Contrasting life-cycle impacts of stream flow on two Chinook salmon populations

Stream flow affects many aspects of freshwater fish biology, but the extent to which variation in stream flow influences productivity of anadromous salmonid populations across their entire life cycle is not well known. We compared relationships of stream flow and productivity for Chinook salmon (Oncorhynchus tshawytscha) from two systems in the Salmon River basin in Idaho: the Lemhi River, a watershed subjected to intensive water use for irrigation, and Marsh Creek, a drainage with a natural hydrograph. We estimated rates of productivity based on monitoring at four life stages: the number of eggs initiating each cohort, juveniles migrating from the natal tributary past an outmigrant trap, smolts surviving to the Snake River, and adults returning to spawn. Using model selection techniques, we examined whether river flow experienced during these life stages explained variation above and beyond predictors of climate associated with each stage. In the Lemhi River, tributary stream flow during early residence exhibited strong correlations with egg–trap, egg–smolt, and egg–adult return rates, and was consistently a better predictor of productivity than stream flow occurring during late summer. Model selection indicated that early rearing flow was the single best predictor of both egg–trap and trap–smolt transition rates in the Lemhi River, and path analysis revealed a strong set of pathways linking rearing flow to adult return rate primarily through egg–trap productivity. These patterns were much less strongly exhibited or nonexistent in Marsh Creek. However, for both populations, migration flow in the Columbia River was the best predictor of smolt–adult return rates. Potentially confounding climatic variables exhibited relatively weak effects upon both early life histories and tributary flow, but were included in the best models of migration flows and smolt–adult return rate. These results suggest that effects of stream flow on juvenile salmonids in flow-altered systems can have substantial impacts on returning adults.     

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.     

Changes in scale circulus spacings of an endangered Atlantic salmon Salmo salar population: evidence of a shift in marine migration?

Post‐smolt scale circulus spacing patterns for two Atlantic salmon Salmo salar populations from the Southern Upland (SU) of Nova Scotia, Canada, were compared with spacings from two endangered populations from the inner Bay of Fundy (iBoF) Nova Scotia and New Brunswick, to determine if growth patterns differed among these populations, and if growth patterns had changed as the abundance of these populations declined. An analysis of numbers of marine circuli from scales of post‐smolts and one‐sea‐winter adults of known age indicated that circuli were deposited at a rate of about one circulus per week in summer and slowed to one every 2 weeks in winter. During the summer and the autumn, mean circulus spacing in the iBoF populations, known to have occupied the outer Bay of Fundy during these seasons, was lower than in the SU populations, which are known to migrate to the North Atlantic. Similar circulus spacing patterns within SU populations is suggestive of a common marine distribution for these populations. In contrast, a cluster analysis revealed that within the geographically intermediate Big Salmon River (iBoF), some individuals exhibited wider spacing patterns that resemble the distant migrating SU populations, while others exhibited narrower spacing similar to other iBoF S. salar. Within the Big Salmon River, the relative abundance of the wider and the narrower spacing patterns varied in the earlier years, but all fish sampled since 1999, exhibited wider spacings similar to distant migrating SU S. salar. The apparent disappearance of the narrower pattern, characteristic of localized migration and indicative of historical iBoF populations, suggests that local migration may not presently be a successful strategy for these populations.     

Effects of hydropeaking on the spawning behaviour of Atlantic salmon Salmo salar and brown trout Salmo trutta

An in situ camera set‐up was used to study the spawning activity of Atlantic salmon Salmo salar and brown trout Salmo trutta throughout two consecutive seasons in a spawning area affected by hydropower‐related pulse flows due to hydropeaking. The purpose was to test whether the flow variation discouraged spawning in shallow areas or motivated spawning into areas with elevated risk of incubation mortality. There were more S. salar observed on the spawning ground during days with high discharge. The presence of S. salar in the spawning grounds was not affected by the hydropeaking cycles of the preceding night. Female S. salar were observed preparing nests within the first hour after water discharge had increased to levels suitable for spawning. In contrast, the number of S. trutta was not correlated with flow and nest preparation was also observed at a discharge corresponding to the lowest discharge levels during a hydropeaking cycle. Survival was generally high in nests excavated the following winter, with only 5·4% suffering mortality due to dewatering. The results suggest that S. salar may respond rapidly to variable‐flow conditions and utilize short windows with suitable flows for spawning. Smaller S. trutta may utilize low‐flow conditions to spawn in areas that are not habitable by larger S. salar during low flow.     

