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The expansion of the agriculture has become the main agent of disturbance in the Amazon region, and such alteration has consequences on soil microbial communities, which represent the majority of biodiversity in terrestrial ecosystems. In this study we assessed the effects of land-use changes on physicochemical soil properties and, consequently, on the bacterial communities in soils from Southeastern Amazon, Brazil. Soil samples were collected in four distinct land-use systems, i.e. native forest, deforested area, agricultural and pasture fields. The soil bacterial community abundance, structure and composition were addressed using qPCR, one molecular marker (T-RFLP) and high-throughput sequencing of the bacterial 16S rRNA gene, respectively. Obtained data were analyzed using multivariate techniques. We found that the type of land-use had a primary effect on the soil bacterial communities, whereas parameters such as pH, C, N, NO3− and K content significantly correlated to overall community structures. We observed that the abundance and taxonomic diversity of the bacterial 16S rRNA changed to a higher extent according to the land-use system, but they also showed significant temporal turnover within sites. From the total 27 bacterial phyla identified, 12 presented clearly differential distribution across the four land-use systems. Comparison among all sites revealed Acidobacteria and Chlamydiae to be higher abundant in forest soil, Actinobacteria in deforested site, Nitrospira and Deinococcus-Thermus in agriculture and Firmicutes in pasture. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as Al saturation index, Al, base saturation index, Mg and Ca presented correlation with the most number of bacterial groups detected. Thus, we suggest that several soil parameters besides pH should be taken into account when assessing the impacts of land-use change on the microbial communities.

Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.

Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N

We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.

Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.

Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.

Soil microorganisms play an important role in the N cycle; however, these communities are sensitive to soil disturbances. Understanding the influence of anthropogenic activities on soil microbial communities would increase our ability to establish conservation strategies in the Amazon region, where deforestation has become a great concern. We hypothesized that forest-to-agriculture conversion in a short- and long-term is responsible for alterations in soil chemical properties, with consequences on the composition, diversity, and potential function of microbial communities. Here, we used 16S rRNA amplicon sequencing and quantitative PCR to assess the bacterial and archaeal composition, diversity, abundance, and the potential functions related to the N-cycle in a natural forest and agricultural fields with 2-, 8-, and 20-years after conversion in the Amazon region. We observed that soil chemical properties were altered by the forest-to-agriculture conversion, which consequently affected the bacterial and archaeal communities. In general, Ca, Al, NH4+, and N-total were significantly correlated to the overall microbial community structure. Forest-to-agriculture conversion also altered the microbial composition and potential functions related to the N-cycle, increasing the nitrification and denitrification processes in agricultural soils, while natural forest demonstrated to be a potential N2O sink. Together, our data demonstrated the impacts of forest-to-agriculture conversion in the Amazon region and add important information for future research that seeks the development of more sustainable agriculture.

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.

There are only some very small undisturbed forest fragments still remaining in the state Sao Paulo, Brazil, and loss of biodiversity and soil functions has been generalized. The few studies undertaken on this subject did not include any microbiological survey and interactions between microbiological and physical–chemical attributes to assist in understanding the development of this system. Therefore, the objective of this study was to identify microbiological indicators of soil quality that vary with seasonality and physical and chemical characteristics or along a time gradient of four areas—undisturbed forest (NT) and 20 (R20), 10 (R10), and 5 year-old (R05) recovering reforested areas—in two seasons (austral summer and winter). All analyzed soils had a high bulk density, due to mechanization during the course of sugar cane plantation. Lower soil bulk density values were found at NT (1.33 g cm −3 ) and R20 (1.37 g cm −3 Macroporosity at NT (0.21 m 3 m −3 ) was about twice as high than at R20 and R10, and four times higher than at R05. Also, total carbon (TC) and total N (TN) were twice as high at NT in both seasons. NO 3 –N contents varied according to season and recovery age, being greatest at the NT site and about three times higher in summer. Microbial biomass of carbon (MBC) and urease varied consistently with recovery age, independently of eventual differences in soil physical attributes. Dehydrogenase, in the winter, was most influenced by soil texture. Attributes as humidity and microporosity had a negative influence on dehydrogenase activity and on MBN. Soil bulk density was negatively correlated with the microbial biomass and urease activity. On the other hand, macroporosity had a positive effect on CO 2 –C evolution, microbial biomass of nitrogen (MBN) and acid phosphatase activity. There was a higher correlation between microbiological attributes, especially between MBC, MBN, and urease or dehydrogenase activity. T-RFLP showed greater similarity of the Bacteria community between NT and R20, only in the summer. We expect that these findings can help to understand and interpret oncoming studies and will be applicable to other systems focusing on the comparison of sites with differences in recovery age or soil chemical and physical attributes.

