Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry.

Pollen and tracheophyte spores are ubiquitous environmental indicators at local and global scales. Palynology is typically performed manually by microscopic analysis; a specialised and time-consuming task limited in taxonomical precision and sampling frequency, therefore restricting data quality used to inform climate change and pollen forecasting models. We build on the growing work using AI (artificial intelligence) for automated pollen classification to design a flexible network that can deal with the uncertainty of broad-scale environmental applications. We combined imaging flow cytometry with Guided Deep Learning to identify and accurately categorise pollen in environmental samples; here, pollen grains captured within c. 5500 Cal yr BP old lake sediments. Our network discriminates not only pollen included in training libraries to the species level but, depending on the sample, can classify previously unseen pollen to the likely phylogenetic order, family and even genus. Our approach offers valuable insights into the development of a widely transferable, rapid and accurate exploratory tool for pollen classification in 'real-world' environmental samples with improved accuracy over pure deep learning techniques. This work has the potential to revolutionise many aspects of palynology, allowing a more detailed spatial and temporal understanding of pollen in the environment with improved taxonomical resolution.

Functional Trait Variation Among and Within Species and Plant Functional Types in Mountainous Mediterranean Forests.

Plant structural and biochemical traits are frequently used to characterise the life history of plants. Although some common patterns of trait covariation have been identified, recent studies suggest these patterns of covariation may differ with growing location and/or plant functional type (PFT). Mediterranean forest tree/shrub species are often divided into three PFTs based on their leaf habit and form, being classified as either needleleaf evergreen (Ne), broadleaf evergreen (Be), or broadleaf deciduous (Bd). Working across 61 mountainous Mediterranean forest sites of contrasting climate and soil type, we sampled and analysed 626 individuals in order to evaluate differences in key foliage trait covariation as modulated by growing conditions both within and between the Ne, Be, and Bd functional types. We found significant differences between PFTs for most traits. When considered across PFTs and by ignoring intraspecific variation, three independent functional dimensions supporting the Leaf-Height-Seed framework were identified. Some traits illustrated a common scaling relationship across and within PFTs, but others scaled differently when considered across PFTs or even within PFTs. For most traits much of the observed variation was attributable to PFT identity and not to growing location, although for some traits there was a strong environmental component and considerable intraspecific and residual variation. Nevertheless, environmental conditions as related to water availability during the dry season and to a smaller extend to soil nutrient status and soil texture, clearly influenced trait values. When compared across species, about half of the trait-environment relationships were species-specific. Our study highlights the importance of the ecological scale within which trait covariation is considered and suggests that at regional to local scales, common trait-by-trait scaling relationships should be treated with caution. PFT definitions by themselves can potentially be an important predictor variable when inferring one trait from another. These findings have important implications for local scale dynamic vegetation models.

Biogeochemical recuperation of lowland tropical forest during succession.

High rates of land conversion and land use change have vastly increased the proportion of secondary forest in the lowland tropics relative to mature forest. As secondary forests recover following abandonment, nitrogen (N) and phosphorus (P) must be present in sufficient quantities to sustain high rates of net primary production and to replenish the nutrients lost during land use prior to secondary forest establishment. Biogeochemical theory and results from individual studies suggest that N can recuperate during secondary forest recovery, especially relative to P. Here, we synthesized 23 metrics of N and P in soil and plants from 45 secondary forest chronosequences located in the wet tropics to empirically explore (1) whether there is a consistent change in nutrients and nutrient cycling processes during secondary succession in the biome; (2) which metrics of N and P in soil and plants recuperate most consistently; (3) if the recuperation of nutrients during succession approaches similar nutrient concentrations and fluxes as those in mature forest in ~100 yr following the initiation of succession; and (4) whether site characteristics, including disturbance history, climate, and soil order are significantly related to nutrient recuperation. During secondary forest succession, nine metrics of N and/or P cycling changed consistently and substantially. In most sites, N concentrations and fluxes in both plants and soil increased during secondary succession, and total P concentrations increased in surface soil. Changes in nutrient concentrations and nutrient cycling processes during secondary succession were similar whether mature forest was included or excluded from the analysis, indicating that nutrient recuperation in secondary forest leads to biogeochemical conditions that are similar to those of mature forest. Further, of the N and P metrics that recuperated, only soil total P and foliar δ15 N were strongly influenced by site characteristics like climate, soils, or disturbance history. Predictable nutrient recuperation across a diverse and productive ecosystem may support future forest growth and could provide a means to quantify successful restoration of ecosystem function in secondary tropical forest beyond biomass or species composition.

