Ecology

Flow velocity thresholdThere were 92 Chinese sturgeon signals from 2016 to 2019, which were identified with the DIDSON dual-frequency video sonar system. The distribution map of Chinese sturgeon signals was shown in Fig. 1. The number of monitored signals in 2016 was significantly higher than in 2017–2019. The latest wild reproduction of the Chinese sturgeon occurred in 2016. Overall, most Chinese sturgeon signals were distributed within 500 m downstream from Gezhouba Dam, and there were more in the right side(facing downstream) than in the left side. The flow field of each sturgeon signal was simulated by the model, and the velocity of each signal location was obtained. According to the statistical analysis of the flow velocity values, the frequency of the sturgeon signal at different flow velocity values was shown in Fig. 2. The results show that most signals were concentrated in areas with flow velocities of 0.6–1.5 m/s, which accounted for 88.1% of the signals; areas with flow velocities below 0.6 m/s accounted for 4.3% of the signals, and areas with flow velocities above 1.5 m/s accounted for 7.6%. Therefore, 0.6–1.5 m/s was selected as the preferred flow velocity range of the Chinese sturgeon for spawning activity. This result was approximately consistent with the ranges proposed by most other researchers. The low limit of the velocity range was lower than that of other researchers. There may be two reasons for this result: the first was that the bottom velocity we analysed was lower than the surface velocity and vertical average velocity under the same conditions; the second was that our research time was after 2016, and the discharge during the spawning period was relatively low, so the velocity of the Chinese sturgeon signal was also relatively low.Figure 1Distribution map of Chinese sturgeon signals, where ○ indicates Chinese sturgeon signals monitored in 2016, ∆ indicates those in 2017, □ indicates those in 2018, and ✩ indicates those in 2019. Map generated in ArcGIS Pro (https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview).Full size imageFigure 2Plots of the frequency for the different flow velocity ranges of Chinese sturgeon signals.Full size imageDifferent opening modes with identical dischargeThe discharge of 6150 m3/s on November 24, 2016, when the latest wild reproduction of Chinese sturgeon occurred, was used to study the flow velocity distribution with different opening modes. The specific opening mode cases are shown in Table 1. Case 1 was the actual situation, and the Dajiang Plant featured 7 open units: #8, #11, #13, #14, #16, #19, and #21. According to the amounts of electricity generated by Dajiang Plant and Erjiang Plant on that day, the proportion of the Dajiang River flow was 58.8%, and the average discharge of each unit was 516.6 m3/s. Case 2 and case 3 featured 7 open units with the same discharge, but in case 2, units #15–21 were continuously open on the right-side (facing downstream), and in case 3, units #8–14 were continuously open near the left side. Case 4 and case 5 were the most concentrated conditions with the discharge of 6150 m3/s because the maximum through-discharge for each unit in the Dajiang Plant is 825 m3/s19. In these cases, at least 5 units were open with an average discharge of 723 m3/s per unit. Case 4 involved continuously opening units #8–12 on the left side, and case 5 involved continuously opening units #17–21 on the right side. Case 6 involved simultaneously opening 14 units on Dajiang River, and the average discharge of each unit was 258.3 m3/s.Table 1 Calculation cases with different opening modes of units under the identical discharge.Full size tableFigure 3 shows the flow fields of the spawning ground under different opening modes with identical discharge. By comparing the areas with a velocity threshold range of 0.6–1.5 m/s in different cases, the most favourable opening mode was determined. In case 1, the velocity at the outlet of the units was higher than the 1.5 m/s velocity threshold, but the discharge of each unit was only 516.6 m3/s, so the high-velocity range was limited, and most areas were suitable. In case 2 and case 3, there was a large difference in proportions of suitable area. Because the left side was deeper than the right side, the flow velocity on the right side was higher under the same discharge, and case 3 more easily exceeded the flow threshold, which resulted in a larger unsuitable area. Case 2 was more suitable than case 1, which also demonstrated that opening the left-side units was more favourable. In case 4 and case 5, the proportions of suitable area were small. Because the units were concentrated, the discharge of each unit was too high, and the outlet velocity was more than 2 m/s, so a large area of high velocity appeared downstream of the units with backflow under the shut-down units. The proportion of suitable area in case 5 was larger than those in case 4 and case 3, which further indicates that opening the left-side units was more favourable than opening the right-side units. Case 6 was greater than that of any other case. Because the discharge of each unit was only 258.3 m3/s, the velocity of the unit outlet was less than 1.5 m/s, and almost all areas were suitable except for the small areas on both sides. The suitable-velocity area was the largest when all units of the Dajiang Plant of Gezhouba Dam were open; therefore, for a given discharge, it was best to open all units.Figure 3Flow field of the spawning ground in different opening modes with identical discharge, where the numbers at the top of each picture are the numbers of units to open, and the arrows indicate the direction of the water flow. Maps generated in Tecplot360 EX 2020 R1 (https://www.tecplot.com/products/tecplot-360/).Full size imageDifferent discharges under identical opening modeThe velocity distribution of the spawning field is affected by the opening mode of the units and discharge of Gezhouba Dam. To study the effect of different