Disproportionate single-species contribution to canopy-soil nutrient flux in an Amazonian rainforest

Rainfall, throughfall and stemflow were monitored on an event basis in an undisturbed open tropical rainforest with a large number of palm trees located in the southwestern Amazon basin of Brazil. Stemflow samples were collected from 24 trees with a diameter at breast height (DBH) > 5 cm, as well as eight young and four full-grown babassu palms (Attalea speciosa Mart.) for 5 weeks during the peak of the wet season. We calculated rainfall, throughfall and stemflow concentrations and fluxes of Na+, K+, Ca2+, Mg2+,, Cl-, SO42-, NO3- and H+ and stemflow volume-weighted mean concentrations and fluxes for three size classes of broadleaf trees and three size classes of palms. The concentrations of most solutes were higher in stemflow than in rainfall and increased with increasing tree and palm size. Concentration enrichments from rainfall to stemflow and throughfall were particularly high (81-fold) for NO3-. Stemflow fluxes of NO3- and H+ exceeded throughfall fluxes but stemflow fluxes of other solutes were less than throughfall fluxes. Stemflow solute fluxes to the forest soil were dominated by fluxes on babassu palms, which represented only 4% of total stem number and 10% of total basal area. For NO3-, stemflow contributed 51% of the total mass of nitrogen delivered to the forest floor (stemflow + throughfall) and represented more than a 2000-fold increase in NO3- flux compared what would have been delivered by rainfall alone on the equivalent area. Because these highly localized fluxes of both water and NO3- persist in time and space, they have the potential to affect patterns of soil moisture, microbial populations and other features of soil biogeochemistry conducive to the creation of hotspots for nitrogen leaching and denitrification, which could amount to an important fraction of total ecosystem fluxes. Because these hotspots occur over very small areas, they have likely gone undetected in previous studies and need to be considered as an important feature of the biogeochemistry of palm-rich tropical forest. (C) 2011 Elsevier B.V. All rights reserved.

Introducing Acacia mangium trees in Eucalyptus grandis plantations: consequences for soil organic matter stocks and nitrogen mineralization

Background and aims Eucalyptus plantations cover 20 million hectares on highly weathered soils. Large amounts of nitrogen (N) exported during harvesting lead to concerns about their sustainability. Our goal was to assess the potential of introducing A. mangium trees in highly productive Eucalyptus plantations to enhance soil organic matter stocks and N availability. Methods A randomized block design was set up in a Brazilian Ferralsol soil to assess the effects of mono-specific Eucalyptus grandis (100E) and Acacia mangium (100A) stands and mixed plantations (50A:50E)on soil organic matter stocks and net N mineralization. Results A 6-year rotation of mono-specific A. mangium plantations led to carbon (C) and N stocks in the forest floor that were 44% lower and 86% higher than in pure E. grandis stands, respectively. Carbon and N stocks were not significantly different between the three treatments in the 0-15 cm soil layer. Field incubations conducted every 4 weeks for the two last years of the rotation estimated net soil N mineralization in 100A and 100E at 124 and 64 kg ha(-1) yr(-1), respectively. Nitrogen inputs to soil with litterfall were of the same order as net N mineralization. Conclusions Acacia mangium trees largely increased the turnover rate of N in the topsoil. Introducing A. mangium trees might improve mineral N availability in soils where commercial Eucalyptus plantations have been managed for a long time.

Amazonian Anthrosols Support Similar Microbial Communities that Differ Distinctly from Those Extant in Adjacent, Unmodified Soils of the Same Mineralogy