Solar radiation and functional traits explain the decline of forest primary productivity along a tropical elevation gradient.

One of the major challenges in ecology is to understand how ecosystems respond to changes in environmental conditions, and how taxonomic and functional diversity mediate these changes. In this study, we use a trait-spectra and individual-based model, to analyse variation in forest primary productivity along a 3.3 km elevation gradient in the Amazon-Andes. The model accurately predicted the magnitude and trends in forest productivity with elevation, with solar radiation and plant functional traits (leaf dry mass per area, leaf nitrogen and phosphorus concentration, and wood density) collectively accounting for productivity variation. Remarkably, explicit representation of temperature variation with elevation was not required to achieve accurate predictions of forest productivity, as trait variation driven by species turnover appears to capture the effect of temperature. Our semi-mechanistic model suggests that spatial variation in traits can potentially be used to estimate spatial variation in productivity at the landscape scale.

Nitrogen and phosphorus availabilities interact to modulate leaf trait scaling relationships across six plant functional types in a controlled-environment study.

Nitrogen (N) and phosphorus (P) have key roles in leaf metabolism, resulting in a strong coupling of chemical composition traits to metabolic rates in field-based studies. However, in such studies, it is difficult to disentangle the effects of nutrient supply per se on trait-trait relationships. Our study assessed how high and low N (5 mM and 0.4 mM, respectively) and P (1 mM and 2 µM, respectively) supply in 37 species from six plant functional types (PTFs) affected photosynthesis (A) and respiration (R) (in darkness and light) in a controlled environment. Low P supply increased scaling exponents (slopes) of area-based log-log A-N or R-N relationships when N supply was not limiting, whereas there was no P effect under low N supply. By contrast, scaling exponents of A-P and R-P relationships were altered by P and N supply. Neither R : A nor light inhibition of leaf R was affected by nutrient supply. Light inhibition was 26% across nutrient treatments; herbaceous species exhibited a lower degree of light inhibition than woody species. Because N and P supply modulates leaf trait-trait relationships, the next generation of terrestrial biosphere models may need to consider how limitations in N and P availability affect trait-trait relationships when predicting carbon exchange.

Light inhibition of foliar respiration in response to soil water availability and seasonal changes in temperature in Mediterranean holm oak (Quercus ilex) forest.

In the present study we investigated variations in leaf respiration in darkness (RD) and light (RL), and associated traits in response to season, and along a gradient of soil moisture, in Mediterranean woodland dominated by holm oak (Quercus ilex L.) in central and north-eastern Spain respectively. On seven occasions during the year in the central Spain site, and along the soil moisture gradient in north-eastern Spain, we measured rates of leaf RD, RL (using the Kok method), light-saturated photosynthesis (A) and related light response characteristics, leaf mass per unit area (MA) and leaf nitrogen (N) content. At the central Spain site, significant seasonal changes in soil water content and ambient temperature (T) were associated with changes in MA, foliar N, A and stomatal conductance. RD measured at the prevailing daily T and in instantaneous R-T responses, displayed signs of partial acclimation and was not significantly affected by time of year. RL was always less than, and strongly related to, RD, and RL/RD did not vary significantly or systematically with seasonal changes in T or soil water content. Averaged over the year, RL/RD was 0.66±0.05s.e. (n=14) at the central Spain site. At the north-eastern Spain site, the soil moisture gradient was characterised by increasing MA and RD, and reduced foliar N, A, and stomatal conductance as soil water availability decreased. Light inhibition of R occurred across all sites (mean RL/RD=0.69±0.01s.e. (n=18)), resulting in ratios of RL/A being lower than for RD/A. Importantly, the degree of light inhibition was largely insensitive to changes in soil water content. Our findings provide evidence for a relatively constrained degree of light inhibition of R (RL/RD ~ 0.7, or inhibition of ~30%) across gradients of water availability, although the combined impacts of seasonal changes in both T and soil water content increase the range of values expressed. The findings thus have implications in terms of the assumptions made by predictive models that seek to account for light inhibition of R, and for our understanding of how environmental gradients impact on leaf trait relationships in Mediterranean plant communities.

