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We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.

It is important to understand the Amazonian Dark Earth (ADE) diversified microbial communities which colonize agricultural soils and interact with plants, allowing a more sustainable way of soil utilization. Genomic prospection of biotechnological interest, such as the phenazine biosynthesis genes, was carried out by the characterization of the bacterial community structure through the analysis of the 16S rRNA gene in ADE rhizospheric and bulk soil sampled in the forest, and in the agriculture managed soil, being subsequently cultivated with caupi bean. Additionally, the phzF gene coding for a key enzyme in the phenazine biosynthesis was detected and quantified. Gene polymophism (Terminal Restriction Fragment Length Polymorphism, T-RFLP) analysis revealed differences in the bacterial community structure between colonized rhizospheric and bulk soil, but there were no differences concerning the 16S rRNA gene copy number. Besides, the phzF gene copy number was higher in the rhizospheric than in the bulk soil, without any difference between forest and agricultural soils. This work confirms that the type of soil and the interaction between plants and microorganisms are key factors that shape the structure and diversity of bacterial communities and represent a biotechnological potential, with the possibility of finding natural compounds for use in biological control. Key words: Amazonian Dark Earth, rhizosphere, quantitative polymerase chain reaction (PCR), terminal restriction fragment length polymorphism (T-RFLP), microbial diversity.

Amazonian Dark Earth (ADE) is a highly fertile soil of anthropogenic origin characterized by higher amount of charred black carbon (BC). ADE is considered a fertility model, however knowledge about the fungal community structure and diversity inhabiting ADE and BC is scarce. Fungal community structure and diversity of ADE and BC from four sites under different land use (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon was evaluated by 18S rRNA gene pyrosequencing. Fungal communities in ADE and BC were dissimilar and showed differential abundances of fungal Operational Taxonomic Units (OTUs). Estimated fungal species richness (ACE and Chao-1) and diversity (Shannon and Simpson's reciprocal) indices were higher in ADE than BC in all agricultural areas. No differences were observed in the same estimators in ADE and BC samples under secondary forest. Pezizomycotina fungi, and OTUs assigned to Cordyceps confragosa, Acremonium vitellinum, Camarops microspora and Hirsutella rhossiliensis were more abundant in BC particles than in ADE. This study is a breakthrough in understanding the fungal communities in BC particles from ADE and can also be valuable in future studies considering biochar application in soil.

Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used a DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture and secondary forest) in the Amazon region. In general, the microbial community structure was influenced by changes in soil physicochemical properties. Aluminum and water-holding capacity significantly correlated to overall community structure and most of microbial phyla. Taxonomic changes were followed by potential functional changes in the soil microbial community, with pasture presenting the most distinct profile in comparison with other sites. Although taxonomic structure was very distinct among sites, we observed a recovery of the potential functions in secondary forest after pasture abandonment. Our findings elucidate a significant shift in belowground microbial taxonomic and potential functional diversity following natural forest re-establishment and have implications for ecological restoration programs in tropical and sub-tropical ecosystems.