Evidence for long‐term change in length,mass and migration phenology of anadromous spawners in French Atlantic salmon Salmo salar

This study provides new data on Atlantic salmon Salmo salar life‐history traits across France. Using a long‐term recreational angling database (1987–2013) covering 34 rivers in three regions (genetic units), a decline in individual length, mass and a delayed adult return to French rivers was reported. Temporal similarities in trait variations between regions may be attributed to common change in environmental conditions at sea. The relative rate of change in phenotypic traits was more pronounced in early maturing fish [1 sea‐winter (1SW) fish] than in late maturing fish (2SW fish). Such contrasted response within populations highlights the need to account for the diversity in life histories when exploring mechanisms of phenotypic change in S. salar. Such detailed life‐history data on returning S. salar have not previously been reported from France. This study on French populations also contributes to reducing the gap in knowledge by providing further empirical evidence of a global pattern in S. salar across its distribution range. Results are consistent with the hypothesis that the observed changes in life‐history traits are primarily associated with environmental changes in the North Atlantic Ocean. They also emphasize the presence of less important, but still significant contrasts between region and life history.     

Environmental change influences the life history of salmon Salmo salar in the North Atlantic Ocean

Annual mean total length (L_T) of wild one‐sea‐winter (1SW) Atlantic salmon Salmo salar of the Norwegian River Imsa decreased from 63 to 54 cm with a corresponding decrease in condition factor (K) for cohorts migrating to sea from 1976 to 2010. The reduction in L_T is associated with a 40% decline in mean individual mass, from 2 to 1·2 kg. Hatchery fish reared from parental fish of the same population exhibited similar changes from 1981 onwards. The decrease in L_T correlated negatively with near‐surface temperatures in the eastern Norwegian Sea, thought to be the main feeding area of the present stock. Furthermore, S. salar exhibited significant variations in the proportion of cohorts attaining maturity after only one winter in the ocean. The proportion of S. salar spawning as 1SW fish was lower both in the 1970s and after 2000 than in the 1980s and 1990s associated with a gradual decline in post‐smolt growth and smaller amounts of reserve energy in the fish. In wild S. salar, there was a positive association between post‐smolt growth and the sea survival back to the River Imsa for spawning. In addition, among smolt year‐classes, there were significant positive correlations between wild and hatchery S. salar in L_T, K and age at maturity. The present changes may be caused by ecosystem changes following the collapse and rebuilding of the pelagic fish abundance in the North Atlantic Ocean, a gradual decrease in zooplankton abundance and climate change with increasing surface temperature in the Norwegian Sea. Thus, the observed variation in the life‐history traits of S. salar appears primarily associated with major changes in the pelagic food web in the ocean.     

Influences of multilocus heterozygosity on size during early life

Genetic diversity has been hypothesized to promote fitness of individuals and populations, but few studies have examined how genetic diversity varies with ontogeny. We examined patterns in population and individual genetic diversity and the effect of genetic diversity on individual fitness among life stages (adults and juveniles) and populations of captive yellow perch (Perca flavescens) stocked into two ponds and allowed to spawn naturally. Significant genetic structure developed between adults and offspring in a single generation, even as heterozygosity and allelic richness remained relatively constant. Heterozygosity had no effect on adult growth or survival, but was significantly and consistently positively related to offspring length throughout the first year of life in one pond but not the other. The largest individuals in the pond exhibiting this positive relationship were more outbred than averaged size individuals and also more closely related to one another than they were to average‐sized individuals, suggesting potential heritability of body size or spawn timing effects. These results indicate that the influence of heterozygosity may be mediated through an interaction, likely viability selection, between ontogeny and environment that is most important during early life. In addition, populations may experience significant genetic change within a single generation in captive environments, even when allowed to reproduce naturally. Accounting for the dynamic influences of genetic diversity on early life fitness could lead to improved understanding of recruitment and population dynamics in both wild and captive populations.     

