Makovkina, Aleksandr Myslenkov & Inna Voloshina

    State Nature Reserve Tungusskiy, Krasnoyarsk, Russian Federation
    Artur Meydus, Julia Raiskaya & Vladimir Sopin

    Krasnoyarsk State Pedagogical University named after V.P. Astafyev, Krasnoyarsk, Russian Federation
    Artur Meydus

    Institute of Geography, Russian Academy of Sciences, Moscow, Russian Federation
    Aleksandr Minin

    Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russian Federation
    Aleksandr Minin

    Carpathian National Nature Park, Yaremche, Ukraine
    Mykhailo Motruk

    State Environmental Institution National Park Braslav lakes, Braslav, Belarus
    Nina Nasonova

    National Park Synevyr, Synevyr-Ostriki, Ukraine
    Tatyana Niroda, Ivan Putrashyk, Yurij Tyukh & Yurij Yarema

    Pasvik State Nature Reserve, Nikel, Russian Federation
    Natalja Polikarpova

    Mari Chodra National Park, Krasnogorsky, Russian Federation
    Tatiana Polyanskaya

    State Nature Reserve Vishersky, Krasnovishersk, Russian Federation
    Irina Prokosheva

    State Nature Reserve Olekminsky, Olekminsk, Russian Federation
    Yuri Rozhkov, Olga Rozhkova & Dmitry Tirski

    Crimea Nature Reserve, Alushta, Republic of Crimea
    Marina Rudenko

    Forest Research Institute Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russian Federation
    Sergei Sazonov, Lidia Vetchinnikova & Juri Kurhinen

    Black Sea Biosphere Reserve, Hola Prystan’, Ukraine
    Zoya Selyunina

    Institute of Physicochemical and Biological Problems in Soil Sciences, Russian Academy of Sciences, Pushchino, Russian Federation
    Maksim Shashkov

    State Nature Reserve Nurgush, Kirov, Russian Federation
    Sergej Shubin & Ludmila Tselishcheva

    Caucasian State Biosphere Reserve of the Ministry of Natural Resources, Maykop, Russian Federation
    Yurii Spasovski

    National Nature Park Vyzhnytskiy, Berehomet, Ukraine
    Vitalіy Stratiy

    National Park Khvalynsky, Khvalynsk, Russian Federation
    Guzalya Suleymanova

    State Research Center Arctic and Antarctic Research Institute, Saint Petersburg, Russian Federation
    Aleksey Tomilin

    Information-Analytical Centre for Protected Areas, Moscow, Russian Federation
    Aleksey Tomilin

    State Nature Reserve Malaya Sosva, Sovetskiy, Russian Federation
    Aleksander Vasin & Aleksandra Vasina

    Krasnoyarsk State Medical University named after Prof. V.F.Voino-Yasenetsky, Krasnoyarsk, Russian Federation
    Vladislav Vinogradov

    Surhanskiy State Nature Reserve, Sherabad, Uzbekistan
    Tura Xoliqov

    Mordovia State Nature Reserve, Pushta, Russian Federation
    Andrey Zahvatov

    Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
    Otso Ovaskainen

    The data were collected by the 195 authors starting from M.A. and ending with T.Z. in the author list. J.K., E.M., C.L., G.T. and E.G. contributed to the establishment and coordination of the collaborative network and to the compilation and curation of the resulting dataset. T.R., O.O., L.A., M.H. and M.d.M.D. conceived the idea behind the current study and wrote the first draft of the paper, with O.O. conducting the analyses. All authors provided useful comments on earlier drafts. More