discharges, 14 cases were simulated, as shown in Table 2. All units of the Dajiang Plant were considered open because the proportion of suitable area was expected to be maximal under such circumstances. From 1982 to the present, the discharge during the spawning day of Chinese sturgeon under Gezhouba Dam has a wide range: the highest discharge was 27,290 m3/s in 1990, and the lowest discharge was 5590 m3/s in 2012. However, the highest design discharge of the Gezhouba Dam units is 17,930 m3/s20. Once the design discharge is exceeded, the spillway on Erjiang River discharges water, and the velocity distribution of the study area is not affected. Therefore, case 1 represents the lowest discharge of 5590 m3/s, and case 2 represents a discharge of 6000 m3/s. For each subsequent case, the discharge was increased by 1000 m3/s to case 13 with the highest flow of 17,930 m 3/s. In case 14, all units reached the design discharge, and the discharge of each unit was 825 m3/s19.Table 2 Calculation cases with the same opening mode under different discharges.Full size tableFigure 4 shows the proportion of suitable-velocity area with all units open under different discharges. According to the calculation results, the proportion of suitable area slightly fluctuated at approximately 96.2% for discharges of 5590–11,000 m3/s. Because the discharge of each unit was low, the velocity of the unit outlet was low, and most areas were within the velocity threshold. Therefore, it is advantageous to open all units when the discharge is low. After the discharge reached 12,000 m3/s, the proportion of suitable area rapidly decreased. Because the discharge of each unit was high, on the right side of Dajiang River, the velocity of the unit outlet exceeded the velocity threshold and increased with increases in discharge, and the range of effect gradually increased. In the last case, the proportion of suitable area was only 6% when the units reached the designed discharge of 825 m3/s. Because the discharge of each unit was too high, almost all areas exceeded the velocity threshold except for small areas on both sides. Therefore, at discharges below 12,000 m3/s, opening all units is favourable, and at discharge above 12,000 m3/s, a higher discharge corresponds to more unfavourable conditions.Figure 4Proportions of the suitable-velocity area with all units opened under different discharges.Full size imageOptimal scheme under high-flow conditionsHigh-flow conditions at Gezhouba Dam are considered those that exceed 12,000 m3/s because of the substantive decline in suitable habitat area at higher discharges. Because opening the units on the left side of the Dajiang Plant provides a more uniform, suitable habitat, we evaluated 20 cases with a left-side opening mode under different discharge, as shown in Table 3. Because the highest discharge of each unit in the Dajiang Plant is 825 m3/s, at least 9 units must be open when the discharge is 12,000 m3/s. Case 1 was designed to open 9 units on the left, i.e., units #13–21, and the discharge of each unit was 784 m3/s. Cases 2–5 increased by 1 unit from left to right until 13 units were opened. For discharges of 13,000 m3/s, 14,000 m3/s, 15,000 m3/s, and 16,000 m3/s, at least 10, 10, 11, and 12 units were opened. When the discharge was 17,000 m3/s and 17,930 m3/s, at least 13 units were open.Table 3 Calculation cases with different opening modes under high-flow conditions.Full size tableFigure 5 shows the proportions of suitable area for different opening modes under high-flow conditions. The calculation results show that when the discharge was 12,000 m3/s, 13,000 m3/s, and 14,000 m3/s, the proportion of suitable area showed a parabolic trend with the increase in number of units. When the discharge was 12,000 m3/s, the proportion of suitable area with 11 open units on the left was the largest, which was 8.7% larger than the value for all open units and 15% larger than the value for the lowest number of open units. When the discharge was 13,000 m3/s, 12 open units on the left had the largest proportion of suitable-flow-velocity area. When the discharge was 14,000 m3/s, the proportions of suitable area produced by opening 12 and 13 units on the left were the largest. The proportion of suitable area of the lowest number of open units was usually minimal because the discharge of each unit was too high, which resulted in a large area of high velocity that was not suitable for Chinese sturgeon to spawn. Because of the underwater topography, opening the left-side units was more favourable than opening the right-side units, so for all open units, the proportions of suitable area will be lower, and the number of units opened in the middle will be the most advantageous. For a discharge of 15,000 m3/s, with the increase in number of units, the proportion of suitable area increased, and there was no parabolic trend because the discharge of each unit exceeded 678 m3/s; thus, on the left side, there was a large area of high velocity, and the effect extended very far, which was not suitable for Chinese sturgeon.Figure 5Proportions of the suitable area for different opening modes under high-flow conditions, where 12,000–09 on the x-axis indicates that the discharge is 12,000 m3/s, and 9 units are open on the left.Full size image More

