A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

Importancia de la caracterización de la masa de raíces en la simulación de ecosistemas forestales

Los análisis de sensibilidad son una herramienta importante para comprender el funcionamiento de los modelos ecológicos, así como para identificar los parámetros más importantes en su funcionamiento. Además, los análisis de sensibilidad pueden utilizarse para diseñar de forma más efectiva planes de muestreo de campo dirigidos a calibrar los modelos ecológicos. En los estudios de ecosistemas forestales, el análisis cuantitativo de la parte subterránea es mucho más costoso y complicado que el estudio de la parte aérea, en especial el estudio de la dinámica de producción y descomposición de raíces gruesas y finas de los árboles. En este trabajo se muestra un ejemplo de análisis de sensibilidad del modelo forestal FORECAST a parámetros que definen la biomasa, longevidad y concentración de nitrógeno en las raíces de los árboles. El modelo se calibró para simular dos rodales de pino silvestre (Pinus sylvestris) en los Pirineos de Navarra. Los resultados indican que la tasa de renovación de raíces finas es el parámetro más influyente en las estimaciones del modelo de crecimiento de los árboles, seguida de la concentración de N en las mismas, siendo la relación biomasa subterránea/total el parámetro al cual el modelo es menos sensible. Además, el modelo es más sensible a los parámetros que definen el componente subterráneo de la biomasa arbórea cuando simula un sitio de menor capacidad productiva y mayor limitación por nutrientes.

Sampling tissue for DNA analysis of trees: Trunk cambium as an alternative to canopy leaves

The number of studies of tropical tree species that use molecular tools is increasing, most of which collect leaf tissue for genomic DNA extraction. In tropical trees the canopy is not only frequently inaccessible, but also, once reached, the leaf tissue is often heavily defended against herbivory by high concentrations of anti-predation compounds, which may inhibit downstream applications, particularly PCR. Cambium tissue, accessed directly from the tree trunk at ground level, offers a readily accessible resource that is less hampered by the presence of defensive chemicals than leaf tissue. Here we describe a simple method for obtaining tissue from the cambial zone for DNA extraction and test the applicability of the method in a range of tropical tree species. The method was used successfully to extract DNA from 11 species in nine families. A subset of the DNA extracts was tested in more detail and proved to be highly suitable for AFLP analysis.

Planted forests and biodiversity

Expansion of planted forests and intensification of their management has raised concerns among forest managers and the public over the implications of these trends for sustainable production and conservation of forest biological diversity. We review the current state of knowledge on the impacts of plantation forestry on genetic and species diversity at different spatial scales and discuss the economic and ecological implications of biodiversity management within plantation stands and landscapes. Managing plantations to produce goods such as timber while also enhancing ecological services such as biodiversity involves tradeoffs, which can be made only with a clear understanding of the ecological context of plantations in the broader landscape and agreement among stakeholders on the desired balance of goods and ecological services from plantations.

Nitrogen balance for an agroforestry system irrigated with saline, high nitrogen effluent

Land disposal is commonly used for urban and industrial wastewater, largely due to the high costs involved in alternative treatments or disposal systems. However, the viability of such systems depends on many factors, including the composition of the effluent water, soil type, the plant species grown, growth rate, and planting density. The objective of this study is to establish whether land disposal of nitrogen (N) rich effluent using an agroforestry system is sustainable, and determine the effect of irrigation rate and tree planting density on the N cycle and subsequent N removal. We examined systems for the sustainable disposal of a high strength industrial effluent. The challenge was to leach the salt, by using a sufficiently high rate of irrigation, while simultaneously ensuring that N did not leach from the soil profile. We describe the N balance for two plant systems irrigated with effluent, one comprising Eucalyptus tereticornis and Eucalyptus moluccana and a Rhodes grass (Chloris gayana) pasture, and the other, Rhodes grass pasture alone. Nitrogen balance was assessed from N inputs in effluent and rainfall, accumulation of N in the plant biomass, changes in soil N storage, N loss in run-off water, denitrification and N loss to the groundwater by deep-drainage. Biomass production was estimated from allometric relationships derived from yearly destructive harvesting of selected trees. The N content of that biomass was then calculated from measured N content of the various plant parts, and their mass. Approximately 300 kg N/ha/yr was assimilated into tree biomass at a planting density of 2500 tree/ha of E. moluccana. In addition to tree assimilation, pasture growth between the tree rows, which was regularly harvested, contributed substantially to N uptake. If the trees were harvested after two years of growth and grass harvested regularly, biomass removal of N by the mixed system would be about 700 kg N/ha/yr. The results of this study show that the current system of effluent disposal is not sustainable as the nitrate leaching from the soil profile far exceeds standards set out by the ANZECC guidelines. Hence additional means of N removal will need to be implemented. Biological N removal is an area that warrants further studies as it is aimed at reducing N levels in the effluent before irrigation. This will complement the current agroforestry system.

