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Barthe, S., Gugerli, F., Barkley, N. A., Maggia, L., Cardi, C., & Scotti, I. (2012). Always look on both sides: Phylogenetic information conveyed by simple sequence repeat allele sequences. PLoS ONE, 7(7), e40699.
Abstract: Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.
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Hein, P. R. G., Chaix, G., Clair, B., Brancheriau, L., & Gril, J. (2016). Spatial variation of wood density, stiffness and microfibril angle along Eucalyptus trunks grown under contrasting growth conditions. Trees – Structure and Function, 30(3), 871–882.
Abstract: Sloped terrains tend to produce trees with higher radial variation in wood density while at high wind speeds, the wood tends to present higher stiffness and lower MFA in Eucalyptus.
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Doughty, C. E., Wolf, A., Baraloto, C., & Malhi, Y. (2016). Interdependency of plants and animals in controlling the sodium balance of ecosystems and the impacts of global defaunation. Ecography, 39(2), 204–212.
Abstract: Sodium, an element which is needed by animals but often toxic in high concentrations to plants, may be deficient and limit animal abundance in inland continental regions, but may be overabundant and limit plant productivity in coastal regions. Here we present data from 50 independent plots (including leaf data from more than 2480 individual trees) showing that leaves in the Amazon basin uptake high amounts of sodium (Na) in a manner more similar to the essential cation potassium (K) than to the toxic cation aluminium (Al). Leaf Na increases linearly with soil Na concentrations, and there is no apparent mechanism for selective exclusion of Na in comparison to K, a key attribute of halophytes. This indicates that the Amazon basin is broadly non-halophytic and increased sodium concentrations in non-halophyte plants often decrease plant productivity. Total Na concentrations are ∼ 10 times higher in coastal regions than inland regions. Such concentration gradients in nutrients may have been reduced in the past because large animals that were abundant in the Pleistocene have been hypothesized to play a large role in reducing nutrient concentration gradients at continental scales. We use a diffusion model and a Na loss rate based on empirical data to estimate that large animals may have moved significant quantities of Na inland away from coastal regions in the Amazon Basin. Therefore, our simple model suggests that large animals may play an important, yet diminishing, role in maintaining the sodium balance of the planet. © 2016 Nordic Society Oikos.
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Peguero, G., Sardans, J., Asensio, D., Fernández-Martínez, M., Gargallo-Garriga, A., Grau, O., et al. (2019). Nutrient scarcity strengthens soil fauna control over leaf litter decomposition in tropical rainforests. Proc. Biol. Sci., 286(1910), 20191300.
Abstract: Soil fauna is a key control of the decomposition rate of leaf litter, yet its interactions with litter quality and the soil environment remain elusive. We conducted a litter decomposition experiment across different topographic levels within the landscape replicated in two rainforest sites providing natural gradients in soil fertility to test the hypothesis that low nutrient availability in litter and soil increases the strength of fauna control over litter decomposition. We crossed these data with a large dataset of 44 variables characterizing the biotic and abiotic microenvironment of each sampling point and found that microbe-driven carbon (C) and nitrogen (N) losses from leaf litter were 10.1 and 17.9% lower, respectively, in the nutrient-poorest site, but this among-site difference was equalized when meso- and macrofauna had access to the litterbags. Further, on average, soil fauna enhanced the rate of litter decomposition by 22.6%, and this contribution consistently increased as nutrient availability in the microenvironment declined. Our results indicate that nutrient scarcity increases the importance of soil fauna on C and N cycling in tropical rainforests. Further, soil fauna is able to equalize differences in microbial decomposition potential, thus buffering to a remarkable extent nutrient shortages at an ecosystem level.
Keywords: biogeochemistry; extracellular enzyme activity; litter decomposition; nutrients; soil fauna
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Sellan, G., Brearley, F. Q., Nilus, R., Ttin, J., & Majalap-Lee, N. (2021). Differences in soil properties among contrasting soil types in Northern Borneo. Journal of Tropical Forest Science, 33(2), 191–202.
Abstract: Soil in the tropics is high in diversity, and despite the diversity of Borneo’s forest–soil associations, there is a paucity of data on its soil properties. We investigated the differences between three soil types in the Kabili–Sepilok Forest Reserve, Sabah, Malaysia, encompassing the contrasting alluvial, sandstone and heath forest typologies. We examined the distribution of nutrients between soil types and through soil depths, and assessed the extent of spatial autocorrelation in the three soil types. We confirmed the fertility gradient from alluvial to heath forest soil found by others. Soil elemental concentrations declined in deeper horizons with the exception of exchangeable sodium and aluminium that remained constant through alluvial and sandstone soil profiles. Spatial autocorrelation was present in all three soil types and strongest in the sandstone soil. Overall, we show how bedrock, erosion, leaching and topography influence soil properties across this mosaic of soil types and note their importance in influencing tree communities and their ecological functioning.
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Soong, J. L., Marañon-Jimenez, S., Cotrufo, M. F., Boeckx, P., Bodé, S., Guenet, B., et al. (2018). Soil microbial CNP and respiration responses to organic matter and nutrient additions: Evidence from a tropical soil incubation. Soil Biology and Biochemistry, 122, 141–149.
