Ederson da Conceição Jesus

Changes in land use alter the structure of bacterial communities in Western Amazon soils

Here we show how agricultural practices by indigenous peoples as well as forest recovery relate to the structure and composition of Amazon soil bacterial communities. Soil samples were collected in different land use systems and bacterial community composition and diversity were explored by T-RFLP, cloning and sequencing, and data were analyzed with multivariate techniques. The main differences in bacterial community structure were related to changes in the soil attributes that, in turn, were correlated to land use. Community structure changed significantly along gradients of base saturation, [Al3+] and pH. The relationship with soil attributes accounted for about 31% of the variation of the studied communities. Clear differences were observed in community composition as shown by the differential distribution of Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Actinobacteria. Similarity between primary and secondary forest communities indicates the recovery of bacterial community structure during succession. Pasture and crop soil communities were among the most diverse, showing that these land use types did not deplete bacterial diversity under the conditions found in our sites.

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities

The Amazon rainforest is the Earth’s largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.

A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network

Science has a critical role to play in guiding more sustainable development trajectories. Here, we present the Sustainable Amazon Network (Rede Amazônia Sustentável, RAS): a multidisciplinary research initiative involving more than 30 partner organizations working to assess both social and ecological dimensions of land-use sustainability in eastern Brazilian Amazonia. The research approach adopted by RAS offers three advantages for addressing land-use sustainability problems: (i) the collection of synchronized and co-located ecological and socioeconomic data across broad gradients of past and present human use; (ii) a nested sampling design to aid comparison of ecological and socioeconomic conditions associated with different land uses across local, landscape and regional scales; and (iii) a strong engagement with a wide variety of actors and non-research institutions. Here, we elaborate on these key features, and identify the ways in which RAS can help in highlighting those problems in most urgent need of attention, and in guiding improvements in land-use sustainability in Amazonia and elsewhere in the tropics. We also discuss some of the practical lessons, limitations and realities faced during the development of the RAS initiative so far.

Comparing the Bacterial Diversity of Acute and Chronic Dental Root Canal Infections

This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic) or chronic (asymptomatic) apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs) (at 3% divergence) belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%), Fusobacteria (17%) and Bacteroidetes (13%), while in chronic infections the dominant were Firmicutes (59%), Bacteroidetes (14%) and Actinobacteria (10%). Members of Fusobacteria were much more prevalent in acute (89%) than in chronic cases (50%). The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165) of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic). This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections.

Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering

High-throughput sequencing of 16S rRNA genes has increased our understanding of microbial community structure, but now even higher-throughput methods to the Illumina scale allow the creation of much larger datasets with more samples and orders-of-magnitude more sequences that swamp current analytic methods. We developed a method capable of handling these larger datasets on the basis of assignment of sequences into an existing taxonomy using a supervised learning approach (taxonomy-supervised analysis). We compared this method with a commonly used clustering approach based on sequence similarity (taxonomy-unsupervised analysis). We sampled 211 different bacterial communities from various habitats and obtained ∼1.3 million 16S rRNA sequences spanning the V4 hypervariable region by pyrosequencing. Both methodologies gave similar ecological conclusions in that β-diversity measures calculated by using these two types of matrices were significantly correlated to each other, as were the ordination configurations and hierarchical clustering dendrograms. In addition, our taxonomy-supervised analyses were also highly correlated with phylogenetic methods, such as UniFrac. The taxonomy-supervised analysis has the advantages that it is not limited by the exhaustive computation required for the alignment and clustering necessary for the taxonomy-unsupervised analysis, is more tolerant of sequencing errors, and allows comparisons when sequences are from different regions of the 16S rRNA gene. With the tremendous expansion in 16S rRNA data acquisition underway, the taxonomy-supervised approach offers the potential to provide more rapid and extensive community comparisons across habitats and samples.

Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences

Microbes are key components of the soil environment and are important contributors to the sustainability of agricultural systems, which is especially significant for biofuel crops growing on marginal lands. We studied bacterial communities in the rhizosphere of five biofuel crops cultivated in four locations in Michigan to determine which factors were correlated to changes in the structure of those communities. Three of these sites were marginal lands in that two were not suitable for conventional agriculture and one was regulated as a brownfield due to prior industrial pollution. Bacterial community composition and structure were assessed by 454 sequencing of the 16S rRNA gene. A total of 387,111 sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as plant species, soil attributes, and location. The most abundant bacterial phyla found in the rhizosphere of all crops were Acidobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia. Bacterial communities grouped by location rather than by crop and their structures were correlated to soil attributes, principally pH, organic matter, and nutrients. The effect of plant species was low but significant, and interactions between locations, plant species, and soil attributes account for most of the explained variation in the structure of bacterial communities, showing a complex relationship between bacterial populations and their environment. Bacterial diversity was higher in the agricultural sites compared to adjacent forest sites, indicating that the cultivation of those biofuel crops increased the rRNA diversity.