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The gobi region ecosystem has low stability because of its single species composition and simple structure (Fig. 8a). Large-scale shrub planting destroyed the original stable state (Fig. 8b) and resulted in another stable state via self-adjustment. In this process, the planted shrubs deteriorated the original ecosystem by competing for water and a chain reaction may ensue, leading to greater ecological problems. The original intention of the large-scale planting of shrubs was to maintain regional ecological balance, protect biodiversity, and fix sand, thus improving the environment (Fig. 8c). However, given the poor choice of the planting location, the expected results were not achieved. In fact, the opposite results of the original good intentions were achieved (Fig. 8d).Figure 8Diagram of different development stages of large-scale afforestation in the gobi region (a: original ground surface; b: holes dug for afforestation; c the living trees planted; d: ground surface when the trees are dead).Full size imageChina has a large expanse of arid areas, and has suffered from droughts for a long time. Land afforestation has been at the forefront of China’s policy principles, and there are government departments specializing in this field. In recent years, the Chinese Government has recommended a series of major strategies, for example, the “construction of ecological civilization” and “lucid waters and lush mountains are invaluable assets”, and also promoted greening projects, including “Three North Shelterbelt Project”, “Beijing-Tianjin Sandstorm Source Control Project”, and the “Natural Forest Protection Project”. More recently, desert greening has been conducted by people and enterprises, for example, the Ant Forest and Society of Entrepreneurs & Ecology (SEE). As a result of these projects and initiatives, China’s greening has contributed to global greening totals15,16. For afforestation, China’s policy departments have recommended the principles of “sticking to local conditions, suitable land for green, suitable trees for trees, suitable shrub for shrub, suitable grass for grass” and promoting the overall protection of “Mountain-River-Forest-Farmland-Lake-Grass-Desert system”, with particular references to desert. Their goal is to scientifically promote afforestation of the land and to clarify “where to afforest, what to afforest, how to afforest, how to manage”. However, problems arise very easily when grassroots executors are involved.The total area of the gobi region in China is approximately 56.95 × 104 km2, accounting for 13.36% of the national area, and is primarily distributed in the northwest extreme arid regions17. As mentioned above, gobi refers to a special arid landform that has a notably low water supply and is unsuitable for growing trees and shrubs. As an important natural landform, the gobi plays a key role in ecological protection; hence, its reference as “black vegetation”. However, there is a lack of understanding of the gobi, and it is often regarded as an area that needs to be greened or reformed. However, gobi, as an extremely arid region, is a fragile ecosystem. Once the gravel on the gobi surface is destroyed, it could lead to a series of ecological and environmental problems. Therefore, afforestation in arid areas is both a scientific and technical issue which must be conducted according to different regional characteristics, rather than by blindly planting trees in unsuitable areas. This study aims to attract more attention from the government forestry department and implementation personnel involved in afforestation activities so as to revise relevant policies. In response to the findings of this study, we have several recommendations: (1) it is necessary to popularize the understanding of scientific greening within the general public; (2) scientific understanding of the gobi needs to be increased, and awareness must be raised to promote its protection; (3) afforestation projects and management must be scientifically and systematically improved to ensure long-term effectiveness, and; (4) restoration and protection measures should be taken immediately in the gobi regions that have been afforested or destroyed.One of the most important causes of all these problems is the implementation of national policies on subsidies for greening and planting trees in desert areas. According to our survey, personnel who specifically plant trees and engage in afforestation are businessmen, farmers, or others, with most of them being businessmen from abroad, and only a few being local people. All the personnel are more concerned about the subsidies than greening and planting trees itself. According to the policy, they will receive majority of the subsidy if the planted trees live for three years, irrespective of whether the trees survive after that. Therefore, to guarantee the survival of the planted trees for three years, they even use water tankers to carry water to the trees from a great distance. However, after three years, the people stop watering the trees planted in the Gobi region, thereby leading to the death of trees after a few years as they cannot survive only on natural precipitation and groundwater. In pursuit of maximum profits, these businessmen will pursue larger areas for planting trees, which will cause further damage to the ecological environment in the Gobi region. Based on the current situation, we propose the following suggestions: (1) Trees that are planted must be monitored over a long time period, which will greatly reduce the short-term profit motive of the people engaged in planting trees. (2) We must plan greening and planting trees according to local conditions, respecting the laws of nature. Not all areas should be greened; moreover, we should not plant trees, especially in the gobi region, where planting trees can possibly destroy the gobi ecological environment, which is a very fragile desert ecosystem. (4) Personnel responsible for the destruction of the gobi ecological environment by unscientific greening and planting of trees must be obligated to restore the surface conditions of the gobi to prevent the aggravation of wind erosion and desertification, which will increase their awareness of environmental protection and receive punishment for environmental damage. More

A Psammodromus algirus lizard in Spain, where wildfires can confer long-lasting relief from parasites. Credit: Philippe Clement/Nature Picture Library

Ecology
13 July 2021
Destructive fires serve as pest control for lizards

Mediterranean lizards in burnt areas are less likely to be afflicted by mites than their neighbours in unburnt woodlands.