Data on the biogeochemical cycle of methane in the ocean

Geological, mineralogical and microbiological aspects of the methane cycle in water and sediments of different areas in the oceans are under consideration in the monograph. Original and published estimations of formation- and oxidation rates of methane with use of radioisotope and isotopic methods are given. The role of aerobic and anaerobic microbial oxidation of methane in production of organic matter and in formation of authigenic carbonates is considered. Particular attention is paid to processes of methane transformation in areas of its intensive input to the water column from deep-sea hydrothermal sources, mud volcanoes, and cold methane seeps.

Retrieval of grassland biophysical parameters using multitemporal optical and radar satellite data

The amount and quality of available biomass is a key factor for the sustainable livestock industry and agricultural management related decision making. Globally 31.5% of land cover is grassland while 80% of Ireland’s agricultural land is grassland. In Ireland, grasslands are intensively managed and provide the cheapest feed source for animals. This dissertation presents a detailed state of the art review of satellite remote sensing of grasslands, and the potential application of optical (Moderate–resolution Imaging Spectroradiometer (MODIS)) and radar (TerraSAR-X) time series imagery to estimate the grassland biomass at two study sites (Moorepark and Grange) in the Republic of Ireland using both statistical and state of the art machine learning algorithms. High quality weather data available from the on-site weather station was also used to calculate the Growing Degree Days (GDD) for Grange to determine the impact of ancillary data on biomass estimation. In situ and satellite data covering 12 years for the Moorepark and 6 years for the Grange study sites were used to predict grassland biomass using multiple linear regression, Neuro Fuzzy Inference Systems (ANFIS) models. The results demonstrate that a dense (8-day composite) MODIS image time series, along with high quality in situ data, can be used to retrieve grassland biomass with high performance (R2 = 0:86; p < 0:05, RMSE = 11.07 for Moorepark). The model for Grange was modified to evaluate the synergistic use of vegetation indices derived from remote sensing time series and accumulated GDD information. As GDD is strongly linked to the plant development, or phonological stage, an improvement in biomass estimation would be expected. It was observed that using the ANFIS model the biomass estimation accuracy increased from R2 = 0:76 (p < 0:05) to R2 = 0:81 (p < 0:05) and the root mean square error was reduced by 2.72%. The work on the application of optical remote sensing was further developed using a TerraSAR-X Staring Spotlight mode time series over the Moorepark study site to explore the extent to which very high resolution Synthetic Aperture Radar (SAR) data of interferometrically coherent paddocks can be exploited to retrieve grassland biophysical parameters. After filtering out the non-coherent plots it is demonstrated that interferometric coherence can be used to retrieve grassland biophysical parameters (i. e., height, biomass), and that it is possible to detect changes due to the grass growth, and grazing and mowing events, when the temporal baseline is short (11 days). However, it not possible to automatically uniquely identify the cause of these changes based only on the SAR backscatter and coherence, due to the ambiguity caused by tall grass laid down due to the wind. Overall, the work presented in this dissertation has demonstrated the potential of dense remote sensing and weather data time series to predict grassland biomass using machine-learning algorithms, where high quality ground data were used for training. At present a major limitation for national scale biomass retrieval is the lack of spatial and temporal ground samples, which can be partially resolved by minor modifications in the existing PastureBaseIreland database by adding the location and extent ofeach grassland paddock in the database. As far as remote sensing data requirements are concerned, MODIS is useful for large scale evaluation but due to its coarse resolution it is not possible to detect the variations within the fields and between the fields at the farm scale. However, this issue will be resolved in terms of spatial resolution by the Sentinel-2 mission, and when both satellites (Sentinel-2A and Sentinel-2B) are operational the revisit time will reduce to 5 days, which together with Landsat-8, should enable sufficient cloud-free data for operational biomass estimation at a national scale. The Synthetic Aperture Radar Interferometry (InSAR) approach is feasible if there are enough coherent interferometric pairs available, however this is difficult to achieve due to the temporal decorrelation of the signal. For repeat-pass InSAR over a vegetated area even an 11 days temporal baseline is too large. In order to achieve better coherence a very high resolution is required at the cost of spatial coverage, which limits its scope for use in an operational context at a national scale. Future InSAR missions with pair acquisition in Tandem mode will minimize the temporal decorrelation over vegetation areas for more focused studies. The proposed approach complements the current paradigm of Big Data in Earth Observation, and illustrates the feasibility of integrating data from multiple sources. In future, this framework can be used to build an operational decision support system for retrieval of grassland biophysical parameters based on data from long term planned optical missions (e. g., Landsat, Sentinel) that will ensure the continuity of data acquisition. Similarly, Spanish X-band PAZ and TerraSAR-X2 missions will ensure the continuity of TerraSAR-X and COSMO-SkyMed.