We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We sampled paired anthrosol and unmodified soils from four locations in the Manaus, Brazil, region that differed in their current land use and soil type. Community DNA was extracted from sampled soils and characterized by use of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism. DNA bands of interest from Bacteria and Archaea DGGE gels were cloned and sequenced. In cluster analyses of the DNA fingerprints, microbial communities from the anthrosols grouped together regardless of current land use or soil type and were distinct from those in their respective, paired adjacent soils. For the Archaea, the anthrosol communities diverged from the adjacent soils by over 90%. A greater overall richness was observed for Bacteria sequences as compared with those of the Archaea. Most of the sequences obtained were novel and matched those in databases at less than 98% similarity. Several sequences obtained only from the anthrosols grouped at 93% similarity with the Verrucomicrobia, a genus commonly found in rice paddies in the tropics. Sequences closely related to Proteobacteria and Cyanobacteria sp. were recovered only from adjacent soil samples. Sequences related to Pseudomonas, Acidobacteria, and Flexibacter sp. were recovered from both anthrosols and adjacent soils. The strong similarities among the microbial communities present in the anthrosols for both the Bacteria and Archaea suggests that the microbial community composition in these soils is controlled more strongly by their historical soil management than by soil type or current land use. The anthrosols had consistently higher concentrations of incompletely combusted organic black carbon material (BC), higher soil pH, and higher concentrations of P and Ca compared to their respective adjacent soils. Such characteristics may help to explain the longevity and distinctiveness of the anthrosols in the Amazonian landscape and guide us in recreating soils with sustained high fertility in otherwise nutrient-poor soils in modern times.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

CHARACTERIZATION OF THE MICRO-SITE CONDITIONS FROM RESTORED AREAS WITH DIFFERENT AGES

Regeneration microsites are characterized by diverse combinations of attributes which assure the best conditions for seed germination and seedling establishment. By understanding these attributes, we can contribute to determining better management methodologies for reestablishing ecological process in sites under restoration. Thus, we sought to characterize and differentiate the micro-site conditions of restoration plantings to indentify likely physical-chemical limitations for the establishment of native tree species in the forest understory. This study was carried out in reforestation plantings with different ages (10, 22 and 55 years). The physical-chemical characterization of the micro-site of regeneration of the study areas was carried out by evaluating the soil compression level, porosity, humidity, organic matter and nutrients content and granulometry, as well as litter dry mass and canopy cover. An increase on the canopy cover and soil porosity, humidity, clay and organic matter content were observed in the oldest restored areas, as well as a decrease in soil compression. Thus, these findings demonstrated that the evaluated microsite properties are in process of restoration. Therefore, microsite conditions for seedling establishment become even more similar to reference ecosystems as restoration planting evolve.

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. Citation: Jimenez DJ, Andreote FD, Chaves D, Montana JS, Osorio-Forero C, et al. (2012) Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes. PLoS ONE 7(12): e52069. doi:10.1371/journal.pone.0052069

AMMONIA LOSSES ESTIMATED BY AN OPEN COLLECTOR FROM UREA APPLIED TO SUGARCANE STRAW

The quantification of ammonia (NH3) losses from sugarcane straw fertilized with urea can be performed with collectors that recover the NH3 in acid-treated absorbers. Thus, the use of an open NH3 collector with a polytetrafluoroethylene (PTFE)-wrapped absorber is an interesting option since its cost is low, handling easy and microclimatic conditions irrelevant. The aim of this study was to evaluate the efficiency of an open collector for quantifying NH3-N volatilized from urea applied over the sugarcane straw. The experiment was carried out in a sugarcane field located near Piracicaba, Sao Paulo, Brazil. The NH3-N losses were estimated using a semi-open static collector calibrated with N-15 (reference method) and an open collector with an absorber wrapped in PTFE film. Urea was applied to the soil surface in treatments corresponding to rates of 50, 100, 150 and 200 kg ha(-1) N. Applying urea-N fertilizer on sugarcane straw resulted in losses NH3-N up to 24 % of the applied rate. The amount of volatile NH3-N measured in the open and the semi-open static collector did not differ. The effectiveness of the collection system varied non-linearly, with an average value of 58.4 % for the range of 100 to 200 kg ha(-1) of urea-N. The open collector showed significant potential for use; however, further research is needed to verify the suitability of the proposed method.