Made available in DSpace on 2021-06-25T11:04:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 The mechanized sugarcane harvesting system has been replacing the old manual harvesting system with the burning of the sugarcane field. The purpose of the conversion of these systems is to obtain benefits related to the improvement of soil and environmental quality, minimizing the effects of greenhouse gas (GHG) emissions, especially carbon dioxide (CO2). In this context, this study aimed to investigate the effect of burned and unburned sugarcane harvesting systems on soil CO2 emission and soil chemical, physical, and microbiological attributes. Two adjacent areas were used in this study: an unburned sugarcane area, with an eight-year history without burning the sugarcane field and high amounts of crop residues (mean of 13 t ha−1), and a burned sugarcane area, with manual harvesting after burning the sugarcane field and without crop residues on the soil surface. The soil of both areas is classified as an Oxisol. Soil CO2 emission, soil temperature, and soil moisture were assessed from 20 randomly sampling points placed in each area. Soil samples were collected at the end of the soil CO2 emission, soil temperature, and soil moisture assessments from each point at a depth of 0–0.20 m to determine soil physical, chemical, and microbiological attributes. Soil CO2 emission was, on average, 37% higher in the burned sugarcane area (2.63 µmol m−2 s−1) compared to the unburned sugarcane area (1.92 µmol m−2 s−1). Soil moisture was higher in the unburned sugarcane area (25.30%) than in the burned sugarcane area (16.02%). An opposite effect was observed for soil temperature, which presented values 2.5 °C higher in the burned sugarcane area (21.5 °C) compared to the unburned sugarcane area (19.1 °C). Soil carbon decay constant k indicated that carbon was decomposed faster in the burned sugarcane area (0.00070 days−1) than in the unburned sugarcane area (0.00046 days−1). Thus, soil carbon half-life was longer in the unburned sugarcane area (1,572.82 days) compared to the burned sugarcane area (1,033.95 days), i.e., carbon permanence time in the unburned sugarcane area was 52% higher than in the burned sugarcane area. Soil temperature, soil moisture, air-filled pore space, P, the sum of bases (Ca2+ + K+ + Mg2+), soil bulk density, soil carbon stock, soil C/N ratio, and the abundance of functional gene nifH are the most representative soil attributes that allows characterizing the CO2 emission process in soils managed with sugarcane under unburned and burned harvesting systems. Therefore, the study of these attributes should be taken into account when assessing the variability of CO2 emissions in agricultural soils. In conservationist terms, the unburned sugarcane system presents a higher potential for stabilizing soil carbon and reducing the contribution of agriculture to greenhouse gas emissions, especially CO2, when compared to the burned sugarcane system. Brazilian Biorenewables National Laboratory (LNBR) Brazilian Center for Research in Energy and Materials (CNPEM), Rua Giuseppe Máximo Scolfaro, 10000 School of Agricultural and Veterinary Sciences São Paulo State University (FCAV–UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n University of Marília (UNIMAR), Avenida Hygino Muzzy Filho, 1001, 17525-902, Campus Universitário, Jardim Araxá Center of Nuclear Energy in Agriculture University of São Paulo (CENA–USP), Av. Centenário, 303, 13400-970, São Dimas School of Agricultural and Veterinary Sciences São Paulo State University (FCAV–UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n

Amazonian Dark Earth (ADE) in the Brazilian Amazon is the main evidence left by pre-Columbian indigenous populations indicating that infertile soils can be transformed into highly fertile ground. Changes in vegetation cover and seasonality are likely to influence microbial communities; however, little is known about these effects on ADE. Therefore, this study compared the effects of two land use systems in ADE and adjacent soil (ADJ) during the rainy and dry seasons using biochemical and molecular tools. Bacterial community function was determined by community level physiological profile (CLPP), bacterial community structure by terminal restriction length polymorphism (T-RFLP), and bacterial community composition by pyrosequencing of the V4 16S rRNA gene region. Our results show that the community structure is highly affected by vegetation, in both, ADE and ADJ soils. Regarding community function, Average Well Color Development (from Biolog substrates) were higher in ADE than ADJ during the rainy season and kept the same pattern of substrate utilization during the dry season and finally, community composition showed to be influenced even at the level of family, mostly by soil type rather than vegetation. Collectively, our study provides insights into processes affecting the bacterial community assemblages in both, ADE and adjacent soils. Key words: Amazonian soils, vegetation type, seasonality, soil bacteria.

Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes.

Biochar fragments are found in many tropical soils as a result of natural burning and anthropogenic activities. Such fragments are common constituents of soil organic matter, which can act like sorbents of soluble organic compounds and are involved in the retention of water in soil systems. In addition, biochar may play an important role as host for soil microorganisms. Microbial studies regarding biochar require molecular techniques such as next-generation sequencing. Recent studies demonstrate the importance of biochar as an ecological niche for survival of unique bacterial and archaeal species, along with functional populations like hydrocarbon degraders. Thus, besides the importance of its physical and chemical properties as a soil amendment, biochar can potentially host important microbes with biological implications on global biogeochemical cycles, as well as promoting sustainability and fertility to soils. This chapter explores these concepts but with Amazonian Dark Earths as a specific example of a biochar-impacted ecosystem.

Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in ADE soils were more similar to each other than their ADJ soils, except for only one site. Phosphorus and aluminum saturation were the main soil chemical factors contributing to ADE and ADJ fungal community dissimilarities. Differences in fungal richness were not observed between ADE and ADJ soil pairs regarding to the most sites. In general, the most dominant subphyla present in the soils were Pezizomycotina, Agaricomycotina, and Mortierellomycotina. The most abundant operational taxonomic units (OTUs) in ADE showed similarities with the entomopathogenic fungus Cordyceps confragosa and the saprobes Fomitopsis pinicola, Acremonium vitellinum, and Mortierellaceae sp., whereas OTUs similar to Aspergillus niger, Lithothelium septemseptatum, Heliocephala gracillis, and Pestalosphaeria sp. were more abundant in ADJ soils. Differences in fungal community composition were associated to soil chemical factors in ADE (P, Ca, Zn, Mg, organic matter, sum of bases, and base saturation) and ADJ (Al, potential acidity, Al saturation, B, and Fe) soils. These results contribute to a deeper view of the fungi communities in ADE and open new perspectives for entomopathogenic fungi studies. Electronic supplementary material The online version of this article (doi:10.1007/s00248-015-0703-7) contains supplementary material, which is available to authorized users.

As Terras Pretas de Índio (TPI), também conhecida por Amazonian Dark Earth, apresentam horizonte A antrópico, elevado pH, nutrientes importantes para o crescimento das plantas, elevado teor de carvão pirogênico e intensa atividade biológica quando comparadas aos seus solos de origem. A comunidade microbiana do solo é essencial para o funcionamento dos ecossistemas, sendo fundamentais em processos de decomposição da matéria orgânica, na disponibilização de nutrientes para as plantas e na ciclagem de nutrientes. Este estudo teve como objetivo acessar as estruturas e composição das comunidades de Bacteria e Archaea em fragmentos de carvão pirogênico (provenientes de TPI), TPI e solo adjacente (ADJ) utilizando as técnicas moleculares. Os solos foram coletados em quatro sítios arqueológicos (Balbina, Barro Branco, Costa do Açutuba e Hatahara), localizados na Amazônia Central. Em geral, as TPIs apresentaram elevados valores de pH, P e Ca corroborando com resultados anteriores em TPIs. As amostras de TPI dos sítios Balbina, Barro Branco e Hatahara apresentaram maior número de cópias do gene 16S rRNA de Bacteria quando comparadas com as amostras de solo ADJ. Os resultados obtidos pelas técnicas de fingerprinting (Terminal Restriction Fragment Length Polymorphism - T-RFLP e Denaturing Gradient Gel Electrophoresis - DGGE) utilizando o gene 16S rRNA de Bacteria e Archaea revelaram que as estruturas das comunidades bacterianas em fragmentos de carvão apresentaram diferenças significativas quando comparados com os solos ADJ. A partir da técnica de pirosequenciamento, os filos Proteobacteria, Actinobacteria e Crenarchaeota apresentaram predominância nos fragmentos de carvão. Observou-se também que em fragmentos de carvão, os microorganismos encontrados podem estar diretamente relacionados aos ciclos do N e C. Além disso, a presença desses micro-organismos em fragmentos de carvão pode favorecer a microbiota do solo e, consequentemente, sua qualidade. Neste sentido, o carvão pode também servir como elemento de recuperação em ambientes degradados, agindo como condicionador do solo sendo esta uma alternativa promissora no manejo de solos agrícolas. Amazonian Dark Earth (ADE), also known as Terra Preta de Índio, present tropical A horizon, high pH, important nutrients for plant growth, high pyrogenic charcoal levels and intense biological activity when compared to its soil of origin. Soil microbial community is essential for ecosystem function, which is involved in fundamental processes such as the decomposition of organic matter, availability of nutrients to plants and the nutrient cycling. The objective of this study was to assess the structure and composition of bacterial and archaeal communities in fragments of pyrogenic charcoal (from ADE), ADE and adjacent soil (ADJ) using molecular techniques. The soils were collected in four archaeological sites (Balbina, Barro Branco, Costa do Açutuba and Hatahara), located in the central Amazon. In general, ADE presented high values of pH, P and Ca agreeing with previous results in ADE. ADE samples in Balbina, Barro Branco and Hatahara sites presented higher bacterial 16S rRNA gene copy number in comparison with ADJ soil samples. The results obtained with the fingerprinting techniques (Terminal Restriction Length Polymorphism, T-RFLP and Denaturing Gradient Gel Electrophoresis, DGGE) using the bacterial and archaeal 16S rRNA genes revealed that bacterial community structure in charcoal fragments differed significantly when compared to the ADJ soils. Using the pyrosequencing technique, the phyla Proteobacteria, Actinobacteria and Crenarchaeota were predominant in charcoal fragments. It was also observed that microorganisms from charcoal fragments may be directly related to the N and C cycles. Furthermore, the presence of these microorganisms in charcoal fragments may favor the soil microbiota and, consequently, its quality. In this context, pyrogenic charcoal can serve as an element to recover degraded areas acting as soil conditioner and a promising alternative to the management of agricultural soils.