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Occasional wildfires can help lizards to keep a clean house: the blazes cleanse natural areas of mites that can infest the reptiles’ skin.High-intensity fires in Mediterranean shrublands and woodlands renew vegetation, shoo away seed eaters and keep tree diseases in check. Lola Álvarez-Ruiz at the Desertification Research Centre in Valencia, Spain, and her colleagues were curious to know whether the flames could also be beneficial to animals.Between 2016 and 2018, the researchers sampled Psammodromus algirus, a species of ground-dwelling lizard, in eight burnt and adjacent unburnt areas in Spain. They then counted either how many mites were attached to the creatures’ skin or how many raised scales the lizards had — an indication of previous infection with the parasite.Lizards that lived in unburnt areas were four times more likely to carry mites than were those in recently scorched environments, and were also more likely to have raised scales. The results suggest that there was a lower incidence of parasitism even several years after a fire had occurred.

Proc. R. Soc. B (2021)

Ecology More

Oceanographic context of the sampling locationAll Trichodesmium colonies used in this study were collected from the same phytoplankton net which sampled a surface-ocean Southern Caribbean Sea community (Fig. 1a). At the sampling station the phosphate concentration was low (0.13 μM at 100 m) as is typical in an oligotrophic environment, while the surface dissolved iron concentration was relatively high (2.02 nM at 100 m), consistent with coastal or atmospheric inputs being mobilized in this region (Fig. 1a). By far the most abundant Trichodesmium species at this location was an uncharacterized Trichodesmium thiebautii species, as determined by Trichodesmium-specific metagenome-assembled-genome recruiting (see Table S1).Thirty individual colonies of mixed morphology were separated by hand-picking, immediately examined, and photographed by fluorescent microscopy (385 excitation, >420 nm emission), then frozen individually for particle characterization and metaproteomic analysis (Fig. S1). All colonies used in this study presented as healthy with reddish-orange pigmentation and well-defined shape. When the particles were present they auto-fluoresced in the visual light range, appearing as yellow, red, or blue dots. In general, the particles were concentrated in the center of puff-type colonies, though they were also present in tufts but in smaller numbers. Strikingly, colonies either had many such particles or none at all. Based on prior experimental evidence demonstrating that Trichodesmium colonies can capture mineral particles and access iron from them [14,15,16, 21], we hypothesized that these particles were terrestrially derived minerals (Fig. 1c–h). Therefore, we embarked to understand the morphological heterogeneity by characterizing the particles and the colony’s molecular response to them.Mineralogical characterization of the colony-associated particlesTo find out whether these natural colonies of Trichodesmium had captured iron-rich mineral particles, we performed synchrotron-based micro-X-ray fluorescence (μ-XRF) element mapping of representative colonies with the observed particle associations. Prior evidence of Trichodesmium–particle associations has been based mainly on experimental “feeding” of dust to cultured or captured colonies [15, 16, 20, 22,23,24,25], and it was therefore important to establish these specific Trichodesmium–particle relationships, which developed in nature. We examined one tuft- and two puff-type colonies, all of which had particles associated with them. The element maps were consistent with the hypothesis that there were mineral particles enriched in iron (Fe), copper (Cu), zinc (Zn), titanium/barium (Ti/Ba, which cannot be distinguished by this method), manganese (Mn) and cobalt (Co), though the concentrations approached the limit of detection for the latter two elements (Fig. 2, Figs. S2 and S3). Iron concentrations were particularly high in the particles. Micro-X-ray absorption near-edge structure (μ-XANES) spectra for iron were collected on six particles—three each from the two puffs (Fig. 2 and Fig. S4). The particles contained mineral-bound iron with average oxidation states of 2.6, 2.7, two of oxidation state 2.9, and two of oxidation state 3.0 (Table S2, Fig. S5). While the mineralogy of these particles could not be definitively resolved using μ-XANES, the structure of the absorption edge and post-edge region provided insight into broad mineral groups. Both Fe(III) (oxy/hydro)oxides and mixed-valence iron-bearing minerals consistent with iron silicates were present, suggesting heterogeneous mineral character. While we could not positively identify the silicate mineral phases based on XANES, the spectroscopic similarity of some samples to iron-smectite and the geologic context suggest iron-bearing clays were present (Fig. S5). In this geographic region, iron oxides and clays could be sourced from atmospheric dust deposition, which is common in this region [27, 28] and/or from riverine sources such as the Orinoco and/or Amazon rivers [29, 30].Fig. 2: μ-XRF-based element maps of a Trichodesmium tuft (left) and puff (right) colony (beamsize 3 ×3 μm).White/gray contours, based on the sulfur panel, which is indicative of biomass, have been provided (white = high [S] threshold, gray = lower [S] threshold). The color scale is the same for each image, with the maximum concentration for each element indicated in parentheses; iron is displayed using two scales. Iron oxidation states were determined via μ XANES for three particles in the puff colony, and these are annotated in yellow. The corresponding XANES spectra are shown in Fig. S4 and tabulated data in Table S2.Full size imageThese colony-associated mineral particles likely serve as a simultaneous source of nutritional (Fe, Ni, Co, Mn) and toxic (Cu) metals to the colonies. The elemental composition of the particles is similar to a recent characterization of Trichodesmium-particle associations in the South Atlantic [30]. Release of