Differentiation in the fertility of Inceptisols as related to land use in the upper Solimões river region, western Amazon

The Upper Solimões river region, western Amazon, is the homeland of indigenous populations and contains small-scale agricultural systems that are important for biodiversity conservation. Although traditional slash-and-burn agriculture is being practiced over many years, deforestation there is relatively small compared to other Amazon regions. Pastures are restricted to the vicinity of cities and do not spread to the small communities along the river. Inceptisols are the main soil order (>90%) in the area and have unique attributes including high Al content and high cation exchange capacity (CEC) due to the enrichment of the clay fraction with 2:1 secondary aluminosilicates. Despite its importance, few studies have focussed on this soil order when considering land use effects on the fertility of Amazon soils. Thus, the objective of this study was to evaluate changes in soil fertility of representative land use systems (LUSs) in the Upper Solimões region, namely: primary rainforest, old secondary forest, young secondary forest, agroforestry, pasture and agriculture. LUSs were significantly differentiated by the chemical attributes of their topsoil (0-20 cm). Secondary forests presented soil chemical attributes more similar to primary rainforest areas, while pastures exhibited the highest dissimilarity from all the other LUSs. As a whole, soil chemical changes among Inceptisols dominated LUSs showed patterns that were distinct from those reported from other Amazon soils like Oxisols and Ultisols. This is probably related to the presence of high-activity clays enriched in exchangeable aluminum that heavily influenced the soil chemical reactions over the expected importance of organic matter found in most studies conducted over Oxisol and Ultisol.

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side‐by‐side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.

Dependência de micorrizas para a nodulação de leguminosas arbóreas tropicais

The leguminous species Piptadenia gonoacantha and Piptadenia paniculata do not nodulate and grow well on sterilized substrates. For this reason selection of efficient rhizobial strains for these species becomes hard to perform. Plants growing in the field are well nodulated and colonized with mycorrhizal fungi. Mycorrhizal colonization may be an explanation for the good plant responses in the field. The effect of mycorrhizal inoculation on nodulation and growth of the woody legume species P. gonoacantha and P. paniculata was studied. The experiments were carried out under greenhouse conditions, at Embrapa Agrobiologia, Rio de Janeiro. The species were inoculated with specific rhizobia and with the mycorrhizal fungi Gigaspora margarita and Glomus clarum. Both tree species were highly responsive to mycorrhizal inoculation. Only the plants inoculated with both rhizobium and mycorrhizal fungi were nodulated. Plants inoculated with both rhizobia and mycorrhizal fungi presented higher dry matter than those inoculated only with rhizobia. P. gonoacantha plants presented higher shoot phosphorus content when inoculated with mycorrhizal fungi. These results show that mycorrhizal inoculation is needed for nodulation and growth of the tree species studied. We suggest the use of mycorrhizal fungi to select rhizobial strains for legumes which have difficulty to grow in Leonard jars.

Much beyond Mantel: Bringing Procrustes Association Metric to the Plant and Soil Ecologist’s Toolbox

The correlation of multivariate data is a common task in investigations of soil biology and in ecology in general. Procrustes analysis and the Mantel test are two approaches that often meet this objective and are considered analogous in many situations especially when used as a statistical test to assess the statistical significance between multivariate data tables. Here we call the attention of ecologists to the advantages of a less familiar application of the Procrustean framework, namely the Procrustean association metric (a vector of Procrustean residuals). These residuals represent differences in fit between multivariate data tables regarding homologous observations (e.g., sampling sites) that can be used to estimate local levels of association (e.g., some groups of sites are more similar in their association between biotic and environmental features than other groups of sites). Given that in the Mantel framework, multivariate information is translated into a pairwise distance matrix, we lose the ability to contrast homologous data points across dimensions and data matrices after their fit. In this paper, we attempt to familiarize ecologists with the benefits of using these Procrustean residual differences to further gain insights about the processes underlying the association among multivariate data tables using real and hypothetical examples.