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Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

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Due to their antimicrobial properties, copper nanoparticles (CuNPs) have been proposed to be used in agriculture for pest control. Pesticides removal is mainly done by microorganisms, whose genes usually are found in conjugative catabolic plasmids (CCP). The aim of this work was to evaluate if CuNPs at subinhibitory concentrations modify the conjugation frequency (CF) of two CCP (pJP4 and pADP1). CuNPs were characterized by scanning electron microscopy with an X-ray detector, dynamic light scattering and X-ray diffraction. Mating assays were done in LB broth supplemented with CuNPs (10, 20, 50 and 100 µg mL-1) or equivalent concentrations of CuSO4. Interestingly, we observed that in LB, Cu+2 release from CuNPs is fast as evaluated by atomic absorption spectrophotometry. Donor and recipient strains were able to grow in all copper concentrations assayed, but CF of mating pairs was reduced to 10% in the presence of copper at 20 or 50 µg Cu mL-1 compared to control. Thus, our results indicated that both copper forms, CuNPs or CuSO4, negatively affected the transfer of catabolic plasmids by conjugation. Since dissemination of degradative genes by conjugation contribute to degradation of pesticides by microorganisms, this work improves our understanding of the risks of using copper in agriculture soils, which could affect the biodegradative potential of microbial communities.

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Abstract Edaphic macrofauna must be better studied if we want to take advantage of their full potential for the restoration of tropical ecosystems. We investigated changes in edaphic macrofauna density and diversity along a secondary succession chronosequence in the Atlantic Forest. Our results show some clear patterns of change in soil macrofauna along the chronosequence. Density did not increase along secondary succession, but was correlated with canopy cover. Diversity was characterized by high dominance of social insects and evenness among other groups. We conclude soil macrofauna has a high capacity to recolonize young forests and that its recovery is considerably fast compared to other ecosystem transformations.

Resumo A macrofauna edáfica deve ser mais bem estudada se quisermos aproveitar todo o seu potencial para a restauração de ecossistemas tropicais. Nós investigamos as mudanças de densidade e diversidade da macrofauna edáfica em uma cronossequência durante a sucessão secundária na Mata Atlântica. Nossos resultados mostram padrões claros de mudança. A densidade não aumentou ao longo da sucessão secundária, mas foi correlacionada com a cobertura de dossel. A diversidade foi caracterizada pela alta dominância de insetos sociais e equidade entre os demais grupos. Nós concluímos que a macrofauna edáfica tem alta capacidade de recolonizar florestas jovens e que sua recuperação é relativamente rápida se comparada a outras transformações ecossistêmicas.

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Edaphic macrofauna must be better studied if we want to take advantage of their full potential for the restoration of tropical ecosystems. We investigated changes in edaphic macrofauna density and diversity along a secondary succession chronosequence in the Atlantic Forest. Our results show some clear patterns of change in soil macrofauna along the chronosequence. Density did not increase along secondary succession, but was correlated with canopy cover. Diversity was characterized by high dominance of social insects and evenness among other groups. We conclude soil macrofauna has a high capacity to recolonize young forests and that its recovery is considerably fast compared to other ecosystem transformations.

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Atrazine is a commonly used herbicide for maize production in Chile, but it has recently been shown to be ineffective in soils that receive applications of cow slurries generated from the dairy industry. This effect may be caused either by the sorption of the pesticide to organic matter or more rapid degradation in slurry-amended soils. The objectives of this study were to evaluate the effects of cow slurry on atrazine dissipation, the formation of atrazine metabolites and the modification of bacterial community in Andisol. The cow slurry was applied at doses of 100,000-300,000 Lha(-1). After 4 weeks, atrazine was applied to the slurry-amended soils at concentrations of 1-3 mg kg(-1). The amounts of atrazine and its metabolites were determined by high performance liquid chromatography (HPLC). The soil microbial community was monitored by measurement of CO(2) evolution and changes in bacterial community using PCR-DGGE of 16S rRNA genes. The results show that cow slurry applications had no effect on atrazine dissipation, which had a half-life of 15-19 days. The atrazine metabolites were detected after 20 days and were significantly higher in soils amended with the slurry at both 20 and 40 days after application of the herbicide. Respiration rates were elevated after 10 days in all soils with atrazine addition. Both the atrazine and slurry amendments altered the bacterial community structures, indicated by the appearance of specific bands in the DGGE gels after 10 days. Cloning and sequencing of the 16S rRNA genes from the DGGE gels showed that the bands represented various genera of beta-proteobacteria that appeared in response to atrazine. According to our results, further field studies are required to explain the lower effectiveness of atrazine in weed control. These studies may include the effect of dissolved organic carbon on the atrazine mobility.

