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    High resolution biologging of breaching by the world’s second largest shark species

    In the present study, we used accelerometer enabled animal-borne biologging tags (recording temperature, pressure and three-axis accelerometry) to describe in high temporal resolution the variability and repeatability of 67 breaches made by three sharks over 41 cumulative days (Fig. 1; shark 5 m length (n = 1) 678 kg estimated mass; and sharks 6 m length (n = 2) 160 kg estimated mass). Approximately half (n = 28) of all breaches were single breaches, but we also recorded 13 double breaches, three triple breaches and one shark that breached four times in 47 s (Fig. 2A-D). Consecutive breaches were 18 s apart (mean value ± 6 s.d, range 12–47 s); i.e. sharks ascend from depth to the surface, propel themselves out of the water and swim to depth before commencing the subsequent ascent. Breaching frequency varied among individuals. Shark 1 breached 0.4 ± 0.9 times per day (mean ± 1 s.d.; range 0–2, n = 2 breaches), shark 3 breached 0.9 per day (± 0.9 s.d, range 0–2, n = 5) and shark 2 breached 1.9 times per day (± 1.8 s.d, range 0–6, N = 60) over 4.8, 4.9 and 31.8 tracking days respectively), during both day and night (peak hour of breaching 04:00 am). Multiple breaches by the same sharks have never been empirically demonstrated before, and breaching has not been described to take place at night.
    Figure 1

    Basking shark breaching. Breaching recorded by a towed camera tag deployed in 2018. These data are from a shark that was not instrumented with an accelerometer, they are included to aid visualisation of the breaching process from a point-of-view perspective. For sharks instrumented with accelerometers in 2017, tags where attached flush to the surface of the animal at the base of the dorsal fin. (A) Basking shark breaching (photo: Youen Jacob). The timing and depth associated with each image (C–H) are identified on the breaching depth profile (B). (C,D) the shark starts to ascend from 72 m depth at 0.94 m of vertical gain per second, reaching the surface (in view, E) in 77 s. The shark can be seen completely out of the water (F), before descending (G,H) to depth again.

    Full size image

    Figure 2

    Characteristics of breaching. (A–D) A quadruple breach by a six-metre basking shark over 47 s showing changes in depth (A), tail beat amplitude (B), VeDBA (C) and speed (D) over the series of breaches. (E) Depth profiles of 16 single breaching events performed by a single shark, with time (in seconds) centred on the breach, overlaid on a common timescale showing repeatability of ascent angle and subsequent descent after breaching. (F) Dubai plot showing tri-axial acceleration data as a 3-dimensional histogram, with time spent by sharks in a particular posture on each facet of the sphere extruded as triangular bars, and colour scaling with the cumulative time in a given facet. Data show a right-handed breach of a single shark, where rapid rolling is indicated by short dark blue bars on the right face of the sphere.