Impact of management and habitat on demographic traits of Primula vulgaris in an agricultural landscape

Question: Is demographic performance of Primula vulgaris correlated with habitat characteristics of the small landscape elements in which it occurs? Can we use this species as an indicator for species‐rich semi‐natural habitats? Location: Flanders, Belgium. Methods: To capture differences in demographic traits and habitat characteristics, both within and between populations, a two‐level survey was carried out. Population size and structure of 89 P. vulgaris populations in different types of small landscape elements was recorded in 1999. At plot level, densities of different life stages were determined and these were related to edaphic conditions and vegetation structure and composition. Results: Three different population types were distinguished: (1) dynamic populations, characterized by seedling and juvenile proportions, (2) normal populations with relatively more adults, but with considerable numbers of seedlings and juveniles and (3) senescent populations, mainly consisting of adults. Senescent populations were significantly smaller than populations with a dynamic demographic structure. At plot level, comparison of demographic characteristics between different management regimes revealed that recruitment rates and total plant density of P. vulgaris were highest in plots that received a regime that included mowing and clearing of ditch banks whereas densities were lower along forest edges. For these plots, it was shown that nutrient levels were higher. Densities of adults as well as juvenile and seedling densities were negatively correlated with vegetation height. Conclusions: Local disturbance and heterogeneity may mask the relationship between unfavourable conditions and demographic characteristics at population level, but it is clear that in small populations recruitment needs to be lifted to guarantee its persistence. Performance of P. vulgaris in small landscape elements can be a first indication of plant species diversity in small landscape elements.     

Genome‐wide SNP analysis reveals a genetic basis for sea‐age variation in a wild population of Atlantic salmon (Salmo salar)

Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade‐offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their ‘sea age’). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual‐based genome‐wide association studies (GWAS) and population‐based F_ST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome‐wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context.     

Genetic assessment of Atlantic salmon Salmo salar and sea trout Salmo trutta stocking in a Baltic Sea river

Microsatellite DNA variation was used to assess the outcome of stocking Atlantic salmon Salmo salar and migratory trout Salmo trutta in River Sävarå, N Sweden. No information on pre‐stocking genetic composition of S. salar and S. trutta in River Sävarå was available. In 2 year‐classes of S. salar smolt, microsatellite data indicated that post‐stocking genetic composition differed markedly (F_ST= 0·048) from the main donor strain, Byskeälven S. salar, and from other Gulf of Bothnia S. salar stocks (F_ST 0·047 and 0·132). The STRUCTURE programme failed to detect any substructuring within Sävarå salmon. It was concluded that only minor introgression estimated to a proportion of 0·11 (95% CI 0·07–0·16) has occurred in S. salar. Salmo trutta showed overall low differentiation among populations with maximum F_ST of 0·03 making analysis more cumbersome than in S. salar. Still, the SävaråS. trutta deviated significantly from potential donor populations, and STRUCTURE software supported that majority of trout in Sävarå formed a distinct genetic population. Admixture was more extensive in S. trutta and estimated to 0·17 (95% CI 0·10–0·25).     