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Communities of Actynomicetes fungy in three vegetation types of the Colombian Amazon: abundance, morphotypes and the 16s rDNA gene. Among soil microorganisms, Actinomycetes play an important role in the sustainability of natural and agricultural systems: decomposition of organic matter; degradation of recalcitrant compounds like lignin; nitrogen fixation; degradation of agricultural chemicals and biological control in plants and animals. We evaluated their diversity in soils under three different vegetation covers (pasture, tropical primary forest and stubble) at two depths in the Southern Colombian Amazon border. We collected five replicates per vegetation type (in each, three samples at 0-20cm and three at 20-30cm; for a total of 30 samples). Abundance and phenotypic diversity were determined by plate counting. Genomic DNA was extracted from the isolates: the 16s rDNA gene was amplified with specific primers, and its genetic diversity was estimated by means of an amplified restriction analysis (ARDRA). Actynomicetes abundance varied with vegetation and depth, possibly reflecting presence of earthworms, macro-fauna and physico-chemical characteristics associated to fertility, as well as organic matter, total bases, and optimal capacity to cationic interchange. Primary forests had the highest diversity. Sixteen morpho-types (six genera) were identified; Streptomyces was the most abundant everywhere. The heterogeneity of ARDRA patterns prevented species identification because of the intra-species variability in sequences of 16s rDNA operons. This community is a biological indicator of landscape alteration and could include new bio-active compounds of pharmaceutical interest. Rev. Biol. Trop. 57 (4): 1119-1139. Epub 2009 December 01.

Los actinomicetos son importantes en la sostenibilidad de sistemas naturales. Su diversidad fue evaluada en suelos de bosque, pastizal y rastrojo, y dos profundidades en el Sur del Trapecio Amazónico Colombiano. Se analizaron suelos de cinco repeticiones por cobertura para un total de 15 unidades. Se tomaron seis muestras en cada unidad y dos profundidades, para un total de 30. Los actinomicetos cultivables se determinaron por recuento en placa, se extrajo ADN, se amplificó el gen ADNr 16s y su diversidad genética se estimó por ARDRA. Hubo diferencias de abundancia entre coberturas y profundidades, relacionadas con la vegetación, presencia de lombrices, macrofauna, altos niveles de materia orgánica, y bases totales. Se obtuvieron valores de diversidad fenotípica similares para las tres coberturas, pero los bosques son más diversos. Se identificaron 16 morfotipos, agrupados en séis géneros, siendo Streptomyces el más abundante. La heterogeneidad de los patrones ARDRA no permitió la asignación de especies, reflejándose variaciones en las secuencias de diferentes operones ADNr 16s en un mismo organismo. Las perturbaciones en la cobertura influyen sobre los actinomicetos, generando cambios en su abundancia y diversidad. Su importancia ecológica permite proponerlos como indicadores biológicos de alteración del paisaje.

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Among soil microorganisms, Actinomycetes play an important role in the sustainability of natural and agricultural systems: decomposition of organic matter; degradation of recalcitrant compounds like lignin; nitrogen fixation; degradation of agricultural chemicals and biological control in plants and animals. We evaluated their diversity in soils under three different vegetation covers (pasture, tropical primary forest and stubble) at two depths in the Southern Colombian Amazon border. We collected five replicates per vegetation type (in each, three samples at 0-20cm and three at 20-30cm; for a total of 30 samples). Abundance and phenotypic diversity were determined by plate counting. Genomic DNA was extracted from the isolates: the 16s rDNA gene was amplified with specific primers, and its genetic diversity was estimated by means of an amplified restriction analysis (ARDRA). Actynomicetes abundance varied with vegetation and depth, possibly reflecting presence of earthworms, macro-fauna and physico-chemical characteristics associated to fertility, as well as organic matter, total bases, and optimal capacity to cationic interchange. Primary forests had the highest diversity. Sixteen morpho-types (six genera) were identified; Streptomyces was the most abundant everywhere. The heterogeneity ofARDRA patterns prevented species identification because of the intra-species variability in sequences of 16s rDNA operons. This community is a biological indicator of landscape alteration and could include new bio-active compounds of pharmaceutical interest.

