Modelling seed germination in forest tree species through survival analysis. The Pinus pinea L. case study

The direct application of existing models for seed germination may often be inadequate in the context of ecology and forestry germination experiments. This is because basic model assumptions are violated and variables available to forest managers are rarely used. In this paper, we present a method which addresses the aforementioned shortcomings. The approach is illustrated through a case study of Pinus pinea L. Our findings will also shed light on the role of germination in the general failure of natural regeneration in managed forests of this species. The presented technique consists of a mixed regression model based on survival analysis. Climate and stand covariates were tested. Data for fitting the model were gathered from a 5-year germination experiment in a mature, managed P. pinea stand in the Northern Plateau of Spain in which two different stand densities can be found. The model predictions proved to be unbiased and highly accurate when compared with the training data. Germination in P. pinea was controlled through thermal variables at stand level. At microsite level, low densities negatively affected the probability of germination. A time-lag in the response was also detected. Overall, the proposed technique provides a reliable alternative to germination modelling in ecology/forestry studies by using accessible/ suitable variables. The P. pinea case study highlights the importance of producing unbiased predictions. In this species, the occurrence and timing of germination suggest a very different regeneration strategy from that understood by forest managers until now, which may explain the high failure rate of natural regeneration in managed stands. In addition, these findings provide valuable information for the management of P. pinea under climate-change conditions.

An integral model for natural regeneration of Pinus pinea L. in the Northern Plateau (Spain) = Modelo integral de regeneración natural para Pinus pinea L. en la Meseta Norte (España)

Natural regeneration is an ecological key-process that makes plant persistence possible and, consequently, it constitutes an essential element of sustainable forest management. In this respect, natural regeneration in even-aged stands of Pinus pinea L. located in the Spanish Northern Plateau has not always been successfully achieved despite over a century of pine nut-based management. As a result, natural regeneration has recently become a major concern for forest managers when we are living a moment of rationalization of investment in silviculture. The present dissertation is addressed to provide answers to forest managers on this topic through the development of an integral regeneration multistage model for P. pinea stands in the region. From this model, recommendations for natural regeneration-based silviculture can be derived under present and future climate scenarios. Also, the model structure makes it possible to detect the likely bottlenecks affecting the process. The integral model consists of five submodels corresponding to each of the subprocesses linking the stages involved in natural regeneration (seed production, seed dispersal, seed germination, seed predation and seedling survival). The outputs of the submodels represent the transitional probabilities between these stages as a function of climatic and stand variables, which in turn are representative of the ecological factors driving regeneration. At subprocess level, the findings of this dissertation should be interpreted as follows. The scheduling of the shelterwood system currently conducted over low density stands leads to situations of dispersal limitation since the initial stages of the regeneration period. Concerning predation, predator activity appears to be only limited by the occurrence of severe summer droughts and masting events, the summer resulting in a favourable period for seed survival. Out of this time interval, predators were found to almost totally deplete seed crops. Given that P. pinea dissemination occurs in summer (i.e. the safe period against predation), the likelihood of a seed to not be destroyed is conditional to germination occurrence prior to the intensification of predator activity. However, the optimal conditions for germination seldom take place, restraining emergence to few days during the fall. Thus, the window to reach the seedling stage is narrow. In addition, the seedling survival submodel predicts extremely high seedling mortality rates and therefore only some individuals from large cohorts will be able to persist. These facts, along with the strong climate-mediated masting habit exhibited by P. pinea, reveal that viii the overall probability of establishment is low. Given this background, current management –low final stand densities resulting from intense thinning and strict felling schedules– conditions the occurrence of enough favourable events to achieve natural regeneration during the current rotation time. Stochastic simulation and optimisation computed through the integral model confirm this circumstance, suggesting that more flexible and progressive regeneration fellings should be conducted. From an ecological standpoint, these results inform a reproductive strategy leading to uneven-aged stand structures, in full accordance with the medium shade-tolerant behaviour of the species. As a final remark, stochastic simulations performed under a climate-change scenario show that regeneration in the species will not be strongly hampered in the future. This resilient behaviour highlights the fundamental ecological role played by P. pinea in demanding areas where other tree species fail to persist.