Scaling leaf respiration with nitrogen and phosphorus in tropical forests across two continents.

Leaf dark respiration (Rdark ) represents an important component controlling the carbon balance in tropical forests. Here, we test how nitrogen (N) and phosphorus (P) affect Rdark and its relationship with photosynthesis using three widely separated tropical forests which differ in soil fertility. Rdark was measured on 431 rainforest canopy trees, from 182 species, in French Guiana, Peru and Australia. The variation in Rdark was examined in relation to leaf N and P content, leaf structure and maximum photosynthetic rates at ambient and saturating atmospheric CO2 concentration. We found that the site with the lowest fertility (French Guiana) exhibited greater rates of Rdark per unit leaf N, P and photosynthesis. The data from Australia, for which there were no phylogenetic overlaps with the samples from the South American sites, yielded the most distinct relationships of Rdark with the measured leaf traits. Our data indicate that no single universal scaling relationship accounts for variation in Rdark across this large biogeographical space. Variability between sites in the absolute rates of Rdark and the Rdark  : photosynthesis ratio were driven by variations in N- and P-use efficiency, which were related to both taxonomic and environmental variability.

Leaf respiration in darkness and in the light under pre-industrial, current and elevated atmospheric CO2 concentrations.

Our study sought to understand how past, low atmospheric CO2 concentrations ([CO2]) impact respiration (R) of soybean (Glycine max), when compared to plants grown under current and future [CO2]s. Experiments were conducted using plants grown under 290, 400 and 700 ppm [CO2]. Leaf R was measured in both darkness (RD) and in the light (RL; using the Kok method), with short-term changes in measurement [CO2] and [O2] being used to explore the relationship between light inhibition of leaf R and photorespiration. Root R, photosynthesis (A), leaf [N] and biomass allocation traits were also quantified. In contrast to the inhibitory effect of low growth [CO2] on A, growth [CO2] had no significant effect on leaf RD or root R. Irrespective of growth [CO2], RL was always lower than RD, with light inhibiting leaf R by 17-47%. Importantly, the degree of light inhibition of leaf R was lowest in plants grown under low [CO2], with variations in RL being positively correlated with RD and photorespiration. Irrespective of whether leaf R was measured in the light or dark, a greater proportion of the carbon fixed by leaf photosynthesis was released by leaf R in plants grown under low [CO2] than under current/future [CO2]'s. Collectively, our results highlight the differential responses of A and R to growth of plants under low to elevated atmospheric [CO2].

Evidence for strong seasonality in the carbon storage and carbon use efficiency of an Amazonian forest.

The relative contribution of gross primary production and ecosystem respiration to seasonal changes in the net carbon flux of tropical forests remains poorly quantified by both modelling and field studies. We use data assimilation to combine nine ecological time series from an eastern Amazonian forest, with mass balance constraints from an ecosystem carbon cycle model. The resulting analysis quantifies, with uncertainty estimates, the seasonal changes in the net carbon flux of a tropical rainforest which experiences a pronounced dry season. We show that the carbon accumulation in this forest was four times greater in the dry season than in the wet season and that this was accompanied by a 5% increase in the carbon use efficiency. This seasonal response was caused by a dry season increase in gross primary productivity, in response to radiation and a similar magnitude decrease in heterotrophic respiration, in response to drying soils. The analysis also predicts increased carbon allocation to leaves and wood in the wet season, and greater allocation to fine roots in the dry season. This study demonstrates implementation of seasonal variations in parameters better enables models to simulate observed patterns in data. In particular, we highlight the necessity to simulate the seasonal patterns of heterotrophic respiration to accurately simulate the net carbon flux seasonal tropical forest.

Light inhibition of leaf respiration in field-grown Eucalyptus saligna in whole-tree chambers under elevated atmospheric CO2 and summer drought.