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils. O conhecimento acerca da ecologia de comunidades microbianas do solo em relevantes escalas espaciais é primordial na ampla região da Amazônia devido às mudanças de uso da terra. Neste estudo, a diversidade do Domínio Archaea (estrutura da comunidade) e Archaea oxidadora de amônia (riqueza e composição da comunidade) foi investigada usando-se técnicas moleculares em solos sob diferentes sistemas de uso da terra na Amazônia ocidental brasileira. Amostras de solo foram coletadas em dois períodos distintos de elevada intensidade pluviométrica (março de 2008 e janeiro de 2009) em Cambissolos sob floresta primária, floresta secundária (5 a 20 anos de regeneração), sistemas agrícolas de povos indígenas e pastagem. A eletroforese em gel com gradiente desnaturante de produtos amplificados pela reação em cadeia da polimerase (PCR-DGGE) usando o gene 16S rRNA como marcador filogenético indicou que as estruturas de comunidades de Archaea em solos sob cultivo agrícola e pastagem são diferentes daquelas encontradas em solos sob floresta primária. Estas, por sua vez, foram mais similares às estruturas de comunidades em solos sob floresta secundária. A análise de sequências de bandas excisadas de géis de DGGE revelou a presença de organismos dos filos Crenarchaeota e Euryarchaeota. Com base em análise de bibliotecas de clones do gene que codifica para a subunidade A da enzima amônia monoxigenase (amoA ) de Archaea (306 sequências), os índices de Shannon-Wiener e Simpson mostraram maior diversidade de Archaea oxidadora de amônia em solos sob floresta primária (H' = 2,1486; D = 0,1366), seguido por menor diversidade em solos sob pastagem (H' = 1,9629; D = 0,1715), cultivo agrícola (H' = 1,4613; D = 0,3309) e floresta secundária (H' = 0,8633; D = 0,5405). Todos os insertos clonados foram similares a clones do gene amoA de Crenarchaeota (identidade >95 %) previamente detectados em solos e sedimentos; e distribuíram-se em três agrupamentos filogenéticos principais. Os resultados indicaram que a estrutura de comunidades de Archaea e a diversidade de Archaea oxidadora de amônia na Amazônia ocidental são afetadas em solos sob sistemas agrícolas de povos indígenas e pastagem.

Studies on keratinolytic microorganisms have been mainly related to their biotechnological applications and association with animal pathologies. However, these organisms have an ecological relevance to recycling keratinous residues in nature. This work aimed to select and identify new culturable feather-degrading bacteria isolated from soils of Brazilian Amazon forest and Atlantic forest. Bacteria that were isolated from temperate soils and bacteria from Amazonian basin soil were tested for their capability to grow on feather meal agar (FMA). Proteolytic bacteria were tested for feather degradation and were further identified according to their morphological and biochemical characteristics. Also, molecular identification based on 16S rDNA gene sequencing was carried out. A total of 24 proteolytic and 20 feather-degrading isolates were selected; Most of the isolates were from the Bacillus genus (division Firmicutes), but one Aeromonas, two Serratia (γ-Proteobacteria), and one Chryseobacterium (Cytophaga–Flavobacterium group).

The Anthropogenic Amazon Dark Earth soil is considered one of the world's most fertile soils. These soils differs from conventional Amazon soils because its higher organic content concentration. Here we describe the metagenome sequencing of microbial communities of two sites of Anthropogenic Amazon Dark Earth soils from Amazon Rainforest, Brazil. The raw sequence data are stored under Short Read Accession number: PRJNA344917.

The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn”) the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes.