Modelling Pinus pinea forest management to attain natural regeneration under present and future climatic scenarios

Natural regeneration-based silviculture has been increasingly regarded as a reliable option in sustainable forest management. However, successful natural regeneration is not always easy to achieve. Recently, new concerns have arisen because of changing future climate. To date, regeneration models have proved helpful in decision-making concerning natural regeneration. The implementation of such models into optimization routines is a promising approach in providing forest managers with accurate tools for forest planning. In the present study, we present a stochastic multistage regeneration model for Pinus pinea L. managed woodlands in Central Spain, where regeneration has been historically unsuccessful. The model is able to quantify recruitment under different silviculture alternatives and varying climatic scenarios, with further application to optimize management scheduling. The regeneration process in the species showed high between-year variation, with all subprocesses (seed production, dispersal, germination, predation, and seedling survival) having the potential to become bottlenecks. However, model simulations demonstrate that current intensive management is responsible for regeneration failure in the long term. Specifically, stand densities at rotation age are too low to guarantee adequate dispersal, the optimal density of seed-producing trees being around 150 stems·ha−1. In addition, rotation length needs to be extended up to 120 years to benefit from the higher seed production of older trees. Stochastic optimization confirms these results. Regeneration does not appear to worsen under climate change conditions; the species exhibiting resilience worthy of broader consideration in Mediterranean silviculture.

Climatic factors control rodent seed predation in Pinus pinea L. stands in Central Spain

- Context: Pinus pinea L. presents serious problems of natural regeneration in managed forest of Central Spain. The species exhibits specific traits linked to frugivore activity. Therefore, information on plant–animal interactions may be crucial to understand regeneration failure. - Aims: Determining the spatio-temporal pattern of P. pinea seed predation by Apodemus sylvaticus L. and the factors involved. Exploring the importance of A. sylvaticus L. as a disperser of P. pinea. Identifying other frugivores and their seasonal patterns. - Methods: An intensive 24-month seed predation trial was carried out. The probability of seeds escaping predation was modelled through a zero-inflated binomial mixed model. Experiments on seed dispersal by A. sylvaticus were conducted. Cameras were set up to identify other potential frugivores. - Results: Decreasing rodent population in summer and masting enhances seed survival. Seeds were exploited more rapidly nearby parent trees and shelters. A. sylvaticus dispersal activity was found to be scarce. Corvids marginally preyed upon P. pinea seeds. - Conclusions: Survival of P. pinea seeds is climate-controlled through the timing of the dry period together with masting occurrence. Should germination not take place during the survival period, establishment may be limited. A. sylvaticus mediated dispersal does not modify the seed shadow. Seasonality of corvid activity points to a role of corvids in dispersal.

Can seed production and restricted dispersal limit recruitment in Pinus pinaster Aiton from the Spanish Northern Plateau?

Natural regeneration faces increasing difficulties in dry forests from the Mediterranean basin, including for normally well-regenerating species such as maritime pine (Pinus pinaster Aiton). In this paper, we studied female fertility, seed dispersal and spread rates in P. pinaster from the Spanish Northern Plateau, where natural regeneration failure is a main concern for forest managers. For this purpose we periodically collected data from seed traps and trees located at two core locations across several years. We found significant variation in interannual cone production, with the best seed trees being the same across years. In addition, we found highly skewed distributions of female reproductive effort and large fertility differences across stands located few kilometres away. Annual seed dispersal kernels fitted lognormal or 2Dt models depending on the stand analysed, with median dispersal distances between 14 and 25 m. Kernels fitted for maximum dispersal periods showed an outstanding intraseasonal variation of median dispersal distances, from 10 to 54 m, in association to variable patterns of rainfall and maximum wind speed. The amount of seed produced appeared to be enough to guarantee the natural regeneration of the stands during the typical 20-year regeneration period. Colonisation simulations concluded that Mediterranean maritime pine has a notable dispersion capacity, which is strongly influenced by levels of fecundity and, especially, by the number and frequency of long-distance dispersal events. The latter play a key role in tree dispersion processes through enlarging the occupied area and fostering the invasion of abandoned crop land.

Directed seed dispersal by bellbirds in a tropical cloud forest

A fundamental goal of plant population ecology is to understand the consequences for plant fitness of seed dispersal by animals. Theories of seed dispersal and tropical forest regeneration suggest that the advantages of seed dispersal for most plants are escape from seed predation near the parent tree and colonization of vacant sites, the locations of which are unpredictable in space and time. Some plants may gain in fitness as a fortuitous consequence of disperser behavior if certain species of dispersers nonrandomly place seeds in sites predictably favorable for seedling establishment. Such patterns of directed dispersal by vertebrates long have been suggested but never demonstrated for tropical forest trees. Here we report the pattern of seed distribution and 1-year seedling survival generated by five species of birds for a neotropical, shade-tolerant tree. Four of the species dispersed seeds to sites near the parent trees with microhabitat characteristics similar to those at random locations, whereas the fifth species, a bellbird, predictably dispersed seeds under song perches in canopy gaps. The pattern of seedling recruitment was bimodal, with a peak near parent trees and a second peak, corresponding to bellbird song perches, far (>40 m) from parent trees. Seedling survival was higher for seeds dispersed by bellbirds than by the other species, because of a reduction in seedling mortality by fungal pathogens in gaps. Thus, bellbirds play a significant role in seed dispersal by providing directed dispersal to favorable sites and therefore may influence plant recruitment patterns and species diversity in Neotropical forests.