We investigated whether the degree of light inhibition of leaf respiration (R) differs among large Eucalyptus saligna grown in whole-tree chambers and exposed to present and future atmospheric [CO(2) ] and summer drought. Associated with month-to-month changes in temperature were concomitant changes in R in the light (R(light) ) and darkness (R(dark) ), with both processes being more temperature dependent in well-watered trees than under drought. Overall rates of R(light) and R(dark) were not significantly affected by [CO(2) ]. By contrast, overall rates of R(dark) (averaged across both [CO(2) ]) were ca. 25% lower under drought than in well-watered trees. During summer, the degree of light inhibition of leaf R was greater in droughted (ca. 80% inhibition) than well-watered trees (ca. 50% inhibition). Notwithstanding these treatment differences, an overall positive relationship was observed between R(light) and R(dark) when data from all months/treatments were combined (R(2) = 0.8). Variations in R(light) were also positively correlated with rates of Rubisco activity and nitrogen concentration. Light inhibition resulted in a marked decrease in the proportion of light-saturated photosynthesis respired (i.e. reduced R/A(sat) ). Collectively, these results highlight the need to account for light inhibition when assessing impacts of global change drivers on the carbon economy of tree canopies.

Thermal acclimation of leaf dark respiration of beech seedlings experiencing summer drought in high and low light environments.

Little is known about how environmental factors shape the short- and long-term responses of leaf respiration to temperature under field conditions despite the importance of respiration for plant and stand carbon balances. Impacts of water availability and canopy cover on leaf dark respiration (R) and temperature sensitivity were assessed in beech (Fagus sylvatica L.) seedlings in a sub-Mediterranean population. We studied seedlings established within canopy gaps (39% global site factor; GSF) that were subject to either no watering (unwatered plants; UW) or regular watering (2-10% higher volumetric topsoil water content as summer progressed; W plants) and seedlings established beneath the adjacent understorey (12% GSF). Leaf R rose exponentially with diurnal increases in temperature; the same temperature sensitivity (Q(10): 2.2) was found for understorey and gap plants, irrespective of watering treatment. Respiration estimated at 25 degrees C (R(25)) was lower in the understorey than the gaps and was significantly lower in the unwatered than in the watered gap plants by the end of summer (0.65 versus 0.80 micromol m(-2) s(-1)). R(25) declined with increasing summer temperature in all plants; however, respiration estimated at the prevailing ambient temperature did not change through the summer. There were parallel declines in R(25) and concentrations of starch and soluble sugars with increasing summer temperature for gap plants. We conclude that seasonal shifts in temperature-response curves of beech leaf R occur in both low- and high-light environments; since leaf R decreased with increasing plant water deficit, such shifts are likely to be greater whenever plants experience summer drought compared to scenarios where plants experience high rainfall in summer.

Is shade beneficial for mediterranean shrubs experiencing periods of extreme drought and late-winter frosts?

BACKGROUND AND AIMS: Plants are naturally exposed to multiple, frequently interactive stress factors, most of which are becoming more severe due to global change. Established plants have been reported to facilitate the establishment of juvenile plants, but net effects of plant-plant interactions are difficult to assess due to complex interactions among environmental factors. An investigation was carried out in order to determine how two dominant evergreen shrubs (Quercus ilex and Arctostaphylos uva-ursi) co-occurring in continental, Mediterranean habitats respond to multiple abiotic stresses and whether the shaded understorey conditions ameliorate the negative effects of drought and winter frosts on the physiology of leaves. METHODS: Microclimate and ecophysiology of sun and shade plants were studied at a continental plateau in central Spain during 2004-2005, with 2005 being one of the driest and hottest years on record; several late-winter frosts also occurred in 2005. KEY RESULTS: Daytime air temperature and vapour pressure deficit were lower in the shade than in the sun, but soil moisture was also lower in the shade during the spring and summer of 2005, and night-time temperatures were higher in the shade. Water potential, photochemical efficiency, light-saturated photosynthesis, stomatal conductance and leaf 13C composition differed between sun and shade individuals throughout the seasons, but differences were species specific. Shade was beneficial for leaf-level physiology in Q. ilex during winter, detrimental during spring for both species, and of little consequence in summer. CONCLUSIONS: The results suggest that beneficial effects of shade can be eclipsed by reduced soil moisture during dry years, which are expected to be more frequent in the most likely climate change scenarios for the Mediterranean region.

Transient shade and drought have divergent impacts on the temperature sensitivity of dark respiration in leaves of Geum urbanum.