The Rodrigo de Freitas lagoon (RFL) is a tropical eutrophic coastal ecosystem located in the urban area of Rio de Janeiro, Brazil. This environment consists of freshwater but has communication with the ocean through a channel (Jardim de Alah’s Channel). The aim of this study was to evaluate the influence of lagoon water on the nearby ocean using molecular and traditional microbiological methods. We hypothesised that due to the eutrophic low-salinity environment, the bacterioplankton community from the RFL would have a native “brackish” composition influenced by both freshwater and marine phylotypes, and that bacterial phylotypes of this community would be detected in oceanic samples closer to the channel between the lagoon and the ocean. The cultivation and microscopy experiments clearly showed this influence. Bacterial cell counts revealed that the greater amounts of bacterial cells present in the lagoon increased the observed values seen at oceanic stations near the channel. The Denaturing gradient gel eletrophoresis community profiles also showed a clear influence of Rodrigo de Freitas lagoon waters on the adjacent beaches. The band patterns found for the stations near the channel showed that these communities were mixtures of the communities of the lagoon and sea, and as the distance from the channel increased, the samples became more similar to ocean bacterial communities. A 16S rRNA gene clone library was constructed using a sample acquired from the connection point between the lagoon and the ocean. Around 52% of the sequences in the library showed similarity to the genus Proteobacteria (1% Alpha, 21% Beta, 19% Gamma and 29% unclassified Proteobacteria), and the second most abundant genus was Bacteroidetes, with 15% of the total clones. The results showed that the structure of the bacterial community had both freshwater and marine characteristics.

A Bacillus sp. strain producing a bacteriocin-like substance was characterized by biochemical profiling and 16S rDNA sequencing. The phylogenetic analysis indicated that this strain has low sequence similarity with most Bacillus spp., suggesting a new species was isolated. The antimicrobial activity was detected starting at the exponential growth phase, and maximum activity was observed at stationary phase. The substance was inhibitory to a broad range of indicator strains, including pathogenic and food spoilage bacteria such as Listeria monocytogenes, B. cereus, Aeromonas hydrophila, Erwinia carotovora, Pasteurella haemolytica, Salmonella Gallinarum, among other. The antibacterial substance was stable over a wide pH range, but it was sensitive to pronase E and lipase. The antibacterial substance was bactericidal and bacteriolytic to L. monocytogenes and B. cereus at 160 AU ml(-1). The identification of a broad range bacteriocin-like inhibitory substance active against L. monocytogenes addresses an important aspect of food protection against pathogens and spoilage microorganisms.