metals from the particles likely vary over time, with copper, nickel, zinc, and cobalt continually leaching and iron leaching initially, then re-adsorbing back onto particles unless organic chelates assist in solubilization [31].Proteome composition is altered by particle presenceTo understand the impact of the particles on colony diversity and function, we performed comparative metaproteomic analysis of the individual Trichodesmium colonies and their microbiota. Seven puffs without particles, 14 puffs with particles, and 4 tufts with particles were analyzed by a new single-colony metaproteomic method. This approach allowed for the first time the molecular profiles of heterogeneous Trichodesmium colonies to be examined individually. Compared to bulk population-level metaproteomes from this location, which achieved deeper resolution of low-abundance proteins by integrating biomass from 50 to 100 colonies (4478 proteins identified) [32], proteome coverage for the low-biomass single colonies was lower yet sufficient for characterizing colony function (2078 proteins identified, Fig. S6) [32]. In total, 1591 Trichodesmium and 487 epibiont proteins were identified across the 25 single-colony metaproteomes versus 2944 Trichodesmium and 1534 epibiont proteins across triplicate population-level metaproteomes (Tables S3 and S4). Phylogenetic exclusivity was checked such that peptides used to identify epibiont proteins were not present in the Trichodesmium genome (Table S5 and Fig. S7) [33, 34].Trichodesmium’s epibiont community plays crucial roles in colony health and physiology, and together the single-colony proteomes demonstrated a diverse and functionally active microbiome associated with the colonies (Fig. 1b and Fig. S8). The proteomic analysis generally reflected the more abundant, “core” members of the epibiont community as was expected given their low-biomass proportion relative to Trichodesmium cells. Many commonly identified epibiont groups were present including Alphaproteobacteria, Microscilla, and non-Trichodesmium cyanobacteria [12, 35, 36]. In general, epibiont abundance was unaffected by particle presence, with one exception: Firmicute proteins were more abundant in tufts and puffs with particles, suggesting enhanced, possibly anaerobic, metabolism. Greater differences were identified between the puff and tuft morphologies, independent of particle presence and consistent with prior characterizations finding that puffs and tufts harbor distinct epibiont communities [12]. Specifically, eukaryotic proteins were more abundant in puffs compared to tufts. These proteins likely represent copepods due to sequence similarity to the model organism Calanus finmarchicus, and this result is consistent with observed associations between copepods and puffs at this location (Fig. S8B). Notably, proteins from the PVC superphylum, particularly an uncharacterized eukaryote pathogen species related to Chlamydia, were also more abundant in puffs. Eukaryotes are often observed in association with Trichodesmium colonies, but are not always identified due to differences in sampling protocols that could wash them away [12], as well as due to biases in analytical methods, for instance in studies with a focus on bacterial 16S or metagenomic analyses. Overall, the differences in the epibiont community were small, suggesting that these do not explain the observed morphological heterogeneity. We therefore turn our attention to describing how the particles impacted the proteome of Trichodesmium specifically.Mineral presence was associated with significant differences in the Trichodesmium proteome. In total, 131 proteins were differently abundant in puffs with particles versus without particles (p  More

We collected and analysed hourly GPS data from Antarctic fur seal pups tracked from birth until moulting in order to investigate the drivers of movement patterns and activity levels during this critical life stage. We found that pup movement was characterised by a star-like pattern, with individuals repeatedly returning to a central location of low activity after bouts of directed exploration. The HMM showed that the probability of such active movement was highest during the day and was mainly influenced by breeding season, colony of birth, and age. Our findings provide new insights into the movement patterns of pinnipeds prior to nutritional independence and highlight the importance of the life-history stage and the neonatal environment on behaviour.Movement in fur seal pupsA recent study of movement in Antarctic fur seal pups found evidence for sex-specific differences in habitat use prior to nutritional independence and the onset of overt sexual size dimorphism. Specifically, male pups were found to exhibit more risk prone behaviour with increasing age, traveling further at sea and spending more time in exposed beach habitats26. While this study highlighted the importance of an intrinsic factor, sex, on neonatal movement, the contributions of other factors, both extrinsic and intrinsic, remained largely unexplored. Our HMM incorporated multiple environmental and individual-based variables including the time of day, air temperature, wind speed, age, body condition, and sex. Rather than focusing on animals from a single colony, our study used tracking data from two breeding colonies with contrasting population density and terrain, while replication across two consecutive breeding seasons also allowed us to account for inter-annual variation in food availability.Our hourly GPS data revealed a distinct pattern of terrestrial pup movement that has not been reported in previous studies. Specifically, we documented a star-like pattern characterised by directed movement away from and subsequent return to a location of low activity. This appears to be a genuine behavioural pattern rather than an artefact of our temporal scale of sampling, as GPS locations collected every five minutes from a subset of individuals revealed a very similar picture (Supplementary Fig. S4). Star-like movement patterns are typified by central place foragers, which make round trips between a central location and a