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.

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.

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.

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.

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.