Terra Preta Antropogênica (TPA) é um dos tipos de solos mais \"férteis\" do mundo. A TPA recebe esta denominação por ser encontrada em sítios arqueológicos onde viveram grupos pré-históricos. São pequenas faixas de solos que apresentam altas concentrações de nutrientes, matéria orgânica e encontram-se distribuídas aleatoriamente pela região Amazônica. A verdadeira origem destes solos ainda não está bem esclarecida. Devido à falta de informações sobre sua diversidade bacteriana, este trabalho estudou a diversidade bacteriana em amostras de solos TPA coletadas em duas regiões: Lagoa Balbina - sítio Terra preta (Amazônia Central- Amazonas) e Floresta Nacional de Caxiuanã - sítio arqueológico Mina I (Amazônia Oriental - Pará), através de técnicas moleculares independentes de cultivo. O DNA genômico total das amostras de solo foi extraído e usado como molde em uma reação de PCR utilizando oligonucleotídeos específicos do gene 16S rRNA para o Domínio Bactéria. O produto de PCR amplificado foi clonado no vetor pGEM-T e 980 clones foram selecionados e comparados com o banco de dados de 16S rRNA do RDP II e GenBank (NCBI-EUA). Os resultados apresentaram predominância com microrganismos não-conhecidos representando 41,6 % das seqüências de solo TPA- Balbina, 68,3 % das seqüências de ADJ-Balbina, 84,8% das seqüências de solo TPAMina e 47,7 % das seqüências de ADJ-Mina. O filo mais predominante nas amostras TPABalbina foi Firmicutes, representando 37,1% do total de seqüências analisadas. Os filos em destaque foram Proteobacteria (9,6%), seguidos de Verrucomicrobia (5,6%), Acidobacteria (2,5%), Gemmatimonadetes (2,5%), Actinobacteria (0,5%) e Nitrospira (0,5%). Por outro lado, em ADJ-Balbina destacaram-se os filos Proteobacteria 15,1%, Acidobacteria (12,5%), Firmicutes (2,3%), Nitrospira (1,1%) e Verrucomicrobia (0,8%). Em TPA-Mina, os filos apresentados foram Proteobacteria (6,5%), Acidobacteria (4,7%), Firmicutes (1,4%), Nitrospira (1,1%), Planctomycetes (1,1%) e Verrucomicrobia (0,4%). Contudo, na biblioteca ADJ-Mina verificou a presença dos filos Acidobacteria (27,2%), Proteobacteria (14,2%), Firmicutes (3,8%), Verrucomicrobia (3,8%), Nitrospira (1,3%), Planctomycetes (1,3%), Actinobacteria (0,4%) e Gemmatimonadetes (0,4%). O pH do solo pode ser um dos atributos do solo que pode ter influência direta na diversidade bacteriana dos solos estudados, assim como pode ter efeito uma floresta natural sobre as populações microbianas em seu solo, fato observado na adjacência do solo Terra Preta em Caxiuanã - PA. A estimativa da riqueza de UTOs pelo Bootstrap corroborou diretamente os valores de diversidade obtidos pelos índices de Simpson e Shannon. De um modo geral, uma maior probabilidade de ocorrência de UTOs únicas empregadas pelo estimador Jackknife se correlacionou com uma maior percentagem de baixas frequências de filotipos nas quatro bibliotecas. Os métodos não-paramétricos ACE e Chao1 para a estimativa da riqueza de UTOs também corroboraram com os valores obtidos com o estimador Jackknife. Anthropogenic Dark Earth (ADE) is one of the most fertile soils in the world. ADE soils have received this nomination due to the pre-historical origin of these archaeological sites, established by pre-colombian populations. ADEs are small areas of soil which present high nutrient and organic matter contents and are randomly distributed throughout the Amazonian region. The true origin of these soils is not known yet. Due to the lack of information concerning the bacterial diversity, this work studied the bacterial diversity in ADE soils collected from two regions: Lagoa Balbina - site Terra Preta (Central Amazonia- Amazonas state) and National Forest of Caxiuanã - archaeological site Mina I (Oriental Amazonia - Pará state), using culture-independent molecular techniques. The total genomic DNAs extracted from the soil samples were used as templates in the PCR reactions using the universal primers for the 16S rRNA bacterial gene. The PCR-products were cloned into the pGEM-T vector and 980 clones were selected and searched using the GenBank (NCBI-USA) and the RDP II program. Data analyses indicated predominance of unknown microorganisms, representing 41.6 % among the sequences from ADE-Balbina, 68.3 % from Adjacent-Balbina, 84.8% from ADE-Mina and 47.7 % from Adjacent-Mina. The predominant phylum in ADEBalbina was Firmicutes, representing 37.1% of the total sequences from that site, followed by Proteobacteria (9.6%), Verrucomicrobia (5.6%) Acidobacteria (2,5%), Gemmatimonadetes (2,5%), Actinobacteria (0,5%) and Nitrospira (0.5%). On the other hand, in the adjacent soil ADJ-Balbina, the predominant phylla were Proteobacteria (15.1%), Acidobacteria (12.5%), Firmicutes (2.3%), Nitrospira (1.1%) and Verrucomicrobia (0.8%). In the Oriental Amazon, the prevalent phylla from the ADE-Mina soil were Proteobacteria (6.5%), Acidobacteria (4.7%), Firmicutes (1.4%), Nitrospira (1.1%), Planctomycetes (1.1%) and Verrucomicrobia (0.4%). In the ADJ-Mina verificou a presença dos filos Acidobacteria 27.2%, Proteobacteria 14.2%, Firmicutes 3.8%, Verrucomicrobia 3.8%, Nitrospira 1.3%, Planctomycetes 1.3%, Actinobacteria 0.4% e Gemmatimonadetes 0.4%. The soil pH may be of the soil attributes which may have directly influenced the bacterial diversity in those soils, as well as the above-ground vegetation from the natural forest in Caxiuanã-Pará. The estimates of the Operational Taxonomic Units (OTUs) richness using Bootstrap directly corroborated the diversity values obtained from the Simpson and Shannon indexes. Unique UTOs using Jackknife estimator were correlated with a higher percentage of the low frequencies of phylla in all the four clone libraries. The nonparametric ACE and Chao1 methods to estimate the OTUs richness also corroborated the Jackknife values.