foraging patch37. However, as fur seal pups are entirely reliant on their mothers for food until they moult, repeated movements away from a central location are unlikely to be related to resource acquisition. Instead, our results appear to be indicative of bouts of exploration within a defined radius around a suckling location, which would imply that Antarctic fur seal pups are ‘central place explorers’.We would expect central place exploration in fur seal pups to be adaptive given that it entails energetic costs37 and might even make it more difficult for pups to be located by their mothers when they return from foraging trips38. We can envisage a number of possible explanations for this behaviour. First, high levels of activity may facilitate the development of the muscle mass necessary for future foraging success. Second, movement both within and beyond the confines of the beach where a pup is born may increase the scope for social interactions, which might be important for future mating success18. Third, a transition from beach habitats to the tussock grass offers increased protection against harsh weather conditions and may reduce the risk of a pup either being crushed by a territorial male or predated.While all tracked individuals displayed this pattern of central place exploration, the distance travelled during bouts of exploration differed depending on the colony of birth. On average, pups born at FWB travelled shorter distances and stayed closer to their colony of birth, whereas SSB pups moved farther and in a larger variety of directions. Given that SSB pups tend to transition into the tussock grass later in life (see discussion below), one explanation for this difference may be that mother–pup pairs need to travel further inland to find an appropriate, unoccupied suckling location.Results of the HMMWe used an HMM framework to infer the discrete behavioural states underlying pup movement and the probability of switching between these states given certain environmental and individual covariates. This integrated approach to decompose behavioural patterns has been applied across a wide range of species and habitats and has emerged as a powerful tool for animal movement modelling5. Our model uncovered a strong influence of year, with the probability of occupying the active state being higher in the first breeding season (2019), particularly for FWB pups. One possible explanation for this pattern could be that inter-annual differences in movement are adaptive. The first breeding season in our study had among the lowest breeding female numbers, pup birth weights, and foraging trip durations on record28, reflecting poor environmental conditions and low prey abundance39. In 2019, local densities at both colonies were correspondingly below average28. Given a greater risk of predation at low density28, pups might increase their activity to avoid harassment, pecking injuries, and predation by generalist seabirds such as southern and northern giant petrels40. Alternatively, higher levels of activity could be a consequence of increased stress hormone levels. As mothers spent more time at sea foraging in 201928, pups were subjected to longer periods of food deprivation. Such extended bouts of starvation in pinniped pups have been associated with an increase in glucocorticoids41, which are known to increase activity levels in some species42. Understanding the interrelationships among prolonged fasting, glucocorticoids levels, and activity in fur seal pups may help to shed further light on individual responses to environmental challenges.Another clear extrinsic determinant was the time of day, with activity levels peaking just before solar noon. This observation is in line with a previous study of Galápagos fur seal pups18, but otherwise very little is known in general about diurnal patterns of activity among fur seals while ashore. Daily meter-resolution location data from densely packed territory holding Antarctic fur seal males reveal negligible movements from day to day29, implying that these animals remain more or less stationary. By contrast, telemetry studies of adult females have reported associations between nocturnal foraging behaviour and diel variation in the time of arrival and departure from the breeding colony43. Consequently, it is unclear to what extent our results can be extrapolated across the life history, especially given the likelihood of an ontogenetic shift in times of peak activity as pups transition from being reliant on milk to nutritional independence.The HMM also revealed an increase in pup activity with age, but only for pups born at FWB. One explanation for this colony-specific difference could be that FWB pups are able to express their full behavioural repertoire throughout the course of ontogeny, becoming more active as they grow, whereas pups born on SSB are constrained by the high density of conspecifics. In particular, pups that traverse tightly packed harems on SSB run a higher risk of being crushed by a territorial male or bitten by a breeding female21,22. Alternatively, we recently found that FWB pups are more likely to be predated by generalist seabirds28. This might translate into an increase of predator-avoidance activity as pups mature, which would help to explain why activity no longer increases after around 40 days of age, when the majority of individuals have transitioned to the more sheltered tussock grass.We found that pups from FWB tended to move into the tussock grass earlier than pups from SSB and spent proportionally more time in the tussock grass than in their colony of birth. While this earlier shift toward residing mainly in the tussock grass could simply be a consequence of increased activity, it might also be adaptive for FWB pups to move inland as quickly as possible given the higher risk of predation at low density28. In other words, pups may move into the more sheltered tussock grass earlier in life and remain there for longer periods of time in order to avoid predatory seabirds. However, differences in the topography of the two colonies might also influence the timing of this transition, as a steep gully