Application of dendrogeomorphology on the study of soil sediment deposition in the stems of Guarea guidonea trees in a disturbed riparian forest in Goias state, Brazil

The sediments resulting of natural or anthropic erosion are deposited on the soil surface and around the trunks of trees occurring in riparian forests. For assessment of the erosion, tree-rings of roots and stems were analyzed. Guarea guidonea trees from a riparian forest affected by the sedimentation of soil erosion from pastures and soybean fields in state of Goias were selected. Wood samples were extracted through a non-destructive method at three heights from trunks of trees located in three positions (top, middle and bottom) of a riparian slope. The evaluation revealed a deposition of a thick sediment layer up to 34 cm around the base of tree trunks during the past 24 years. The inter-correlations between the tree-rings widths present in wood samples at the base and at 50 and 100 cm from Guarea guidonea tree trunks presented low, medium and high values. These values resulted from the low tree-rings distinctiveness in the wood; the absence of some rings as well as the eccentricity of the pith. The analyses of dendrogeomorphology allowed the determination of the date of seed germination and tree growth and inference on the periods of sediment deposition in the trunk of the trees.

Soil profile, relief features and their relation to structure and distribution of Brazilian Atlantic rain forest trees

In tropical forests, the environmental heterogeneity can provide niche partitioning at local scales and determine the diversity and plant species distribution. Thus, this study aimed to investigate the variations of tree species structure and distribution in response to relief and soil profile features in a portion of the largest remnant of Brazilian Atlantic rain forest. All trees >= 5 cm diameter at breast height were recorded in two 0.99 ha plots. Topographic survey and a soil characterization were accomplished in both plots. Topsoil samples (0-20 cm) were taken from 88 quadrats and analyzed for chemical and particle size properties. Differences for both diversity and tree density were identified among three kinds of soils. A canonical correspondence analysis (CCA) indicated that the specific abundance varied among the three kinds of soils mapped: a shallow Udept - Orthent / Aquent gradient, probably due to differences in soil drainage. Nutrient content was less likely to affect tree species composition and distribution than relief, pH, Al3+, and soil texture. Some species were randomly distributed and did not show restriction to relief and soil properties. However, preferences in niche occupation detected in this study, derived from the catenary environments found, rise up as an important explanation for the high tree species diversity in tropical forests.

Soil-mediated effects on potential Euterpe edulis (Arecaceae) fruit and palm heart sustainable management in the Brazilian Atlantic Forest

Euterpe edulis is an endangered species due to palm heart overharvesting, the most important non-timber forest product of the Brazilian Atlantic Forest, and fruit exploitation has been introduced as a low impacting alternative. However, E. edulis is a keystone species for frugivores birds, and even the impact of fruit exploitation needs to be better investigated. Since this species occurs over contrasting habitats, the establishment of site-specific standards and limits for exploitation may also be essential to achieve truly sustainable management. In this context, we sought to investigate how soil chemical composition would potentially affect E. edulis (Arecaceae) palm heart and fruit exploitation considering current standards of management. We studied natural populations found in Restinga Forest and Atlantic Rainforest remnants established within Natural Reserves of Sao Paulo State, SE Brazil, where 10.24 ha permanent plots, composed of a grid of 256 subplots (20 m x 20 m), were located. In each of these subplots, we evaluated soil chemical composition and diameter at breast height of E. edulis individuals. Additionally, we evaluated fruit yield in 2008 and 2009 in 20 individuals per year. The Atlantic Rainforest population had a much higher proportion of larger diameter individuals than the population from the Restinga Forest, as a result of habitat-mediated effects, especially those related to soil. Sodium and potassium concentration in Restinga Forest soils, which have strong negative and positive effect on palm growth, respectively, played a key role in determining those differences. Overall, the number of fruits that could be exploited in the Atlantic Rainforest was four times higher than in Restinga Forest. If current rules for palm heart and fruit harvesting were followed without any restriction to different habitats, Restinga Forest populations are under severe threat, as this study shows that they are not suitable for sustainable management of both fruits and palm heart. Hence, a habitat-specific approach of sustainable management is needed for this species in order to respect the demographic and ecological dynamics of each population to be managed. These findings suggest that any effort to create general management standards of low impacting harvesting may be unsuccessful if the species of interest occur over a wide range of ecosystems. (C) 2012 Elsevier B.V. All rights reserved.