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2014-02-26T17:15:29Z No. of bitstreams: 1 WOS000180834300035.pdf: 1288581 bytes, checksum: c80b0ab1625eeba1cd15e9da6e465b26 (MD5) Made available in DSpace on 2014-02-26T17:15:29Z (GMT). No. of bitstreams: 1 WOS000180834300035.pdf: 1288581 bytes, checksum: c80b0ab1625eeba1cd15e9da6e465b26 (MD5) Previous issue date: 2003-02-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:25:38Z No. of bitstreams: 1 WOS000180834300035.pdf: 1288581 bytes, checksum: c80b0ab1625eeba1cd15e9da6e465b26 (MD5) Made available in DSpace on 2014-05-20T15:25:38Z (GMT). No. of bitstreams: 1 WOS000180834300035.pdf: 1288581 bytes, checksum: c80b0ab1625eeba1cd15e9da6e465b26 (MD5) Previous issue date: 2003-02-01 Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X.fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X.fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X.fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X.fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies. Univ São Paulo, Inst Biociencias, Dept Bot, BR-05508900 São Paulo, Brazil Univ São Paulo, Inst Quim, BR-05508900 São Paulo, Brazil Univ São Paulo, Inst Ciências Biomed, BR-05508900 São Paulo, Brazil Univ São Paulo, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, Brazil Univ São Paulo, Ctr Energia Nucl Agr, BR-13400970 Piracicaba, Brazil Inst Agron Campinas, Ctr Citricultura Sylio Moreira, BR-13490970 Cordeiropolis, Brazil Univ Estadual Paulista, Fac Ciências Agr & Vet, BR-14884900 Jaboticabal, Brazil Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Inst Biol, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Inst Comp, BR-13083970 Campinas, SP, Brazil Univ São Paulo, Fac Ciências Farmaceut, BR-14040901 Ribeirao Preto, Brazil Univ São Paulo, Fac Filosofia Ciências & Letras, BR-14040901 Ribeirao Preto, Brazil Inst Ludwig Pesquisa Canc, BR-01509010 São Paulo, Brazil Univ Mogi das Cruzes, Nucleo Integrado Biotecnol, BR-08780911 Mogi das Cruzes, Brazil Inst Agron Campinas, BR-13001970 Campinas, SP, Brazil Inst Biol, BR-04014002 São Paulo, Brazil Univ Estadual Paulista, Fac Med Vet & Zootecnia, BR-18603970 Botucatu, SP, Brazil Univ Estadual Paulista, Fac Ciências Agron, BR-18603970 Botucatu, SP, Brazil Univ Estadual Paulista, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil Univ Fed Sao Carlos, BR-13600970 São Paulo, Brazil Univ Fed Mato Grosso do Sul, Dept Comp & Estatist, BR-79070900 Campo Grande, MS, Brazil USDA ARS, Parlier, CA 93648 USA Univ Estadual Paulista, Fac Ciências Agr & Vet, BR-14884900 Jaboticabal, Brazil Univ Estadual Paulista, Fac Med Vet & Zootecnia, BR-18603970 Botucatu, SP, Brazil Univ Estadual Paulista, Fac Ciências Agron, BR-18603970 Botucatu, SP, Brazil Univ Estadual Paulista, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil

The anthropogenic addition of organic amendments, including plant and animal material, pottery, and charcoal, into extant soil formed what are known as Terra Preta do Indio (TPI) or Amazonian Dark Earth (ADE). Whether or not these soil amendments were part of an agricultural management strategy by pre-Colombian cultures, today ADE soils are prized by farmers for their sustained fertility, in regions where chronic soil infertility has lead, in part, to on-going destruction of primary forest to create marginal cropland. However, although prehistoric practices have left a legacy of fertile soil for a few isolated farmers, expanding the benefits of ADE to other soils will require more than serendipity. The unusual chemistry resulting from organic amendments to ADE results in distinct microbial communities that are involved in nutrient cycling and ecological processes. The ongoing biogeochemical activity in ADE is the true legacy of prehistoric practices, and the microbial processes at work in these unique soils are crucial to these

The genus Xanthomonas is a diverse and economically important group of bacterial phytopathogens, belonging to the gamma-subdivision of the Proteobacteria. Xanthomonas axonopodis pv. citri (Xac) causes citrus canker, which affects most commercial citrus cultivars, resulting in significant losses worldwide. Symptoms include canker lesions, leading to abscission of fruit and leaves and general tree decline. Xanthomonas campestris pv. campestris (Xcc) causes black rot, which affects crucifers such as Brassica and Arabidopsis. Symptoms include marginal leaf chlorosis and darkening of vascular tissue, accompanied by extensive wilting and necrosis. Xanthomonas campestris pv. campestris is grown commercially to produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilizing agent in many industries. Here we report and compare the complete genome sequences of Xac and Xcc. Their distinct disease phenotypes and host ranges belie a high degree of similarity at the genomic level. More than 80% of genes are shared, and gene order is conserved along most of their respective chromosomes. We identified several groups of strain-specific genes, and on the basis of these groups we propose mechanisms that may explain the differing host specificities and pathogenic processes.