The respiratory response of plants to temperature is a critical biotic feedback in the study of global climate change. Few studies, however, have investigated the effects of environmental stresses on the short-term temperature response of dark respiration (Rdark) at the leaf level. We investigated the effect of shade and transient drought on the temperature sensitivity (Q10; the proportional increase in respiration per 10°C increase in temperature) of Rdark of Geum urbanum L. in controlled experiments. Shade effects were most pronounced following sustained, near-darkness, when rates of leaf Rdark at a set measuring temperature (25°C) and the Q10 of Rdark were both reduced. By contrast, rates of leaf Rdark and the Q10 of Rdark both increased in response to the onset of severe water stress. Water stress was associated with a rapid (but reversible) decline in rates of light-saturated photosynthesis (Psat), stomatal closure (gs) and progressive wilting. Re-watering resulted in a rapid recovery of Psat, gs and a decline in the Q10 of Rdark (due to larger proportional reductions in the rate of Rdark measured at 25°C compared with those measured at 14°C). The concentration of soluble sugars in leaves did not decline during drought (5-7 day cycles) or shading, but during drought the starch concentration dropped, suggesting starch to sugar conversion helped to maintain homeostatic concentrations of soluble sugars. Thus, the drought and shade induced changes in Rdark were unlikely to be due to stress-induced changes in substrate supply. Collectively, the data highlight the dynamic responses of respiratory Q10 values to changes in water supply and sustained reductions in growth irradiance. If widespread, such changes in the Q10 of leaf respiration could have important implications for predicted rates of ecosystem carbon exchange in the future, particularly in areas that experience more frequent droughts.

Acclimation of photosynthesis and respiration is asynchronous in response to changes in temperature regardless of plant functional group.

Gas exchange, fluorescence, western blot and chemical composition analyses were combined to assess if three functional groups (forbs, grasses and evergreen trees/shrubs) differed in acclimation of leaf respiration (R) and photosynthesis (A) to a range of growth temperatures (7, 14, 21 and 28 degrees C). When measured at a common temperature, acclimation was greater for R than for A and differed between leaves experiencing a 10-d change in growth temperature (PE) and leaves newly developed at each temperature (ND). As a result, the R : A ratio was temperature dependent, increasing in cold-acclimated plants. The balance was largely restored in ND leaves. Acclimation responses were similar among functional groups. Across the functional groups, cold acclimation was associated with increases in nonstructural carbohydrates and nitrogen. Cold acclimation of R was associated with an increase in abundance of alternative and/or cytochrome oxidases in a species-dependent manner. Cold acclimation of A was consistent with an initial decrease and subsequent recovery of thylakoid membrane proteins and increased abundance of proteins involved in the Calvin cycle. Overall, the results point to striking similarities in the extent and the biochemical underpinning of acclimation of R and A among contrasting functional groups differing in overall rates of metabolism, chemical composition and leaf structure.

Does growth irradiance affect temperature dependence and thermal acclimation of leaf respiration? Insights from a Mediterranean tree with long-lived leaves.

Understanding the response of leaf respiration (R) to changes in irradiance and temperature is a prerequisite for predicting the impacts of climate change on plant function and future atmospheric CO2 concentrations. Little is known, however, about the interactive effects of irradiance and temperature on leaf R. We investigated whether growth irradiance affects the temperature response of leaf R in darkness (Rdark) and in light (Rlight) in seedlings of a broad-leaved evergreen species, Quercus ilex. Two hypotheses concerning Rdark were tested: (1) the Q10 (i.e. the proportional increase in R per 10 degrees C rise in temperature) of leaf Rdark is lower in shaded plants than in high-light-grown plants, and (2) shade-grown plants exhibit a lower degree of thermal acclimation of Rdark than plants exposed to higher growth irradiance. We also assessed whether light inhibition of Rlight differs between leaves exposed to contrasting temperatures and growth irradiances, and whether the degree of thermal acclimation of Rlight is dependent on growth irradiance. We showed that while growth irradiance did impact on photosynthesis, it had no effect on the Q10 of leaf Rdark. Growth irradiance had little impact on thermal acclimation when fully expanded, pre-existing leaves were exposed to contrasting temperatures for several weeks. When Rlight was measured at a common irradiance, Rlight/Rdark ratios were higher in shaded plants due to homeostasis of Rlight between growth irradiance treatments and to the lower Rdark in shaded leaves. We also showed that Rlight does not acclimate to the same degree as Rdark, and that Rlight/Rdark decreases with increasing measuring and growth temperatures, irrespective of the growth irradiance. Collectively, we raised the possibility that predictive carbon cycle models can assume that growth irradiance and photosynthesis do not affect the temperature sensitivity of leaf Rdark of long-lived evergreen leaves, thus simplifying incorporation of leaf R into such models.