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

HETEROSIS AND HERITABILITY ESTIMATES OF PURINE ALKALOIDS AND POLYPHENOLS IN COCOA

Cocoa ( Theobroma cacao L. ) is an important allogamous tropical tree crop, whose centre of diversity is considered to be in Central America. Dry cocoa beans from five cocoa clones, and their intercrossed hybrids were analysed based on the variation of alkaloids and polyphenolic compounds contents, in order to gain insights on the heterosis and broad-sense heritability. Polyphenols and alkaloids were analysed at 280 nm by HPLC, using a Photodiode Array Detector (PDA); while anthocyanins were separated with the SEP-PAK Vac 6cc 1000 mg (waters) column and measured at 520 nm with a PDA. Dry cocoa beans displayed high content of purine alkaloids (2.1 and 8.8 mg g-1 for caffein and theobromine, respectively), and polyphenols (25 and 2978 µg g-1 for catechin and epicatechin, respectively). Among the five cocoa clones, SNK16 was the highest in purine alkaloid (caffein and theobromin) and flavanol (catechin and epicatechin); while T79/467 possessed the greatest quantity of cyanidin-3-galactoside and cyanidin-3-arabinoside. From all the parameters studied, anthocyanins (Cyanidin-3-galactoside and cyanidin-3-arabinoside) exhibited the highest level of heterosis. Parental genotypes SNK16 and T79/467 showed good aptitudes for the combination of characters because their reciprocal hybrids F5 and F9, distinguished themselves by better levels of mid-parent heterosis values. Besides, the heritability value in strict sense of this Cyanidin-3-galactoside was very high. Absence of significant difference between genotypes, coming from reciprocal crossbreeding for Cyanidin-3-galactoside, suggests that this character in cocoa would be nuclear contrary to purine alkaloids and flavan-3-ols, where their transmission to offsprings can be stated as cytoplasmic.

Indirect and expedite assessment of Ilex paraguariensis commercial yield.

A produção de biomassa comercial é uns dos principais indicadores para seleção de progênies e clones de erva-mate. Técnicas tradicionais para se obter tais informações dependem da colheita das árvores e apresentam, dentre outras limitações, elevado custo e reduzida praticidade. Assim, objetivou-se avaliar a eficiência de métodos indiretos, por meio de estimativa de biomassa comercial e escore de produtividade em função de diferentes procedências, sexo e morfotipos. Em um teste de progênies e procedências instalado em 1997, foram avaliadas em agosto de 2015 (dois anos após a última colheita) duas metodologias de análise visual. Para tanto, participaram cinco avaliadores treinados que determinaram, para cada planta, uma estimativa de biomassa comercial (kg), e uma nota, com base em um escore de produtividade (0-10). Para avaliação da produtividade pelas técnicas tradicionais, todas as plantas foram podadas e tiveram sua biomassa comercial (folhas e ramos finos menores de 7 mm de diâmetro) colhida e avaliada por meio de pesagem (Kg.planta-1). As avaliações foram realizadas em experimento instalado em blocos ao acaso, com cinco repetições, sete procedências e 126 progênies, totalizando 5292 plantas avaliadas. Os métodos avaliados foram eficientes na estimativa da biomassa comercial. Os avaliadores apresentaram boa acuidade nas estimativas, expressando de forma eficiente a maior produtividade determinada por comparação de médias entre as procedências, sexo das matrizes e morfotipos. As maiores correlações foram verificadas na análise geral das médias e a estimativa de biomassa comercial é a melhor metodologia para estimar a biomassa comercial aferida em plantas adultas de erva-mate.