Abstract: Soil nutrient availability has a strong influence on the fate of soil carbon (C) during microbial decomposition, contributing to Earth's C balance. While nutrient availability itself can impact microbial physiology and C partitioning between biomass and respiration during soil organic matter decomposition, the availability of labile C inputs may mediate the response of microorganisms to nutrient additions. As soil organic matter is decomposed, microorganisms retain or release C, nitrogen (N) or phosphorus (P) to maintain a stoichiometric balance. Although the concept of a microbial stoichiometric homeostasis has previously been proposed, microbial biomass CNP ratios are not static, and this may have very relevant implications for microbial physiological activities. Here, we tested the hypothesis that N, P and potassium (K) nutrient additions impact C cycling in a tropical soil due to microbial stoichiometric constraints to growth and respiration, and that the availability of energy-rich labile organic matter in the soil (i.e. leaf litter) mediates the response to nutrient addition. We incubated tropical soil from French Guiana with a 13C labeled leaf litter addition and with mineral nutrient additions of +K, +N, +NK, +PK and +NPK for 30 days. We found that litter additions led to a ten-fold increase in microbial respiration and a doubling of microbial biomass C, along with greater microbial N and P content. We found some evidence that P additions increased soil CO2 fluxes. Additionally, we found microbial biomass CP and NP ratios varied more widely than CN in response to nutrient and organic matter additions, with important implications for the role of microorganisms in C cycling. The addition of litter did not prime soil organic matter decomposition, except in combination with +NK fertilization, indicating possible P-mining of soil organic matter in this P-poor tropical soil. Together, these results point toward an ultimate labile organic substrate limitation of soil microorganisms in this tropical soil, but also indicate a complex interaction between C, N, P and K availability. This highlights the difference between microbial C cycling responses to N, P, or K additions in the tropics and explains why coupled C, N and P cycle modeling efforts cannot rely on strict microbial stoichiometric homeostasis as an underlying assumption.
Keywords: 13c; Cnp; Microbial stoichiometry; Priming; Soil respiration; Tropics
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Quesada, C. A., Lloyd, J., Schwarz, M., Patino, S., Baker, T. R., Czimczik, C., et al. (2010). Variations in chemical and physical properties of Amazon forest soils in relation to their genesis. Biogeosciences, 7(5), 1515–1541.
Abstract: Soil samples were collected in six South American countries in a total of 71 different 1 ha forest plots across the Amazon Basin as part of the RAINFOR project. They were analysed for total and exchangeable cations, C, N, pH with various P fractions also determined. Physical properties were also examined and an index of soil physical quality proposed. A diverse range of soils was found. For the western areas near the Andean cordillera and the southern and northern fringes, soils tend to be distributed among the lower pedogenetic levels, while the central and eastern areas of Amazonia have more intensely weathered soils. This gives rise to a large variation of soil chemical and physical properties across the Basin, with soil properties varying predictably along a gradient of pedogenic development. Nutrient pools generally increased slightly in concentration from the youngest to the intermediate aged soils after which a gradual decline was observed with the lowest values found in the most weathered soils. Soil physical properties were strongly correlated with soil fertility, with favourable physical properties occurring in highly weathered and nutrient depleted soils and with the least weathered, more fertile soils having higher incidence of limiting physical properties. Soil phosphorus concentrations varied markedly in accordance with weathering extent and appear to exert an important influence on the nitrogen cycle of Amazon forest soils.
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Fortunel, C., Stahl, C., Heuret, P., Nicolini, E., & Baraloto, C. (2020). Disentangling the effects of environment and ontogeny on tree functional dimensions for congeneric species in tropical forests. New Phytol., 226(2), 385–395.
Abstract: Soil water and nutrient availability are key drivers of tree species distribution and forest ecosystem functioning, with strong species differences in water and nutrient use. Despite growing evidence for intraspecific trait differences, it remains unclear under which circumstances the effects of environmental gradients trump those of ontogeny and taxonomy on important functional dimensions related to resource use, particularly in tropical forests. Here, we explore how physiological, chemical, and morphological traits related to resource use vary between life stages in four species within the genus Micropholis that is widespread in lowland Amazonia. Specifically, we evaluate how environment, developmental stage, and taxonomy contribute to single-trait variation and multidimensional functional strategies. We find that environment, developmental stage, and taxonomy differentially contribute to functional dimensions. Habitats and seasons shape physiological and chemical traits related to water and nutrient use, whereas developmental stage and taxonomic identity impact morphological traits –especially those related to the leaf economics spectrum. Our findings suggest that combining environment, ontogeny, and taxonomy allows for a better understanding of important functional dimensions in tropical trees and highlights the need for integrating tree physiological and chemical traits with classically used morphological traits to improve predictions of tropical forests’ responses to environmental change. © 2019 The Authors New Phytologist © 2019 New Phytologist Trust
Keywords: chemistry; developmental stage; habitats; Micropholis; morphology; physiology; plant traits; seasons; developmental stage; ecosystem function; forest ecosystem; habitat selection; habitat structure; nutrient availability; ontogeny; physiological response; soil water; taxonomy; tropical forest; Amazonia
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Le Guen, V., Rodier-Goud, M., Troispoux, V., Xiong, T. C., Brottier, P., Billot, C., et al. (2004). Characterization of polymorphic microsatellite markers for Microcyclus ulei, causal, agent of South American leaf blight of rubber trees. Mol. Ecol. Notes, 4(1), 122–124.
Abstract: South American leaf blight caused by the ascomycete Microcyclus Wei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus).
Keywords: Hevea brasiliensis; Microcyclus ulei; microsatellite markers; phytopathogenic fungi; South American leaf blight
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Gomes, V. H. F., IJff, S. D., Raes, N., Amaral, I. L., Salomão, R. P., de Souza Coelho, L., et al. (2018). Species Distribution Modelling: Contrasting presence-only models with plot abundance data. Sci. Rep., 8, 1003.
Abstract: Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species’ area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
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