    Full size image

    At the onset of a breach, sharks switched from slow swimming at 0.3 m.s-1 (mean value ± 0.16 s.d., range 0.17–0.4 m.s-1) at 14.8 m depth (± 5, range 4.6–28 m), to swimming towards the surface (Fig. 1C-E) at an angle of 38.9° (± 13.2, 23.08 to 81.6°), and an average (mean) ascent speed of 2.7 m.s-1 ± 0.5 (1.2–3.8 m.s-1). The peak ascent phase of a breach was observed when the rates of ascent and swimming speed rapidly increased. Breaching metrics were calculated separately for this peak ascent phase, where basking sharks reached the surface in 6 s (± 2.1, 2–17), before breaching near vertically at 76° (± 9, 43.3–87.9°), leaving the water at a mean exit speed of 3.9 m.s-1 ± 0.6. range: 2.2–5.6 m.s-1) (Fig. 1F). To contextualise our observations, an 8 m basking shark breached at 5.1 m.s-1 from 28 m depth10 and oceanic whitetip sharks (Carcharhinus longimanus)11 and great white sharks (Carcharodon carcharias)11,12 ambush-breach their prey at 4 and up to 6.5 m s−1 respectively, but from considerably deeper ( > 100 m11) and are smaller sharks. The peak forces generated by the three tagged basking sharks (which were estimated to weigh up to 1160 kg) were 20 G at the peak of breaching. Breaches could be further characterised by whether sharks exited the water on a particular side of their body. Sharks rolled to their right side in 45 of the 67 breaches (representing 67% of breaches), which may be suggestive of lateralisation (Fig. 2F), the preference for breaching on one side consistently across events13,14. Dynamic body acceleration (VeDBA) (linear mixed effects model; χ2 7.6, p = 0.006) along with tailbeat amplitude (linear mixed effects model; χ2 5.54, p = 0.019) increased with the sharks’ ascent pitch towards the surface. Breaching events were highly repeatable, both among and between sharks, following a similar ascent rate, speed and angle, and from a similar starting depth (Fig. 2E). Breaching was more energetically demanding than routine swimming (breaching VeDBA 7.7 m s−2 ± 4.5, range 0.4–14.7 vs routine swimming VeDBA 0.24 m.s-2 ± 0.04, 0.2–0.27), requiring double the tail beat frequency (breaching 0.49 Hz ± 0.12 vs routine swimming 1.08 Hz ± 0.51) and 15 times the tail beat amplitude (breaching 1.5 ± 1.1 Hz vs. routine swimming 0.1 ± 0.05 Hz). During multiple breaching events, the ascent rate, swimming speed and acceleration were similar for every subsequent breach, although the ascent starting depth was often shallower than for the initial breach. The relatively low field metabolic rate that comes with being ectothermic makes energetically demanding behaviour relatively more expensive for sharks. Therefore, the costs of performing multiple breaches may accumulate more rapidly compared to endothermic whales, such as humpback whales (Megaptera novaeangliae), which have been recorded breaching 17 times in a 6.5 h deployment15. On average, sharks required an estimated 11.5 kJ (range 3–22 kJ) of mechanical energy (({E}_{m})) to perform a breach, and expended the same ({E}_{m}) for each breach, regardless of whether they breached once or several times (Wilcoxon rank sum test, W = 198.5, p = 0.87; ({E}_{m} single) = 11.5 to 11.8 kJ, ({E}_{m} multi) = 9.98 to 10.3 kJ). Comparatively, the energetic cost of breaching for an 8 m basking shark weighing 2700 kg was estimated six times greater (63 to 72 kJ10). These differences may be attributed to the sharks in the present study being smaller, with the cost of breaching found to increase with increasing body mass15. A breach likely constitutes approximately 0.05 to 0.09% of their daily metabolic cost, which ranged from 12.8 to 21.5 MJ per day16. For comparison, the relative cost of performing a single breach in a 7.8 m (7000 kg) humpback whale represents 0.08 to 0.5% of its daily field metabolic rate15.
    The question remains what the function of breaching is for basking sharks. We are still far from certain what the function of breaching is for many aquatic species, but spinner dolphins, blacktip sharks and humpback whales are known to breach to dislodge epiparasites17. Gore et al.9 noted that epiparasitic lampreys were not dislodged from basking sharks following breaching, suggesting that it may not function for parasite removal, or may require several breaches to dislodge such parasites. Breaching may be used to visually signal between spinner dolphins, and between humpback whales17. Basking sharks breached during the night-time as well as the daytime, and have small eyes, suggesting that breaching is unlikely to be a visual signal. However, breaching may play a role in acoustic communication between distant groups of sharks. Basking sharks can apparently detect weak electric signals produced by zooplankton18, and some elasmobranchs use electro-sensory cues during courtship19, suggesting that breaching could convey readiness to mate. It thus seems possible that the acoustic signal of breaching could be detectable and useful to basking sharks. We have no information in the present study about the presence of other sharks during breaching, although future work using animal-borne acoustic proximity receivers on large numbers of sharks, or aerial drones, could provide insight into the social networks of basking sharks, and whether they breach in proximity to conspecifics. We propose that in the absence of a better explanation and given the predictable and persistent aggregations of basking sharks in Scottish waters, that breaching may be more likely to be related to intra-specific signalling, than anything else yet described.
    We show using repeated direct measurements from three individuals, that the mechanical forces required for basking sharks to breach are considerable, but that basking sharks can breach repeatedly in quick succession. The role of breaching seems most likely to be related to intra-specific signalling and may add to a weight of evidence suggesting that Scottish waters may be an important site for breeding for the species. More