Aluminum toxicity to tropical montane forest tree seedlings in southern Ecuador: response of biomass and plant morphology to elevated Al concentrations

In acid tropical forest soils (pH < 5.5) increased mobility of aluminum might limit aboveground productivity. Therefore, we evaluated Al phytotoxicity of three native tree species of tropical montane forests in southern Ecuador. An hydroponic dose-response experiment was conducted. Seedlings of Cedrela odorata L., Heliocarpus americanus L., and Tabebuia chrysantha (Jacq.) G. Nicholson were treated with 0, 300, 600, 1200, and 2400 mu M Al and an organic layer leachate. Dose-response curves were generated for root and shoot morphologic properties to determine effective concentrations (EC). Shoot biomass and healthy leaf area decreased by 44 % to 83 % at 2400 mu M Al, root biomass did not respond (C. odorata), declined by 51 % (H. americanus), or was stimulated at low Al concentrations of 300 mu M (T. chrysantha). EC10 (i.e. reduction by 10 %) values of Al for total biomass were 315 mu M (C. odorata), 219 mu M (H. americanus), and 368 mu M (T. chrysantha). Helicarpus americanus, a fast growing pioneer tree species, was most sensitive to Al toxicity. Negative effects were strongest if plants grew in organic layer leachate, indicating limitation of plant growth by nutrient scarcity rather than Al toxicity. Al toxicity occurred at Al concentrations far above those in native organic layer leachate.

Forest structure and live aboveground biomass variation along an elevational gradient of tropical Atlantic moist forest (Brazil)

Live aboveground biomass (AGB) is an important source of uncertainty in the carbon balance from the tropical regions in part due scarcity of reliable estimates of live AGB and its variation across landscapes and forest types. Studies of forest structure and biomass stocks of Neotropical forests are biased toward Amazonian and Central American sites. In particular, standardized estimates of aboveground biomass stocks for the Brazilian Atlantic forest are rarely available. Notwithstanding the role of environmental variables that control the distribution and abundance of biomass in tropical lowland forests has been the subject of considerable research, the effect of short, steep elevational gradients on tropical forest structure and carbon dynamics is not well known. In order to evaluate forest structure and live AGB variation along an elevational gradient (0-1100 m a.s.l.) of coastal Atlantic Forest in SE Brazil, we carried out a standard census of woody stems >= 4.8 cm dbh in 13 1-ha permanent plots established on four different sites in 2006-2007. Live AGB ranged from 166.3 Mg ha(-1) (bootstrapped 95% CI: 1444,187.0) to 283.2 Mg ha(-1) (bootstrapped 95% CI: 253.0,325.2) and increased with elevation. We found that local-scale topographic variation associated with elevation influences the distribution of trees >50 cm dbh and total live AGB. Across all elevations, we found more stems (64-75%) with limited crown illumination but the largest proportion of the live AGB (68-85%) was stored in stems with highly illuminated or fully exposed crowns. Topography, disturbance and associated changes in light and nutrient supply probably control biomass distribution along this short but representative elevational gradient. Our findings also showed that intact Atlantic forest sites stored substantial amounts of carbon aboveground. The live tree AGB of the stands was found to be lower than Central Amazonian forests, but within the range of Neotropical forests, in particular when compared to Central American forests. Our comparative data suggests that differences in live tree AGB among Neotropical forests are probably related to the heterogeneous distribution of large and medium-sized diameter trees within forests and how the live biomass is partitioned among those size classes, in accordance with general trends found by previous studies. In addition, the elevational variation in live AGB stocks suggests a large spatial variability over coastal Atlantic forests in Brazil, clearly indicating that it is important to consider regional differences in biomass stocks for evaluating the role of this threatened tropical biome in the global carbon cycle. (C) 2010 Elsevier B.V. All rights reserved.

Biomass and nutrient cycling in pure and mixed stands of native tree species in southeastern Bahia, Brazil

