Rooting theories of plant community ecology in microbial interactions

Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant–soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and propose that these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance and invasion ecology.

Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri

In Xanthomonas axonopodis pv. citri (Xac or X citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala(38) and Ser(151), are shown to be part of the ligand-binding pocket. (c) 2007 Elsevier B.V All rights reserved.

Animal–plant–microbe interactions : direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands

Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH₄. Microbial processes catalyzing nutrient recycling and CH₄ production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick’s swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH₄ production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH₄ oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH₄ production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH₄ cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH₄ emission from wetland systems.

Spatial variability of forage yield and soil physical attributes of a Brachiaria decumbens pasture in the Brazilian Cerrado

The objective of this study was to analyze variability, linear and spatial correlations of forage dry mass yield (FDM) and dry matter percentage (DM%) of Brachiaria decumbens with the bulk density (BD), gravimetric (GM) and volumetric (VM) moisture, mechanical resistance to penetration (RP) and organic matter content (OM), at depths 1 (0-0.10 m) and 2 (0.10-0.20 m), in a Red Latosol (Oxisol), in order to select an indicator of soil physical quality and identify possible causes of pasture degradation. The geostatistical grid was installed to collect soil and plant data, with 121 sampling points, over an area of 2.56 ha. The linear correlation between FDM × DM% and FDM × BD2 was low, but highly significant. Spatial correlations varied inversely and positively, respectively. Except for DM% and BD, at both depths, the other attributes showed average to high variability, indicating a heterogeneous environment. Thus, geostatistics emerges as an important tool in understanding the interactions in pasture ecosystems, in order to minimize possible causes of degradation and indicate better alternatives for soil-plant-animal management. The decrease in FDM and increased BD1 are indicators of physical degradation (compaction) of Red Latosol (Oxisol), particularly in the places with the highest concentration of animals and excessive trampling, in Cerrado conditions, in the municipality of Selvíria, Mato Grosso do Sul State, Brazil.

Antagonistic interactions between garden yeasts and microfungal garden pathogens of leaf-cutting ants

We investigate the diversity of yeasts isolated in gardens of the leafcutter ant Atta texana. Repeated sampling of gardens from four nests over a 1-year time period showed that gardens contain a diverse assemblage of yeasts. The yeast community in gardens consisted mostly of yeasts associated with plants or soil, but community composition changed between sampling periods. In order to understand the potential disease-suppressing roles of the garden yeasts, we screened isolates for antagonistic effects against known microfungal garden contaminants. In vitro assays revealed that yeasts inhibited the mycelial growth of two strains of Escovopsis (a specialized attine garden parasite), Syncephalastrum racemosum (a fungus often growing in gardens of leafcutter lab nests), and the insect pathogen Beauveria bassiana. These garden yeasts add to the growing list of disease-suppressing microbes in attine nests that may contribute synergistically, together with actinomycetes and Burkholderia bacteria, to protect the gardens and the ants against diseases. Additionally, we suggest that garden immunity against problem fungi may therefore derive not only from the presence of disease-suppressing Pseudonocardia actinomycetes, but from an enrichment of multiple disease-suppressing microorganisms in the garden matrix.

Laboratory study on the bioremediation of diesel oil contaminated soil from a petrol station

O objetivo do presente estudo foi investigar possíveis métodos para aumentar a taxa de biodegradação aeróbia de hidrocarbonetos (tratamentos ex-situ). Neste trabalho, processos de biorremediação foram aplicados a um solo arenoso com alto nível de contaminação ocasionada por um vazamento de um tanque de armazenamento de óleo diesel subterrâneo em um posto de combustíveis. Experimentos em escala laboratorial (respirômetros de Bartha) foram utilizados para avaliar a biodegradação do óleo diesel. Estímulo da biodegradação foi realizado utilizando-se as técnicas de bioestímulo (adição de soluções de nitrogênio e fósforo ou surfactante Tween 80) e de bioaumento (consórcio bacteriano isolado de um sistema de landfarming). Para investigar as interações entre os fatores otimizadores, e encontrar a melhor combinação entre esses agentes, o estudo foi baseado em um delineamento experimental fatorial completo. A eficiência de biodegradação foi simultaneamente medida com dois métodos: respirométrico (produção de CO2 microbiano) e cromatografia gasosa. Testes de toxicidade aguda com Daphnia similis foram aplicados para examinar a eficiência dos processos em termos de geração de produtos menos tóxicos. Resultados mostraram que todas as estratégias de biorremediação aceleraram a biorremediação natural do solo contaminado e os melhores resultados foram obtidos quando os tratamentos tinham adição de nutrientes. Dados respirométricos indicaram uma máxima mineralização de hidrocarbonetos de 19,8%, obtida com a combinação dos três agentes, com uma remoção de hidrocarbonetos totais de petróleo (TPH) de 45,5% em 55 dias de tratamento. No final dos experimentos, duas espécies predominantes de bactéria foram isoladas e identificadas como Staphylococcus hominis e Kocuria palustris.