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    Competition between strains of Borrelia afzelii in the host tissues and consequences for transmission to ticks

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    Nesting of Ceratina nigrolabiata, a biparental bee

    Phenology
    Ceratina nigrolabiata excavate new nests mainly in May and June, however, some newly excavated nests were also recorded later in the season (Figs. 1, 2). Active brood nests (Table 1) occurred from half of June and appeared in high proportion through whole July. First full brood nests first occurred at the end of June, but the main peak of full brood nests was in July. Full brood nests were also frequent in August. Full-mature and mature brood nests occurred from the end of July, and they were very frequent through August. Other types of nests occurred mainly in the beginning and at the end of season. At the beginning of the season occurred mainly old hibernacula or adults of C. nigrolabiata visiting nests of other Ceratina. In the late phases of season occurred abandoned nests with only parasites and newly excavated burrows for hibernation.
    Figure 1

    Nesting cycle of C. nigrolabiata. (a) newly excavated nests—burrow which contains only adult(s) and sometimes fillings. (b) discarded nest—burrow where previous nest was discarded, and there are pollen remnants on the walls (c) active brood nest—nest in phase brood cell provisioning (d) large active brood nest, where egg is present at the top, but young adults already developed at the bottom of nest (f) guarded full brood nest—mother guards this nest (f) plugged full brood nest—nest is unguarded and closed by a thick filling plug (g) orphaned full brood nest—last brood cell partition is thin and above it is commonly pollen from incompletely provisioned brood cell (h) full-mature brood nest—this nest contains juveniles, young adults, and sometimes mother (i) mature brood nest—this nest contains young adults and sometimes mother. All these figures are hypothetical examples, they are not based on concrete dissected nests.

    Full size image

    Figure 2

    Phenology of C. nigrolabiata through nesting season.

    Full size image

    Table 1 Criteria for classification of nest stages.
    Full size table

    Type of nest founding
    We found two types of newly founded nests. Newly excavated nests, which were built by excavating pith from a twig. Discarded nests are the other type. These nests were built from previous nest of Ceratina (probably other C. nigrolabiata in most cases) by discarding a part of or all original offspring (Figs. S1 and S2). We observed nests of C. nigrolabiata, where nest partitions were destroyed and pollen from brood cells was placed on side of the nest. We suppose that original offspring were discarded out of the nest (and on several occasions, we observed discarding of offspring out of the nest). Pollen provisions of the previous nest owner were usually moved to the sides of the nest (Fig. S1). From newly founded nests, 82.69% (86/104) were newly excavated and 17.30% (18/104) were discarded nests. When we counted only nests founded after half of June, the proportion of discarded nests was 22.78% (18/79). From active brood nests, 4.66% (29/622) had apparent relics of usurpation and discarding.
    Presence of parents
    Newly excavated nests
    In newly founded nests, only male was present in 53.48% of nests (46/86, Table 2), only female was present in 10.46% of nests (9/86) and male and female together were present in 36.04% (31/86) nests. Newly founded nests were on average 5.47 cm long (SD = 4.68, range 1–22.1, N = 86). Nests with only male were on average 3.82 cm long (SD = 3.26, range 1.2–16.7, N = 46), nests with only female were on average 5.73 cm long (SD = 4.72, range 1–14.1, N = 9), nests with both male and female were on average 7.85 cm long (SD = 5.49, range 1.9–22.1, N = 31). Nests with both parents were significantly longer than nests with only a male (Tukey HSD test on logarithmic data, difference = 0.6743, p = 0.0003), but not significantly longer than nests with only a female (Tukey HSD test on logarithmic data, difference 0.4427 p = 0.2256).
    Table 2 Presence of individuals of parental generation in different nest stages.
    Full size table