Understanding variation in salamander ionomes: A nutrient balance approach

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Disparate patterns of thermal adaptation between life stages in temperate vs. tropical Drosophila melanogaster

Many terrestrial ectothermic species exhibit limited variation in upper thermal tolerance across latitude. However, these trends may not signify limited adaptive capacity to increase thermal tolerance in the face of climate change. Instead, thermal tolerance may be similar among populations because behavioural thermoregulation by mobile organisms or life stages may buffer natural selection for thermal tolerance. We compared thermal tolerance of adults and embryos among natural populations of Drosophila melanogaster from a broad range of thermal habitats around the globe to assess natural variation of thermal tolerance in mobile vs. immobile life stages. We found no variation among populations in adult thermal tolerance, but embryonic thermal tolerance was higher in tropical strains than in temperate strains. We further report that embryos live closer to their upper thermal limits than adults – that is, thermal safety margins are smaller for embryos than adults. F1 hybrid embryos from crosses between temperate and tropical populations had thermal tolerance that matched that of tropical embryos, suggesting the dominance of heat‐tolerant alleles. Together, our findings suggest that thermal selection has led to divergence in embryonic thermal tolerance but that selection for divergent thermal tolerance may be limited in adults. Further, our results suggest that thermal traits should be measured across life stages to better predict adaptive limits.     

Small-scale spatial variation in the elemental composition of otoliths of Stegastes nigricans (Pomacentridae) in French Polynesia

Solution-based inductively coupled plasma-mass spectrometry (ICP-MS) was used to determine if Stegastes nigricans collected from 15 sites in French Polynesia could be distinguished by the trace element composition of their otoliths. A total of 293 adults were collected by spearing and their otoliths were analysed. We found that elemental signatures differed significantly among sites within and between the islands of Tahiti and Moorea (p<0.001), primarily due to variation in concentrations of the elements Ba, Ca, Li, Mg, Mn, Na, Sr and Y. The otoliths of fish collected within Papeete Harbour in Tahiti had distinctive elemental signatures characterised by relatively high concentrations of Mn. Otoliths of these fish could be distinguished from others that were collected only a small distance (200 m) from the harbour. This is the first time that differences in chemical composition of otoliths have been reported at such small spatial scales and this trait may prove useful for the studies of connectivity of populations at within reef scales.     

Geographical variation in photoperiodic induction of larval diapause in the bruchid beetle, Bruchidius dorsalis: polymorphism in overwintering stages

The bruchid beetle, Bruchidius dorsalis Fahraeus (Coleoptera: Bruchidae), has a multivoltine life cycle and shows geographical variation of overwintering stages in Japan. Our previous study found that B. dorsalis enters larval diapause in the final instar under short photoperiods. In cooler areas, we observed that most individuals overwinter in the final larval stage in diapause, whereas beetles at different developmental stages (non‐diapausing young instars, diapausing instars, and adults) were overwintering in warmer areas. In this study, we investigated geographical variation in the photoperiodic response for induction of larval diapause at 20 °C (three populations) and 24 °C (two populations) to clarify the overwintering strategy of B. dorsalis. We observed that (1) diapause incidence at 20 °C changed sharply from ca. 100% to 0% with a change in photoperiod in all the populations, (2) critical photoperiod was longer at 20 °C in populations from cooler areas, and (3) critical photoperiod at 24 °C was shorter than at 20 °C and a fraction of the larvae did not enter diapause, even under short photoperiods. Overwintering stages estimated from these results were consistent with those actually observed in the field. This study indicates that the geographical variation of overwintering stages is likely to reflect adaptive diapause induction in each local environment.     

Trichome production and variation in young plant resistance to the specialist insect herbivore Plutella xylostella among natural populations of Arabidopsis lyrata

The strength of plant‐herbivore interactions varies spatially and through plant ontogeny, which may result in variable selection on plant defense, both among populations and life‐history stages. To test whether populations have diverged in herbivore resistance at an early plant stage, we quantified oviposition preference and larval feeding by Plutella xylostella (L.) (Lepidoptera: Plutellidae) on young (5–6 weeks old) Arabidopsis lyrata (L.) O'Kane & Al‐Shehbaz (Brassicaceae) plants, originating from 12 natural populations, six from Sweden and six from Norway. Arabidopsis lyrata can be trichome‐producing or glabrous, with glabrous plants usually receiving more damage from insect herbivores in natural populations. We used the six populations polymorphic for trichome production to test whether resistance against P. xylostella differs between the glabrous and the trichome‐producing morph among young plants. There was considerable variation among populations in the number of eggs received and the proportion of leaf area consumed by P. xylostella, but not between regions (Sweden vs. Norway) or trichome morphs. Rosette size explained a significant portion of the variation in oviposition and larval feeding. The results demonstrate that among‐population variation in resistance to insect herbivory can be detected among very young individuals of the perennial herb A. lyrata. They further suggest that trichome densities are too low at this plant developmental stage to contribute to resistance, and that the observed among‐population variation in resistance is related to differences in other plant traits.     