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Nitrogen mineralization in PAHs contaminated soil in presence of Eisenia fetida amended with biosolid or vermicompost was investigated. Sterilized and unsterilized soil was contaminated with PAHs, added with E. fetida and biosolid or vermicompost and incubated aerobically for 70 days, while dynamics of inorganic N were monitored. Addition of E. fetida to sterilized soil increased concentration of NH(4)(+) 100> mg N kg(-1), while concentrations in unsterilized remained <60 mg N kg(-1) except for soil amended with biosolid plus PAHs where it increased to >80 mg kg(-1). Addition of PAHs had no significant effect on concentration of NH(4)(+) compared to the unamended soil, except in the soil added with biosolid. Addition of E. fetida to sterilized soil increased concentration of NO(2)(-) 15> mg N kg(-1) while concentrations in unsterilized soil remained <7.5 mg N kg(-1) except for soil amended with biosolid where it increased to >20 mg kg(-1). Addition of PAHs had no significant effect on concentration of NO(2)(-) compared to the unamended soil. Addition of biosolid and vermicompost increased concentration of NO(3)(-), while addition of E. fetida decreased concentration of NO(3)(-) in biosolid amended soil. It was found that NH(4)(+) and NO(2)(-) oxidizers were present in the gut of E. fetida, but their activity was not sufficient enough to inhibit a temporarily increase in concentrations of NH(4)(+) and NO(2)(-). Contamination with PAHs induced immobilization of N in biosolid or vermicompost amended soil, as did feeding of E. fetida on biosolid or vermicompost.

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Polycyclic aromatic hydrocarbons (PAHs) such as phenanthrene, anthracene and Benzo[a]pyrene (BaP) are toxic for the environment. Removing these components from soil is difficult as they are resistant to degradation and more so in soils with high pH and large salt concentrations as in soil of the former lake Texcoco, but stimulating soil micro-organisms growth by adding nutrients might accelerate soil restoration. Soil of Texcoco and an agricultural Acolman soil, which served as a control, were spiked with phenanthrene, anthracene and BaP, added with or without biosolid or inorganic fertilizer (N, P), and dynamics of PAHs, N and P were monitored in a 112-day incubation. Concentrations of phenanthrene did not change significantly in sterilized Acolman soil, but decreased 2-times in unsterilized soil and >25-times in soil amended with biosolid and NP. The concentration of phenanthrene in unsterilized soil of Texcoco was 1.3-times lower compared to the sterilized soil, 1.7-times in soil amended with NP and 2.9-times in soil amended with biosolid. In unsterilized Acolman soil, degradation of BaP was faster in soil amended with biosolid than in unamended soil and soil amended with NP. In unsterilized soil of Texcoco, degradation of BaP was similar in soil amended with biosolid and NP but faster than in the unamended soil. It was found that application of biosolid and NP increased degradation of phenanthrene, anthracene and BaP, but to a different degree in alkaline-saline soil of Texcoco compared to an agricultural Acolman soil.

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New and exciting molecular methods, many using the 16S small sub-unit ribosomal nucleic acid molecule, are opening the microbial "black box" in soil. These studies have added much to our knowlodge of microbial diversity in soils, and are beginning to advance our understanding of the relationship between this diversity and its function in soil processes. Over the next few years, the knowlodge gained from molecular studies will, we hope, lead to improvements in sustainable land management and sustainable exploitation of soil genetic resources. As we enter the third millenium, it is appropriate to review the application of 16S rDNA methods to soil microbiology. This review examines 16S ribosomal DNA (rDNA) methods and their application to soil. It mentions their limits and suggests how they may be applied in the future.

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Se estudió la interacción entre hongos vam nativos de suelos agrícolas de la provincia de Buenos Aires (Argentina), Glomus epigaeus y Bradyrhizobium japonicum en plantas de soja. La inoculación tripartita: vam nativas, G. epigaeus y B. japonicum produjeron plantas más vigorosas, con mayor número de nódulos y de mayor tamaño en relación a plantas no inoculadas. El contenido de nitrogeno en la porción aérea de las plantas aumentó un 102 porciento y el del fósforo un 233 porciento en plantas con inoculación tripartita, en relación al testigo no inoculado

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