Study of the effects of climate warming on seed germination and seed longevity of snowbed species

Understanding how climate change will affect the distribution and the phenology of plants is becoming an increasingly important topic in ecological studies. In response to climate warming, there are documented upward shift and alterations of phenology and physiology of several plant species. Despite this, the effects of climate change on plant regeneration from seeds have largely been neglected. However, regeneration from seeds, a key event in the plant life cycle, could be significantly affected by climate warming. In this regard, we investigated how climatic changes will affect the seasonal dynamics of seed germination and seedling survival in two different alpine context. The first part refers to five species inhabiting a snowbed located at the Gavia pass (Parco Naturale dello Stelvio). Here, plants were exposed, in the field, to natural conditions and to artificial warming using Open Top Chambers proposed by the ITEX (International Tundra Experiment). The germination curves of seeds produced were compared in order to highlight differences in seed germination ecology and in seed physiology induced by the climate warming. In the second part, we considered two tree species that form the treeline in Davos (Switzerland). As a surrogate of climate warming we used the natural thermal gradient driven by the altitude and we compared the germination behavior of the species studied in three sites at three different elevations in order to evaluate the likelihood of treeline shift under the predicted climate warming.

Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Somatic embryogenesis, organogenesis and plant regeneration in taro (Colocasia esculenta var. esculenta)

Callus was initiated in three different ‘‘esculenta’’ taro cultivars by culturing corm slices in the dark on half-strength MS medium supplemented with 2.0 mg/l 2,4- dichlorophenoxyacetic acid (2,4-D) for 20 days followed by subculture of all corm slices to half-strength MS medium containing 1.0 mg/l thidiazuron (TDZ). Depending on the cultivar, 20–30% of corm slices produced compact, yellow, nodular callus on media containing TDZ. Histological studies revealed the presence of typical embryogenic cells which were small, isodiametric with dense cytoplasms. Somatic embryos formed when callus was transferred to hormone-free medium and *72% of the embryos germinated into plantlets on this medium. Simultaneous formation of roots and shoots during germination, and the presence of shoot and root poles revealed by histology, confirmed that these structures were true somatic embryos. Plants derived from somatic embryos appeared phenotypically normal following 2 months growth in a glasshouse. This method is a significant advance on those previously reported for the esculenta cultivars of taro due to its efficiency and reproducibility.

Initiation of embryogenic cell suspensions of taro (Colocasia esculenta var. esculenta) and plant regeneration

Embryogenic callus was initiated by culturing in vitro taro corm slices on agar-solidified half-strength MS medium containing 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) for 20 days followed by transfer to 1.0 mg/L thidiazuron (TDZ). Callus was subsequently proliferated on solid medium containing 1.0 mg/L TDZ, 0.5 mg/L 2,4- D and 800 mg/L glutamine before transfer to liquid medium containing the same components but with reduced glutamine (100 mg/L). After 3 months in liquid culture on an orbital shaker, cytoplasmically dense cell aggregates began to form. Somatic embryogenesis was induced by plating suspension cells onto solid media containing reduced levels of hormones (0.1 mg/L TDZ, 0.05 mg/L 2,4-D), high concentrations of sucrose (40–50 g/L) and biotin (1.0 mg/L). Embryo maturation and germination was then induced on media containing 0.05 mg/L benzyladenine (BA) and 0.1 mg/L indole-3-acetic acid (IAA). Histological studies of the developing embryos revealed the presence of typical shoot and root poles suggesting that these structures were true somatic embryos. The rate of somatic embryos formation was 500–3,000 per mL settledcell volume while approximately 60% of the embryos regenerated into plants.

Utilisation of seed resources by small mammals : a two-way interaction

Within the Australian wet tropics bioregion, only 900 000 hectares of once continuous rainforest habitat between Townsville and Cooktown now remains. While on the Atherton Tableland, only 4% of the rainforest that once occurred there remains today with remnant vegetation now forming a matrix of rainforest dispersed within agricultural land (sugarcane, banana, orchard crops, townships and pastoral land). Some biologists have suggested that remnants often support both faunal and floral communities that differ significantly from remaining continuous forest. Australian tropical forests possess a relatively high diversity of native small mammal species particularly rodents, which unlike larger mammalian and avian frugivores elsewhere, have been shown to be resilient to the effects of fragmentation, patch isolation and reduction in patch size. While small mammals often become the dominant mammalian frugivores, in terms of their relative abundance, the relationship that exists between habitat diversity and structure, and the impacts of small mammal foraging within fragmented habitat patches in Australia, is still poorly understood. The relationship between foraging behaviour and demography of two small mammal species, Rattus fuscipes and Melomys cervinipes, and food resources in fragmented rainforest sites, were investigated in the current study. Population densities of both species were strongly related with overall density of seed resources in all rainforest fragments. The distribution of both mammal species however, was found to be independent of the distribution of seed resources. Seed utilisation trials indicated that M.cervinipes and R.fuscipes had less impact on seed resources (extent of seed harvesting) than did other rainforest frugivores. Experimental feeding trials demonstrated that in 85% of fruit species tested, rodent feeding increased seed germination by a factor of 3.5 suggesting that in Australian tropical rainforest remnants, small mammals may play a significant role in enhancing germination of large seeded fruits. This study has emphasised the role of small mammals in tropical rainforest systems in north eastern Australia, in particular, the role that they play within isolated forest fragments where larger frugivorous species may be absent.