separates the beach at SSB from the tussock grass, while FWB offers a more gradual transition between the two habitats. To disentangle the effects of density and topography would require a larger study embracing a greater diversity of breeding colonies.Contrary to our initial expectations, the HMM found little to no effect of air temperature or wind speed on pup activity. This is surprising given that the pups in our study lacked the water-repellent fur of adults and were thus poorly protected from the elements23. Reduced activity35 and huddling behaviour44 have been documented in pinniped neonates as effective thermoregulatory behaviours to withstand the respectively hottest and coldest daily temperatures, so we originally anticipated a reduction in pup activity under marginal weather conditions. However, large variation in temperature during the course of this study was not observed on Bird Island (2019 mean temperature = 3.7 °C ± s.d. 1.3; 2020 mean temperature = 3.9 °C ± s.d. 1.4). Consequently, behavioural adjustments in activity for effective thermoregulation may not have been necessary in the context of our study. Alternatively, other climatic variables that we could not account for, such as precipitation or humidity, may have a disproportionate influence on activity levels. Future studies involving the direct observation of focal individuals under specific climatic conditions would help to address this question.The HMM also showed that pup activity levels were largely unaffected by body condition. This was unexpected because Antarctic fur seal pups rely on their mother’s milk for nutrition before moulting and must tolerate bouts of starvation lasting up to 11 days while their mothers forage at sea19. As a result, pup growth is known to decline with prolonged maternal absence45, implying that fewer resources should be available for movement. Taken at face value, the lack of a relationship between body condition and movement may suggest that the short-term benefits of high activity, such as muscle mass development and increased social interaction, may outweigh the costs associated with diverting resources from growth. This would be in line with a previous study that found that Galápagos fur seal pups maintained high activity levels throughout bouts of starvation18. However, it is also possible that an effect of body condition could not be detected in our study because our model assumed that condition was constant between successive measurements, whereas in practice it will vary to some extent from day to day.Despite a number of studies having shown that sex-specific differences in activity, habitat use, foraging, and diving behaviour are established early in life in several pinniped species13,14,15,16,17,46, including Antarctic fur seals26, our HMM did not uncover any obvious sex differences in activity. This is probably a consequence of the timeframe of our study. Jones et al.26, for example, only detected sex-specific differences in habitat use in Antarctic fur seal pups greater than 41 days old. Given that we focused on the time window from birth until moulting at around 60 days of age, the results of these two studies are consistent and lend support to the notion that sex-specific movement patterns take several weeks to become established.Results of the post-hoc analysisThe post-hoc analysis showed that pups were significantly less active when their mothers were ashore, suggesting that pup activity is correlated to some extent with maternal foraging behaviour. This association is most likely a reflection of the utmost importance of milk consumption for pup survival and development. A mother may spend as little as 24 h and on average only two days ashore during each nursing bout43, so pups must maximise nutrient update during this time. Moreover, adult female fur seals frequently display aggressive behaviour towards foreign pups21, potentially limiting a pup’s opportunity for social interactions when the mother is present18. It is important to note, however, that although significant, the effect size of the correlation between pup activity and maternal presence was fairly small. This suggests that pups may not remain with their mothers for the entire maternal attendance period, but rather alternate between nursing and bouts of activity.We also found that pups that died tended to be considerably less active. In our dataset, cause of death was assigned to all but one pup as either starvation (n = 5) or predation (n = 6), two factors that are difficult to untangle given that smaller, weaker (i.e. starving) pups may be more likely to be predated. It is possible that the reduced activity of pups that died could be related to poor body condition. While this would appear to contradict the lack of an overall association between activity and condition in the HMM, it is possible that activity may decline only after body condition falls below a critical threshold18, an effect we may not have captured due to the small number (n = 13) and early occurrence (median = 15 days) of mortalities in our dataset. Alternatively, causality could flow in the other direction, with less active pups being more likely to be predated. This would be more in line with our HMM results as well as with the hypothesis that increased activity is related to predator-avoidance behaviour.Strengths, limitations, and future directionsRecent advancements in bio-logging technology and analytical methods have made tracking studies of small, juvenile individuals ethically feasible, cost effective, and analytically approachable. In this study, we have taken advantage of these advancements to implement one of the first in-depth analyses of the movement and activity patterns of Antarctic fur seal pups prior to moulting. We were able to uniquely incorporate individual, ecological, and environmental variation into our analyses by collecting time-series biometric data for all tagged individuals, which were sampled at two breeding colonies across two subsequent breeding seasons. Finally, we were able to tease apart how these intrinsic and extrinsic factors may influence movement by inferring behavioural