    Discarded nests
    In 72.22% (13/18) of discarded nests one male and one female were present. Female and two males were present in two nests, only a male was present in one nest, only a female was present in one nest and no adult was found in one nest.
    Active brood nests
    We found male–female pair in 84.72% of nests (527/622), female and two males were found in 1.29% of nests (8/622), female and three males were found in 0.16% (1/622) of nests, no adult was present in 1.76% (11/622) of nests, only male was in 5.6% (35/622) and only female in 6.43% (40/622) of nests.
    Full brood nests
    Most of full brood nests (73.51%, 493/672) were not guarded by any parent (Table 2). When a full brood nest was guarded, then usually by a female (15.18%, 102/672). Only male was present in 4.31% (29/672) and male and female were present in 7.14% (48/672). Males were significantly more often present in nests, where female was also present, than in nests without a female (Chi-square test, Chi = 81.06, df = 1, p  More

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    The comprehensive changes in soil properties are continuous cropping obstacles associated with American ginseng (Panax quinquefolius) cultivation

    Pot experiment of AG planting
    As shown in Fig. 1, compared to CS, the survival rate of 10-year rotation AG decreased, indicating that 2-year-old AG survival rate in RS was lower than that of AG in CS. This confirmed the continued existence of AG continuous cropping obstacles in RS.
    The decrease of physicochemical properties and enzyme activity
    Plant growth requires water and nutrients. Because soil physicochemical properties influence water and nutrient availability, changes in soil physicochemical properties directly affect AG growth. In the present study, the water content of RS was significantly higher than that of CS under the same management conditions (Table 1). Shu et al.29 found that high soil water content induced root rot disease in AG when sandy loam water content exceeded 30% or that of clay exceeded 50%. Similarly, according to Wang et al.30, the incidence of rust rot positively correlated with soil moisture and rainfall. Therefore, high soil water content, caused by changes in soil physicochemical properties, may negatively affect AG replanting. Furthermore, the pH of RS was significantly lower than that of CS (Table 1). According to Rahman and Punja24, root rot severity at soil pH 5.05 was greater than that at pH 7.0, indicating that acidic conditions can negatively affect AG health. In addition, the available K content in RS was lower than that in CS (Table 1). Sun31 found that AG should be fertilized (N, P, K fertilizer) from emergence to early flowering, when its demand for potassium fertilizer is the highest, suggesting that AG has a high potassium requirement. The levels of ammonium N, nitrate N, available P, and available K, but not of total N and total C, were generally lower in RS than in CS (Table 1), indicating that the cultivation of AG may have long-term negative effects on these soil nutrients. The same trend was observed for soil enzyme activity. Urease, a nickel-containing enzyme, catalyzes the hydrolysis of urea into carbonate and ammonia. Here, urease activity was significantly higher in CS than in RS. Average phosphatase and sucrase activities were also higher in CS than those in RS, although these differences were not significant (Table 2). Yang32 also found that the activities of sucrase, urease, and phosphatase decreased during AG cultivation. In summary, compared to that of CS, RS had lower fertility, but higher soil water content and lower pH, two conditions which are conducive to AG disease, and that may, therefore, present obstacles to AG replanting.
    The dual effects of phenolic acids
    The results showed that the content of salicylic acid in RS was significantly higher than that in CS. Yang16 found that among the various phenolic acids tested, salicylic acid had the strongest inhibitory effect on AG radicle growth. In our study, higher salicylic acid content in RS may have posed direct autotoxicity to AG. As a major defense hormone, salicylic acid has the function of enhancing immune signals and reprogramming defense transcriptomes33. After planting AG, the soil salicylic acid content increased, which indicated that AG might release more salicylic acid in the growth process to improve immune response to the surrounding environment. Therefore, the role of salicylic acid in the continuous cropping obstacles to AG cultivation deserves further study.