O Brasil é considerado o maior produtor mundial de cana-de-açúcar, voltada para a produção de açúcar, etanol e derivados. O aproveitamento de resíduos da usina, como torta de filtro e vinhaça no condicionamento do solo pode contribuir com a manutenção da sua fertilidade. Por outro lado, a cada operação agrícola necessária para o cultivo da cana-de-açúcar está associada uma emissão de GEE que deve ser contabilizada. O objetivo desta pesquisa foi estimar a emissão dos principais GEE (CO2, N2O e CH4) pela torta de filtro, e avaliar as alterações de alguns atributos das comunidades microbianas durante o processo de decomposição. Após avaliação de uma enquete sobre o modo de utilização da torta de filtro por diversas usinas, um estudo foi desenvolvido na Usina Costa Pinto localizada em Piracicaba (SP). A torta aplicada no sulco de plantio da cana foi monitorada quanto à emissão dos gases, sendo que as concentrações dos mesmos nas amostras foram determinadas por cromatografia gasosa. Os atributos microbiológicos examinados foram a biomassa, a atividade enzimática (fosfatase ácida, alcalina e ?-glicosidase) e a estrutura da comunidade através do polimorfismo de fragmento de restrição terminal (T-RFLP). Foi observada emissão significativa dos principais GEE predominantemente da torta quando aplicada nos sulcos de plantio, com destaque para o N2O, com uma proporção doze vezes maior em massa do que o CH4, em 56 dias de experimento. Quanto aos aspectos microbiológicos, o maior valor encontrado de carbono e nitrogênio da biomassa microbiana para a dose usualmente aplicada (25 Mg ha-1), foi com dois meses de experimento, com respectivamente 484,89 ?g C g solo seco-1 e 62,95 ?g N g solo seco-1, e correlacionado pelo coeficiente de Pearson com a atividade enzimática no material. Pela técnica de T-RFLP foi possível avaliar a estrutura dos Domínios de Archaea, Bacteria e Fungi na comunidade microbiana da torta de filtro. Não houve modificação dessa estrutura ao longo do tempo analisado. Os resultados obtidos reforçam a importância dos atributos microbiológicos aliados a fatores químicos e físicos e a influência dos mesmos sobre as emissões de GEE. Brazil is the greatest worldwide producer of sugarcane with production of sugar, ethanol and derived. Usually applied to soil as fertirrigation, filter cake and vinasse on soil conditioning have contributed to the maintenance of fertility. On the contrary, each agricultural operation is associated to GHG emissions that must be accounted for the balance of products. This work aims evaluate GHG emissions (CO2, N2O and CH4) from the filter cake, as well as evaluate the main differences in the microbiological community available within the decomposition process. After evaluation of a survey about to use the filter cake by industries, the study has been developed at Usina Costa Pinto located in Piracicaba (SP). The filter cake applied to the row of sugarcane planting have been monitored by taking regular samples of the emissions. The concentration of the three gases in the samples has been determined by gas chromatography. The microbiological aspects has been evaluated by biomass, enzymatic activity (acid phosphatase, alkaline phosphatase, and beta-glycosidase) and the community structure through terminal restriction fragment length polymorphism (T-RFLP). Significant GHG emission has been observed; mainly from the filter cake applied to the row of sugarcane planting especially N2O, with ratio twelve times greater than CH4 in 56 days of experiment. For microbiological aspects, the maximum of carbon and nitrogen from the microbial biomass for the treatment usually applied (25 Mg ha-1), within two months of experimentation, with respectively 484,89 ?g C g dry soil-1 e 62,95 ?g N g dry soil-1, and correlated by the coefficient of Pearson with the enzymatic activity existent in the material. The T-RFLP analysis has allowed evaluate the community structures of Archaea, Bacteria e Fungi in the microbiological community of the filter cake. Modification in the community structures was not observed over this time examined. The results obtained reinforce the importance of microbiological aspects combined with chemical and physical factors and their influence on GHG emissions.