The objective of this paper is to study selected components of the nutrient cycle of pure and mixed stands of native forest species of Atlantic Forest in southeastern Brazil. Tree diameter, height, above-ground biomass, and nutrient content were determined in 22-year-old stands. Litterfall, litter decomposition, and nutrient concentration were evaluated from August 1994 to July 1995. The following species were studied: Peltogyne angustiflora, Centrolobium robustum, Arapatiella psilophylla, Sclerolobium chrysophyllum, Cordia trichotoma, Macrolobium latifolium. The litter of a natural forest and a 40-year-old naturally regenerated second-growth forest was sampled as well. The mixed-species outmatched pure stands in height, stem volume and total biomass (29.4 % more). The greatest amount of forest litter was observed in the natural forest (9.3 Mg ha-1), followed by the mixed-species stand (7.6 Mg ha-1) and secondary forest (7.3 Mg ha-1), and least litterfall was measured in the pure C. robustum stand (5.5 Mg ha-1). Litterfall seasonality varied among species in pure stands (CV from 44.7 to 91.4 %), unlike litterfall in the mixed-tree stand, where the variation was lower (CV 31.2 %). In the natural and second-growth forest, litterfall varied by 57.8 and 34.0 %, respectively. The annual rate of nutrient return via litterfall varied widely among forest ecosystems. Differences were detected between forest ecosystems in both the litter accumulation and quantity of litterlayer nutrients. The highest mean nutrient accumulation in above-ground biomass was observed in mixed-species stands. The total nutrient accumulation (N + P + K+ Ca + Mg) ranged from 0.97 to 1.93 kg tree-1 in pure stands, and from 1.21 to 2.63 kg tree-1 in mixed-species stands. Soil fertility under mixed-species stands (0-10 cm) was intermediate between the primary forest and pure-stand systems. The litterfall rate of native forest species in a mixed-species system is more constant, resulting in a more continuous decomposition rate. Consequently, both nutrient availability and quantity of organic matter in the soil are higher and the production system ecologically more sustainable.

Tropical terrestrial model ecosystems for evaluation of soil fauna and leaf litter quality effects on litter consumption, soil microbial biomass and plant growth

The aim of this work was to evaluate whether terrestrial model ecosystems (TMEs) are a useful tool for the study of the effects of litter quality, soil invertebrates and mineral fertilizer on litter decomposition and plant growth under controlled conditions in the tropics. Forty-eight intact soil cores (17.5-cm diameter, 30-cm length) were taken out from an abandoned rubber plantation on Ferralsol soil (Latossolo Amarelo) in Central Amazonia, Brazil, and kept at 28ºC in the laboratory during four months. Leaf litter of either Hevea pauciflora (rubber tree), Flemingia macrophylla (a shrubby legume) or Brachiaria decumbens (a pasture grass) was put on top of each TME. Five specimens of either Pontoscolex corethrurus or Eisenia fetida (earthworms), Porcellionides pruinosus or Circoniscus ornatus (woodlice), and Trigoniulus corallinus (millipedes) were then added to the TMEs. Leaf litter type significantly affected litter consumption, soil microbial biomass and nitrate concentration in the leachate of all TMEs, but had no measurable effect on the shoot biomass of rice seedlings planted in top soil taken from the TMEs. Feeding rates measured with bait lamina were significantly higher in TMEs with the earthworm P. corethrurus and the woodlouse C. ornatus. TMEs are an appropriate tool to assess trophic interactions in tropical soil ecossistems under controlled laboratory conditions.

Photosynthesis and carbon gain under contrasting light levels in seedlings of a pioneer and a climax tree from a Brazilian Semideciduous Tropical Forest

In this study we evaluated photosynthetic characteristics and patterns of biomass accumulation in seedlings of two tree species from a Semideciduous Tropical Forest of Brazil. Seedlings of Trema micrantha (L.) Blum. (pioneer) and Hymenaea courbaril (L.) var. stilbocarpa (Hayne) Lee & Langenh. (climax) were grown for 4 months under low light (LL) (5%-8% of sunlight) and high light (HL) (100% of sunlight). Under HL, T. micrantha showed higher CO2 assimilation rates (A CO2) and light saturation than H. courbaril. Under LL, A CO2 were higher in H. courbaril. Under LL, total chlorophyll and carotenoid contents per unit leaf area were higher in H. courbaril. Chlorophyll a/b ratio was higher in T. micrantha under both light regimes. A CO2 and Fv/Fm ratio at both pre-dawn and midday in H. coubaril were lower in HL indicating chronic photoinhibition. Thus, the climax species was more susceptible to photoinhibition than the pioneer. However, H. courbaril produced higher total biomass under both treatments showing high efficiency in the maintenance of a positive carbon balance. Thus, both species expressed characteristics that favor growth under conditions that resemble their natural microenvironments, but H. courbaril also grew under HL. The ecophysiological range of responses to contrasting light levels of this climax plant seems to be broader than generally observed for other rainforest climax species. We propose that this could be related to the particular spatio-temporal light regime of the semideciduous forests.