    In addition, we found that the content of most phenolic acids, such as p-coumaric, p-hydroxybenzoic, vanillic, caffeic, and cinnamic acid, decreased after AG cultivation, and had not returned to the levels in CS even after 10 years of subsequent crop rotation. AG requires a suitable environment for growth. Before germination in spring, the ginseng farmers’ association uses wheat straw to cover the soil, which not only maintains soil temperature and retains soil moisture, but also improves soil quality and promotes the growth of AG seedlings. Jia et al.34 detected the increase in ferulic, vanillic, cinnamic, and p-hydroxybenzoic acid in a wheat-corn rotation area. In addition, Zheng et al.35 found that straw return, a common method for soil improvement, also increased the concentration of phenolic acids in soil. In our study, the increased phenolic acid content in CS relative to RS may have been beneficial to the growth of AG. Similar to our research results, Jiao et al.36 also found that the content of phenolic acid substances such as syringic, vanillic, p-coumaric, and ferulic acid decreased by 49.1–81% after adding AG root residues (simulating the seasonal AG leaf and fibrous root senescence). Therefore, decreases in the soil contents of some phenolic acids after planting AG may underlie the decline of other soil properties, which is not conducive to the subsequent growth of AG.
    As described above, some phenolic acids may be beneficial to the growth of AG; if so, by what mechanism do these beneficial phenolic acids exert their role? Phenolic acids are produced by plants under external stress37,38,39,40. They do have many beneficial functions, such as antibacterial, antioxidant and so on, which can alleviate the stress of plants41. However, with the increase of phenolic acid secretion, some phenolic acids will penetrate into the soil and affect the soil microorganisms. Li et al.42 found that cinnamic acid inhibits Cylindrocarpon destructans (a pathogen of ginseng) growth at high concentrations, while promoting it at low concentrations. Yang et al.43 found that vanillic acid promoted the growth of the pathogens Rhizoctonia solani and Fusarium solani at low concentrations, but inhibited it at high concentrations; many phenolic acid compounds can inhibit the proliferation of Phytophthora cactorum (a pathogenic bacterium that causes AG phytophthora disease) at high concentrations. In addition, Yuan et al.44 found that p-coumaric acid strongly suppressed the in vitro growth of fungi, significantly reducing the decay caused by Alternaria alternata. Therefore, it can be seen that phenolic acids have inhibitory effects on pathogens at higher concentrations. With a decrease in soil phenolic acid content, this inhibitory effect on pathogenic bacteria will be weakened, resulting in an imbalance in the soil microbial composition that affects AG growth performance. Overall, soil phenolic acid content may indirectly affect AG growth performance by affecting soil microorganisms.
    The change in the relative abundance of key bacteria
    Our results showed that there was no significant difference in bacterial α-diversity between 10-year post-ginseng RS and CS, but there were differences in β-diversity, which reflects community composition and structure, between CS and RS. In other words, there were significant differences in the relative abundance of key bacteria in the bacterial community, such as Chlamydiae (phylum level, RS: 0.28%, CS: 0.10%, P = 0.035), within this phylum, the c_Chlamydiae, o_Chlamydiales, f_Simkaniaceae, and g_uncultured; Acidothermus (genus level, RS: 2.40%, CS: 5.40%, P = 0.030); Sphingomonadales (order level, CS: 2.98%, RS: 1.68%, P = 0.002), Sphingomonadaceae (family level, CS: 2.88%, RS: 1.48%, P = 0.004), genera Novosphingobium (CS: 0.03%, RS: 0.20%, P = 0.035) and Sphingomonas (CS: 2.83%, RS: 1.10%, P = 0.000); Rhodanobacter (CS: 0.38%, RS: 3.45%, P = 0.050); Arthrobacter (CS: 0.03%, RS: 0.43%, P = 0.001); Mizugakiibacter (CS: 0.63%, RS: 2.28%, P = 0.048); Jatrophihabitans (CS: 1.15%, RS: 0.75%, P = 0.048); Pseudomonas (RS: 0.15%, CS: 0.03%, P = 0.029) among others (Fig. 4, see Supplementary Table S2).