Stage‐dependent responses to emergent habitat heterogeneity: consequences for a predatory insect population in a coffee agroecosystem

Interactions among members of biological communities can create spatial patterns that effectively generate habitat heterogeneity for other members in the community, and this heterogeneity might be crucial for their persistence. For example, stage‐dependent vulnerability of a predatory lady beetle to aggression of the ant, Azteca instabilis, creates two habitat types that are utilized differently by the immature and adult life stages of the beetle. Due to a mutualistic association between A. instabilis and the hemipteran Coccus viridis – which is A. orbigera main prey in the area – only plants around ant nests have high C. viridis populations. Here, we report on a series of surveys at three different scales aimed at detecting how the presence and clustered distribution of ant nests affect the distribution of the different life stages of this predatory lady beetle in a coffee farm in Chiapas, Mexico. Both beetle adults and larvae were more abundant in areas with ant nests, but adults were restricted to the peripheries of highest ant activity and outside the reach of coffee bushes containing the highest densities of lady beetle larvae. The abundance of adult beetles located around trees with ants increased with the size of the ant nest clusters but the relationship is not significant for larvae. Thus, we suggest that A. orbigera undergoes an ontogenetic niche shift, not through shifting prey species, but through stage‐specific vulnerability differences against a competitor that renders areas of abundant prey populations inaccessible for adults but not for larvae. Together with evidence presented elsewhere, this study shows how an important predator is not only dependent on the existence of two qualitatively distinct habitat types, but also on the spatial distribution of these habitats. We suggest that this dependency arises due to the different responses that the predator's life stages have to this emergent spatial pattern.     

Ontogenetic changes in the drifting of four species of elmid beetles elucidate the complexity of drift-benthos relationships in a small stream in Northwest England

1. This study aimed to quantify ontogenetic changes in the drifting of Elmis aenea, Oulimnius tuberculatus, Esolus parallelepipedus and Limnius volkmari (Coleoptera: Elmidae), and to relate their drift to benthic density. Monthly samples were taken over 39 months, using three surface nets at each of two contrasting sites in a small stream: one in a deep section with abundant macrophytes, and the other in a shallow stony section. 2. Most larvae and adults were taken in the drift at night with little variation between catches in the three nets at each site. Day catches were very low, often zero. No significant relationships could be established between mean numbers in the drift catches and benthic densities. 3. When night catches were converted to drift densities (number caught per 100 m³ of water sampled), the latter were positively related to monthly losses in the benthos, but not to benthic densities. A linear regression described the relationship, and equations for the different life‐stages within each species were not significantly different from the equation for all life‐stages combined. However, drift losses were only about 0.07% of total losses in the benthos. A severe spate in October 1967 increased the number of larvae and adults in the drift, but not drift densities, except for immature adults of E. aenea, O. tuberculatus and E. parallelepipedus. 4. Key life‐stages with the highest drift density were the earliest life‐stage soon after egg hatching for E. aenea, the start of the larval overwintering period for O. tuberculatus and L. volkmari, and mature adults during the mating season for all three species. Drift density for E. parallelepipedus was too low to identify a key life‐stage. These key life‐stages corresponded with critical periods for survival in the life cycle, as identified in an earlier study in the same stream. Mortality was high during these critical periods, hence the strong relationship between drift density and benthic losses. The latter relationship was very consistent for different life‐stages within each species, and partially supported the rarely‐tested hypothesis that drift represents surplus production in the benthos.     