Biogeochemistry of an Amazonian podzol-ferralsol soil system with white kaolin

The podzol-ferralsol soil systems, which cover great areas of Amazonia and other equatorial regions, are frequently associated with kaolin deposits and store and export large amounts of carbon. Although natural organic matter (NOM) plays a key role in their dynamics, little is known about their biogeochemistry. In order to assess the specific role of dissolved organic matter (DOM) on NOM storage in deep horizons and to determine possible relationships between kaolin formation and DOM properties, we studied the groundwater composition of a typical podzol-ferralsol soil catena from the Alto Rio Negro region, Brazil. Groundwater was sampled using tension-free lysimeters placed according to soil morphology. DOC, E-H, p(H), and dissolved Si, Al3+, Fe2+, and Fe3+ were analyzed for all samples and values are given in a database. Quantification of other dissolved ions, small carboxylic acids and SUVA(254) index and acid-base microtitration was achieved on selected samples. Part of the DOM produced by the hydromorphic podzols is directly exported to the blackwater streams; another part percolates at greater depth, and more than 90% of it adsorbs in the Bh-Bhs horizons, allowing carbon storage at depth. Humic substances are preferentially adsorbed with regard to small carboxylic compounds. With regard to kaolin genesis, kaolinite precipitation is favored by Al release from NOM mineralization within the Bh-Bhs and kaolin bleaching is ensured by iron reduction due to acidity and relatively low E-H. Fe2+ mobility can be related to small E-H variations and enhanced by the significant concentration of small carboxylic acids. The long-term result of these processes is the thickening of the kaolin, and it can be inferred that kaolin is likely to occur where active, giant podzols are close to a slope gradient sufficient enough to lower the deep water table.

Home range, movements and diurnal roosts of the endangered thin-spined porcupine, Chaetomys subspinosus (Rodentia: Erethizontidae), in the Brazilian Atlantic Forest

Chaetomys subspinosus is the sole species within the Chaetomyinae subfamily of Caviomorph rodents. This poorly studied porcupine is restricted to the Atlantic Forest in eastern Brazil, where deforestation and habitat fragmentation threaten its survival. Data on the ranging and roosting behavior of C. subspinosus is fairly scarce as it is difficult to observe these behaviors in nature and, consequently, it is very rarely detected during field surveys. We monitored the home ranges of three radio-tagged females over the course of 1 year (2005-2006) and collected data on several aspects of their natural history including movement patterns and the use of diurnal roosts and latrines. The animals were monitored at Parque Estadual Paulo Cesar Vinha, a nature reserve dominated by restinga forests, a subtype of Atlantic Forest occurring on sandy soil. The estimated home range varied little between individuals and was relatively small (mean = 2.14 ha/individual and 1.09 ha/individual using minimum convex polygon and kernel methods, respectively). The animals travelled an average of 147 m/night (range: 21-324 m/night) between two consecutive day roosts. The day roosts were mostly located on vine and liana tangles in the canopy which also aid in connecting the canopy to adjacent trees or the forest floor. Latrines were mostly located near the ground in places heavily protected by spiny bromeliads or by other tangled vegetation. Our data suggests that C. subspinosus has the smallest range among all Neotropical Erethizontids which is likely due to its small size and strictly folivorous diet. Our data also helps explain why C. subspinosus is so difficult to observe in nature: researchers should focus on arboreal masses of tangled vegetation where individuals will normally rest during the day. (C) 2011 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Bamboo overabundance alters forest structure and dynamics in the Atlantic Forest hotspot