states using a HMM.An important limitation of our study, however, is our inability to establish causal relationships between hypothesised explanatory factors and activity. While this is an ever-present challenge when working with wild populations, future studies may consider pairing GPS tracking data with detailed behavioural observations of the focal individuals. This would provide a behavioural context for movement patterns and possibly allow for a more nuanced interpretation of the underlying behavioural states. A higher GPS sampling rate might also facilitate the resolution of finer-scale states. While this was not possible in the current study due to the limited battery capabilities of our tags, as technologies continue to improve future studies may not need to sacrifice sampling resolution for study duration. Finally, it would be interesting in the future to consider GPS tracking both mothers and pups to better understand the relationship between maternal attendance behaviour and pup activity. This approach might also shed light on how mothers find their offspring after returning ashore from foraging trips. More

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Fennoscandian shield genomic database (FSGD)The Fennoscandian Shield bedrock contains an abundance of fracture zones with different groundwater characteristics that vary in water source, retention time, chemistry, and connectivity to surface-fed organic compounds (see Supplementary Data 1). The Äspö Hard Rock Laboratory (HRL) and Olkiluoto drillholes were sampled over time, covering a diversity of aquifers representing waters of differing ages and both planktonic and biofilm-associated communities. In order to provide a genome-resolved view of the Fennoscandian Shield bedrock Archaeal and bacterial communities, collected samples were used for an integrated analysis by combining metagenomes (n = 44), single-cell genomes (n = 564), and metatranscriptomes (n = 9) (see detailed statistics for the generated datasets in the Supplementary Data 1 and Supplementary Information). Assembly and binning of the 44 metagenomes (~1.3 TB sequenced data) resulted in the reconstruction of 1278 metagenome-assembled genomes (MAGs; ≥ 50% completeness and ≤ 5% contamination). By augmenting this dataset with 564 sequenced single-cell amplified genomes (SAGs; 114 of which were ≥ 50% complete with ≤ 5% contamination), we present a comprehensive genomic database for the archaeal and bacterial diversity of these oligotrophic deep groundwaters, hereafter referred to as the Fennoscandian Shield genomic database (FSGD; statistics in Fig. 1A & Supplementary Data 2). Phylogenomic reconstruction using reference genomes in the Genome Taxonomy Database (GTDB-TK; release 86) shows that the FSGD MAGs/SAGs span most branches on the prokaryotic tree of life (Fig. 2). Harboring representatives from 53 phyla (152 archaeal MAGs/SAGs in 7 phyla and 1240 bacterial MAGs/SAGs in 46 phyla), the FSGD highlights the remarkable diversity of these oligotrophic deep groundwaters. Apart from the exceptional case of a single-species ecosystem composed of ‘Candidatus Desulforudis audaxviator’ in the fracture fluids of an African gold mine17, other studies of deep groundwaters as well as aquifer sediments have also revealed a notable phylogenetic diversity of the Archaea and Bacteria10,11,18. For example, metagenomic and single-cell genomic analysis of the CO2-driven Crystal geyser (Colorado Plateau, Utah, USA) resulted in reconstructed genomes of 503 archaeal and bacterial species distributed across 104 different phylum-level lineages11.Fig. 1: Overview of the FSGD MAGs and SAGs.Statistics of the metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) of the Fennoscandian Shield Genomic Database (a). The number of genome clusters present in borehole samples (centerline, median; hinge limits, 25 and 75% quartiles; whiskers, 1.5x interquartile range; points, outliers). Numbers on top of each box plot represent the number of metagenomes generated for borehole samples (b). NMDS plot of unweighted binary Jaccard beta-diversities of presence/absence of all FSGD reconstructed MAGs/SAGs (c) and MAG and SAG clusters belonging to the common core microbiome present in both Äspö HRL and Olkiluoto (d). Numbers in the parenthesis show the number of overlapping points. The data used to generate these plots are available in Supplementary Data 4 and the Source Data.Full size imageFig. 2: Phylogenetic diversity of reconstructed MAGs and SAGs of the fennoscandian shield genomic database (FSGD).Genomes present in genome taxonomy database (GTDB) release 86 were used as reference. Archaea and Bacteria phylogenies are represented separately in the top and bottom panels, respectively. MAGs and SAGs of the FSGD are highlighted in red. Legend in front of each number at the bottom of the figure shows the list of taxa in the tree that are marked with the same number.Full size imageClustering reconstructed FSGD MAGs/SAGs into operationally defined prokaryotic species (≥ 95% average nucleotide identity (ANI) and ≥ 70% coverage) produced 598 genome clusters. Based on the GTDB-TK affiliated taxonomy, a single FSGD cluster may represent a novel phylum, whereas at the lower taxonomic levels, the FSGD harbors genome clusters representing seven novel taxa at class, 58 at order, 123 at family, and 345 at the genus levels. In addition, more than 94% of the reconstructed MAGs/SAGs clusters (n = 568) represent novel species with no existing representative in public databases (Supplementary Data 2). Mapping metagenomic reads against genome clusters represented exclusively by SAGs (n = 38, Fig. 1A) revealed that 14 genome clusters (20 SAGs) were not detectable in the metagenomes, suggesting they might represent rare species in the microbial community of the investigated deep groundwaters (Supplementary Data 3).To explore the community composition of different groundwaters and their temporal dynamics, presence/absence patterns were computed by competitively mapping the metagenomics reads against all reconstructed MAGs/SAGs of the FSGD. Contigs were discarded from the mapping results if More