    There was no difference in soil bacterial α-diversity between RS and CS, which may be due to the recovery of soil bacterial diversity after 10 years of rotation. However, the results of the pot experiment showed that RS still presented continuous cropping obstacles, which indicated that restoring soil microbial α-diversity does not alleviate continuous cropping obstacles for AG. Instead, differences in microbial community composition (i.e., β-diversity), particularly the abundances of bacterial taxa that play key roles, may explain the persistence of AG continuous cropping obstacles in RS after 10 years.
    Among the differences in microbial community composition, CS had higher relative abundances of some bacterial genera that may be beneficial bacteria. The genus Acidothermus had the highest abundance, and it contained a single species, A. cellulolyticus, which is thermophilic, acidophilic, and has the ability to produce many thermostable cellulose-degrading enzymes45. Therefore, higher cellulose-degrading capacity might exist in CS than that in RS. Sphingomonas, a bacterium with the ability to decompose mono- and polycyclic aromatic compounds, as well as heterocyclic compounds, was more abundant in CS than RS, suggesting that bacterial decay of recalcitrant plant compounds was also higher in CS than RS. In addition, Sphingomonas not only decomposes monoaromatic phenolic acids but also improves plant stress resistance, and it is considered a plant probiotic46. Similar to our results, Li and Jiang23 found that Jatrophihabitans relative abundance in soil used for AG for 4 years was significantly (P  root rot group  > control group; in addition, compared with CS, there was a higher abundance of Rhodanobacter in the soil in which Korean ginseng (Panax ginseng) was grown49. We also found that this genus might be increased by the influence of Panax plants, which warrants further study. Our results showed that Arthrobacter was higher in the RS group, and Jiang et al.48 also found that the relative abundance of Arthrobacter in the root rot group was higher than that in the healthy root group; therefore, we speculate that Arthrobacter might be a factor causing root rot of P. quinquefolius, leading to a continuous cropping obstacle to AG growth. Our results showed that the abundance of Pseudomonas sp. in RS was higher than that in CS (RS: 0.15%, CS: 0.03%, P = 0.029, see Supplementary Table S2). Tan et al.50 showed that Pseudomonas sp. was the main pathogen causing root rot disease in P. notoginseng. In addition, Jiang et al.48 also found that Pseudomonas is abundant in the rhizosphere soils of diseased ginseng roots. Therefore, it is necessary to further study the effects of Pseudomonas species on AG growth. To sum up, the relative abundances of a large number of bacteria that are either confirmed or potentially harmful to other plants increased in RS, which may be an important factor leading to the occurrence of continuous cropping obstacles in the 10-year post-ginseng rotation soil.
    As shown in Fig. 6, there are many correlations among the three factors. The abundances of Acidothermus, Sphingomonas, Jatrophihabitans, and Actinospica were each positively correlated with that of available K, caffeic acid, and cinnamic acid, but negatively correlated with that of salicylic acid. Therefore, the interactions among phenolic acids, microorganisms, and soil nutrients evidenced possible “synergistic” or “antagonistic” effects within the microecosystem. Overall, these complex relationships are the main reason for AG continuous cropping obstacles, but it is still unknown which of these factors plays the primary role. Finally, Nitrobacter, Actinospica, Clostridium sensu stricto 1, Thermosporothrix, Holophaga, and Peptoclostridium, also showed significant differences in abundance between RS and CS (Fig. 4), which also should receive more attention. More