With fast growth rates and clonal reproduction, bamboos can rapidly invade forest areas, drastically changing their original structure. In the Brazilian Atlantic Forest, where recent mapping efforts have shown that woody bamboos dominate large areas, the present study assessed the differences in soil and vegetation between plots dominated (>90% of bamboo coverage) and not dominated (<10% of coverage) by the native Guadua tagoara. Surface soil was physically and chemically analyzed, and trees at three size classes (seedling, sapling, and adult) were counted, identified and measured. New inventories were conducted to assess recruitment, mortality, and damage rates. Bamboo plots had more fertile soils (higher bases saturation and lower potential acidity) due to the preferential occurrence of G. tagoara on more clayey soils. Bamboo-dominated plots had lower density of adult trees (diameter >5 cm) and lower species density. In addition, overall tree diameter distribution was very different between environments, with bamboo plots having greater concentration of small-sized trees. Such differences are probably related to the general tendency of higher mortality, recruitment, and damage rates in bamboo plots. Greater physical (wind and bamboo-induced damages) and physiological stress (heat and light) in bamboo plots are probable causes of bamboo-dominated plots being more dynamic. Finally, we discuss the differences between Atlantic and Amazonian Guadua-dominated forests, causes, and possible consequences of bamboo overabundance to the Atlantic Forest conservation. (C) 2012 Elsevier Ltd. All rights reserved.

Gradients in N-cycling attributes along forestry and agricultural land-use systems are indicative of soil capacity for N supply

Indicators of soil quality associated with N-cycling were assessed under different land-use systems (native forest NAT, reforestation with Araucaria angustifolia or Pinus taeda and agricultural use AGR) to appraise the effects on the soil potential for N supply. The soil total N ranged from 2 to 4 g/kg (AGR and NAT, respectively), and the microbial biomass N ranged from 80 to 250 mg/kg, being higher in NAT and A. angustifolia, and lower in P. taeda and AGR sites. Activities of asparaginase (ca. 50200 mg NH4+-N/kg per h), glutaminase (ca. 200800 mg NH4+-N/kg per h) and urease (ca. 80200 mg NH4+-N/kg/h) were also more intense in the NAT and A. angustifolia-reforested soils, indicating greater capacity for N mineralization. The NAT and AGR soils showed the highest and the lowest ammonification rate, respectively (ca. 1 and 0.4 mg NH4+-N/kg per day), but the inverse for nitrification rate (ca. 12 and 26%), indicating a low capacity for N supply, in addition to higher risks of N losses in the AGR soil. A multivariate analysis indicated more similarity between NAT and A. angustifolia-reforested sites, whilst the AGR soil was different and associated with a higher nitrification rate. In general, reforestation with the native species A. angustifolia had less impact than reforestation with the exogenous species P. taeda, considering the soil capacity for N supply. However, AGR use caused more changes, generally decrease in indicators of N-cycling, showing a negative soil management effect on the sustainability of this agroecosystem.

CHEMICAL AND BIOCHEMICAL PROPERTIES OF ARAUCARIA ANGUSTIFOLIA (BERT.) KTZE. FOREST SOILS IN THE STATE OF SAO PAULO

Araucaria angustifolia, commonly named Araucaria, is a Brazilian native species that is intensively exploited due to its timber quality. Therefore, Araucaria is on the list of species threatened by extinction. Despite the importance of soil for forest production, little is known about the soil properties of the highly fragmented Araucaria forests. This study was designed to investigate the use of chemical and biological properties as indicators of conservation and anthropogenic disturbance of Araucaria forests in different sampling periods. The research was carried out in two State parks of Sao Paulo: Parque Estadual Turistico do Alto do Ribeira and Parque Estadual de Campos de Jordao. The biochemical properties carbon and nitrogen in microbial biomass (MB-C and MB-N), basal respiration (BR), the metabolic quotient (qCO(2)) and the following enzyme activities: beta-glucosidase, urease, and fluorescein diacetate hydrolysis (FDA) were evaluated. The sampling period (dry or rainy season) influenced the results of mainly MB-C, MB-N, BR, and qCO(2). The chemical and biochemical properties, except K content, were sensitive indicators of differences in the conservation and anthropogenic disturbance stages of Araucaria forests. Although these forests differ in biochemical and chemical properties, they are efficient in energy use and conservation, which is shown by their low qCO(2), suggesting an advanced stage of succession.