Evidence for episodic acidification effects on migrating Atlantic salmon Salmo salar smolts

Field studies were conducted to determine levels of gill aluminium as an index of acidification effects on migrating Atlantic salmon Salmo salar smolts in the north‐eastern U.S.A. along mainstem river migration corridors in several major river basins. Smolts emigrating from the Connecticut River, where most (but not all) tributaries were well buffered, had low or undetectable levels of gill aluminium and high gill Na⁺/K⁺‐ATPase (NKA) activity. In contrast, smolts emigrating from the upper Merrimack River basin where most tributaries are characterized by low pH and high inorganic aluminium had consistently elevated gill aluminium and lower gill NKA activity, which may explain the low adult return rates of S. salar stocked into the upper Merrimack catchment. In the Sheepscot, Narraguagus and Penobscot Rivers in Maine, river and year‐specific effects on gill aluminium were detected that appeared to be driven by underlying geology and high spring discharge. The results indicate that episodic acidification is affecting S. salar smolts in poorly buffered streams in New England and may help explain variation in S. salar survival and abundance among rivers and among years, with implications for the conservation and recovery of S. salar in the north‐eastern U.S.A. These results suggest that the physiological condition of outmigrating smolts may serve as a large‐scale sentinel of landscape‐level recovery of atmospheric pollution in this and other parts of the North Atlantic region.     

Time and size at seaward migration influence the sea survival of Salmo salar

Whether time of seaward migration of young Atlantic salmon Salmo salar influences their subsequent survival and growth was investigated in the River Imsa, south‐western Norway. Salmo salar were tagged when moving downstream through a trap near the outlet between 1976 and 2010 and recaptured on their adult return. Most descended as smolts in April and May, but some descended during the other months of the year. Annual variation in timing of the smolt migration was significantly correlated with variation in water temperature during spring. Mean total body length of the descending S. salar varied with month of seaward migration. The sea survival of S. salar emigrating from the River Imsa between January and May was 2·8 times higher than for those descending between June and December. The sea survival of the various cohorts decreased with increasing river temperature in April to May, prior to the smolt migration, and decreasing day number when the smolts moved to sea. The size of smolts descending the river between April and May did not affect the survival at sea as much as it affected the survival of migrants descending in any other month of the year. The majority of the downstream migrating S. salar were 2 years old, but proportionally, more 1 year olds moved downstream in the autumn than in the rest of the year. Mean duration between downstream migration of the young and the return migration of the grilse was shortest (12·7 months) for those descending in July and August and longest for those descending in October (21 months). Mean monthly specific growth rate was highest for those migrating downstream between May and July and lowest for those emigrating in September. Based on the present results, it was hypothesized that S. salar emigrating between April and August migrated directly out into the ocean, while those that emigrated between October and March stayed in the estuary until the subsequent spring.     

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill

Although plants introduced for site restoration are pre‐selected for specific traits (e.g. trace element bioaccumulation, rapid growth in poor soils), the in situ success of these plants likely depends on the recruitment of appropriate rhizosphere microorganisms from their new environment. We introduced three willow (Salix spp.) cultivars to a contaminated landfill, and performed soil chemical analyses, plant measurements, and Ion Torrent sequencing of rhizospheric fungal and bacterial communities at 4 and 16 months post‐planting. The abundance of certain dominant fungi was linked to willow accumulation of Zn, the most abundant trace element at the site. Interestingly, total Zn accumulation was better explained by fungal community structure 4 months post‐planting than 16 months post‐planting, suggesting that initial microbial recruitment may be critical. In addition, when the putative ectomycorrhizal fungi Sphaerosporella brunnea and Inocybe sp. dominated the rhizosphere 4 months post‐planting, Zn accumulation efficiency was negatively correlated with fungal diversity. Although field studies such as this rely on correlation, these results suggest that the soil microbiome may have the greatest impact on plant function during the early stages of growth, and that plant–fungus specificity may be essential.