Non-local interactions and the dynamics of dispersal in immature insects

A simple mathematical model is developed to explain the appearance of oscillations in the dispersal of larvae from the food source in experimental populations of certain species of blowflies. The life history of the immature stage in these flies, and in a number of other insects, is a system with two populations, one of larvae dispersing on the soil and the other of larvae that burrow in the soil to pupate. The observed oscillations in the horizontal distribution of buried pupae at the end of the dispersal process are hypothesized to be a consequence of larval crowding at a given point in the pupation substrate. It is assumed that dispersing larvae are capable of perceiving variations in density of larvae buried at a given point in the substrate of pupation, and that pupal density may influence pupation of dispersing larvae. The assumed interaction between dispersing larvae and the larvae that are burrowing to pupate is modeled using the concept of non-local effects. Numerical solutions of integro-partial differential equations developed to model density-dependent immature dispersal demonstrate that variation in the parameter that governs the non-local interaction between dispersing and buried larvae induces oscillations in the final horizontal distribution of pupae. (C) 1997 Academic Press Limited.

Modelling short-term temporal changes of bare soil CO2 emissions in a tropical agrosystem by using meteorological data

Determining the variability of carbon dioxide emission from soils is an important task as soils are among the largest sources of carbon in biosphere. In this work the temporal variability of bare soil CO2 emissions was measured over a 3-week period. Temporal changes in soil CO2 emission were modelled in terms of the changes that occurred in solar radiation (SR), air temperature (T-air), air humidity (AR), evaporation (EVAP) and atmospheric pressure (ATM) registered during the time period that the experiment was conducted. The multiple regression analysis (backward elimination procedure) includes almost all the meteorological variables and their interactions into the final model (R-2 = 0.98), but solar radiation showed to be the one of the most relevant variables. The present study indicates that meteorological data could be taken into account as the main forces driving the temporal variability of carbon dioxide emission from bare soils, where microbial activity is the sole source of carbon dioxide emitted. (C) 2003 Elsevier B.V. All rights reserved.

Molecular identification of fungal communities in a soil cultivated with vegetables and soil suppressiveness to Rhizoctonia solani

Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed in Escherichia coli by cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application. © 2013 Silvana Pompéia Val-Moraes et al.

Biodegradation and Phytotoxicity of Biodiesel, Diesel, and Petroleum in Soil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the spatial and temporal dependence of CO2 emission on soil properties in sugarcane (Saccharum spp.) production

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

From Potential to Implementation: an innovation framework to realize the benefits of soil carbon

This chapter addresses the mismatch between existing knowledge, techniques and management methods for improved soil carbon management and deficits in its implementation. The paper gives a short overview of the evolution of the concept of soil carbon, which illustrates the interactions between scientific, industrial, technical, societal and economic change. It then goes on to show that sufficient techniques are available for the large-scale implementation of soil organic carbon (SOC) sequestration. A subsequent analysis of the bottlenecks that prevent implementation identifies where issues need to be addressed in order to enable robust, integrated and sustainable SOC management strategies.

Performance of cucumber hybrids cultivated in coconut fiber and soil

The objective of this work was to evaluate the performance of three Japanese group cucumber hybrids, which were cultivated in two cultivation systems. The experiment was designed in a split-plot randomized block design with two cultivation systems (coconut fiber and soil) for commercial Japanese cucumber hybrids ('Tsuyataro', 'Yoshinari' and 'Nankyoku'). After harvesting the cucumbers, we evaluated the number of marketable fruits per plant, the average fruit length, the mean fruit diameter, the bottom fruit diameter, the marketable production of fruits per plant and the marketable yield per hectare. There were significant interactions between the cultivation system and the hybrid, as indicated by the number of marketable fruits. The Nankyoku hybrid had the highest average (14.54 fruits pl(-1)), although it did not differ from the Yoshinari hybrid when grown in coconut fiber. In soil culture, the Yoshinari hybrid had the highest average number of fruits per plant (10.12 fruits pl(-1)) and did not differ from the Tsuyataro hybrid. Cultivation in coconut fiber provided better results for production traits and plant productivity. 'Yoshinari' and 'Nankyoku' were the most productive hybrids. Based on the cucumber cultivation results from a protected environment, the cultivation of hybrid Japanese cucumbers and Yoshinari and Nankyoku hybrids in coconut fiber is recommended.

Metabolomic evaluation of interactions in rhizosphere between Senna spectabilis and associated microorganisms

Pós-graduação em Química - IQ

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.