Application of autologous periosteal cells for the regeneration of class III furcation defects in Beagle dogs

The aim of this study was to evaluate the healing of class III furcation defects following transplantation of autogenous periosteal cells combined with b-tricalcium phosphate (b-TCP). Periosteal cells obtained from Beagle dogs’ periosteum explant cultures, were inoculated onto the surface of b-TCP. Class III furcation defects were created in the mandibular premolars. Three experimental groups were used to test the defects’ healing: group A, b-TCP seeded with periosteal cells were transplanted into the defects; group B, b-TCP alone was used for defect filling; and group C, the defect was without filling materials. Twelve weeks post surgery, the tissue samples were collected for histology, immunohistology and X-ray examination. It was found that both the length of newly formed periodontal ligament and the area of newly formed alveolar bone in group A, were significantly increased compared with both group B and C. Furthermore, both the proportion of newly formed periodontal ligament and newly formed alveolar bone in group A were much higher than those of group B and C. The quantity of cementum and its percentage in the defects (group A) were also significantly higher than those of group C. These results indicate that autogenous periosteal cells combined with b-TCP application can improve periodontal tissue regeneration in class III furcation defects.

Clonal characterization of bone marrow derived stem cells and their application for bone regeneration

Tissue engineering allows the design of functionally active cells within supportive bio-scaffolds to promote the development of new tissues such as cartilage and bone for the restoration of pathologically altered tissues. However, all bone tissue engineering applications are limited by a shortage of stem cells. The adult bone marrow stroma contains a subset of nonhematopoietic cells referred to as bone marrow mesenchymal stem cells (BMSCs). BMSCs are of interest because they are easily isolated from a small aspirate of bone marrow and readily generate single- cell-derived colonies. These cells have the capacity to undergo extensive replication in an undifferentiated state ex vivo. In addition, BMSCs have the potential to develop either in vitro or in vivo into distinct mesenchymal tissues, including bone, cartilage, fat, tendon, muscle, and marrow stroma. Thus, BMSCs are an attractive cell source for tissue engineering approaches. However, BMSCs are not homo- geneous and the quantity of stem cells decreases in the bone marrow in aged population. A sequential loss of lineage differentiation potential has been found in the mixed culture of bone marrow stromal cells due to a heterogenous popu- lation. Therefore, a number of studies have proposed that homogenous bone marrow stem cells can be generated from clonal culture of bone marrow cells and that BMSC clones have the greatest potential for the application of bone regeneration in vivo

Repair and regeneration of osteochondral defects in the articular joints

People suffering from pain due to osteoarthritic or rheumatoidal changes in the joints are still waiting for a better treatment. Although some studies have achieved success in repairing small cartilage defects, there is no widely accepted method for complete repair of osteochondral defects. Also joint replacements have not yet succeeded in replacing of natural cartilage without complications. Therefore, there is room for a new medical approach, which outperforms currently used methods. The aim of this study is to show potential of using a tissue engineering approach for regeneration of osteochondral defects. The critical review of currently used methods for treatment of osteochondral defects is also provided. In this study, two kinds of hybrid scaffolds developed in Hutmacher's group have been analysed. The first biphasic scaffold consists of fibrin and PCL. The fibrin serves as a cartilage phase while the porous PCL scaffold acts as the subchondral phase. The second system comprises of PCL and PCL-TCP. The scaffolds were fabricated via fused deposition modeling which is a rapid prototyping system. Bone marrow-derived mesenchymal cells were isolated from New Zealand White rabbits, cultured in vitro and seeded into the scaffolds. Bone regenerations of the subchondral phases were quantified via micro CT analysis and the results demonstrated the potential of the porous PCL and PCL-TCP scaffolds in promoting bone healing. Fibrin was found to be lacking in this aspect as it degrades rapidly. On the other hand, the porous PCL scaffold degrades slowly hence it provides an effective mechanical support. This study shows that in the field of cartilage repair or replacement, tissue engineering may have big impact in the future. In vivo bone and cartilage engineering via combining a novel composite, biphasic scaffold technology with a MSC has been shown a high potential in the knee defect regeneration in the animal models. However, the clinical application of tissue engineering requires the future research work due to several problems, such as scaffold design, cellular delivery and implantation strategies.