Made available in DSpace on 2018-12-11T17:05:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-12-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest. Departamento de Tecnologia Faculdade de Ciências Agrárias e Veterinária FCAV Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N Faculdade de Ciências Biológicas e Ambientais FCBA Universidade Federal da Grande Dourados UFGD, Rodovia Dourados, Itahum, Km 12 - Unidade II, Caixa Postal: 364 Laboratório de Biologia Celular e Molecular Centro de Energia Nuclear na Agricultura CENA Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96 Departamento de Tecnologia Faculdade de Ciências Agrárias e Veterinária FCAV Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N FAPESP: FAPESP 12/13321-7

BACKGROUND: Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

The heavy traffic of agricultural equipment in citric orchards as a result of frequent application of pesticides and fungicides have led to soil compaction and a biological imbalance in these agricultural ecosystems, decreasing crop yields and increasing production costs. The purpose of this work was to assess the effects of spontaneous vegetation (weed) management in interrows following the replacement of agrochemicals with alternative inputs known to have a low impact on the environment. This experiment was conducted in a commercial orchard of ‘Murcott’ tangor ( Citrus reticulata , Blanco × Citrus sinensis , Osbeck). Highly soluble sources of NPK were substituted with a mixture of 65% rice bran + 35% castor bean meal (3.0% N), thermophosphate (17.5% P 2 O 5 ) and potassium sulfate (48% K 2 O). Synthetic pesticides were replaced with alternative pest controls, such as Bordeaux mixture and lime sulfur. Mechanical mowing was used instead of herbicides, and the mowed weeds were spread under the citrus plants canopy for mulch. This treatment, referred to as alternative management (AM), was performed for three years and compared with a control area, referred to as conventional management (CM), in which conventional cultivation practices and pesticide applications were maintained. The soil compaction, the fruit yield and select biological parameters were used for our assessment. When compared to the CM treatment, AM provided a higher vegetation cover and species diversity (especially for grasses), reduced soil resistance to penetration, better root growth in the topsoil layer, increased root colonization by arbuscular mycorrhizal fungi (AMF), increased viable spores in the soil and a higher leaf boron (B) concentration. Furthermore, the infestation of the AM plots with the mealybug, Orthezia praelonga , was significantly lower, and the fruit yield was higher in the third year. These results indicate that agricultural management practices focused on a reduced impact on the agroecosystem, mainly with regard to biological processes, are promising techniques for sustainable agriculture.

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.

The Amazon rainforest is considered the world\'s largest reservoir of plant and animal biodiversity, but in recent years has been subjected to high rates of deforestation for the conversion of native areas into agricultural fields and pasture. The understanding of the effects of land-use change on soil microbial communities is essential, taking into account the importance that these organisms play in the ecosystem. In this context, this thesis evaluated the effect of these changes on microorganism communities in soils under different land-use systems. In the first study, the microbial communities were analyzed using the nextgeneration sequencing Illumina Hiseq2000, considering samples from native forest, deforested area, agriculture and pasture. From the analysis of approximately 487 million sequences was possible to show that microbial communities respond differently in each landuse system, with changes in both taxonomic and functional diversity. Also, we suggested that ecosystem function in forest soils is maintained by the abundance of microorganisms, while in disturbed areas such functioning is maintained by high diversity and functional redundancy. In the second study, we assessed the extent to which a particular plant species, i.e. soybean, is able to select the microbial community that inhabits the rhizosphere. From the metagenomic sequencing by the 454 GS FLX Titanium platform we investigated the taxonomic and functional diversities of soil and rhizosphere communities associated to soybean, and also tested the validity of neutral and niche theories to explain rhizosphere community assembly process. The results suggest that soybean selects a specific microbial community inhabiting the rhizosphere based on functional traits, which may be related to benefits to the plant, such as growth promotion and nutrition. This process of selection follows largely the niche -based theory indicating the selection power of the plant and other environmental variables in shaping the microbial community both at the taxonomic and functional level. This thesis highlights the importance of microbial ecology studies in the context of the Amazon to a better understanding of the effects of deforestation on microorganisms, and provides information that can be suitable for future development of sustainable approaches for the ecosystem use A floresta Amazônica é considerada o maior reservatório de biodiversidade vegetal e animal do mundo, porém, nos últimos anos tem sido submetida à altas taxas de desmatamento para a conversão de áreas de mata nativa em campos de agricultura e pastagem. A compreensão sobre os efeitos dessa mudança de uso da terra sobre as comunidades microbianas do solo é fundamental, levando-se em consideração a importância que esses organismos desempenham no ecossistema. Neste contexto, este trabalho de tese avaliou o efeito dessas mudanças sobre as comunidades de micro-organismos em solos sob diferentes sistemas de uso. No primeiro estudo, as comunidades microbianas foram analisadas por meio do sequenciamento de nova geração Illumina Hiseq2000, sendo consideradas amostras de áreas de floresta nativa, área desmatada, agricultura e pastagem. A partir da análise de aproximadamente 487 milhões de sequências foi possível mostrar que as comunidades microbianas respondem diferentemente em cada sistema de uso do solo, com alterações tanto na diversidade taxonômica quanto funcional. Também, sugere-se que o funcionamento do ecossistema em solos de floresta é mantido pela abundância dos micro-organismos presentes, enquanto nas áreas alteradas esse funcionamento é mantido pela alta diversidade e redundância funcional. No segundo estudo foi avaliado até que ponto uma espécie de planta, i.e. soja, é capaz de selecionar a comunidade habitante de sua rizosfera. A partir do sequenciamento metagenômico pela plataforma 454 GS FLX Titanium da Roche foi investigado a diversidade taxonômica e funcional das comunidades de solo e rizosfera associadas à soja, e testou-se a validade das teorias neutras e de nicho para explicar o processo de formação das comunidades microbianas. Os resultados sugerem que a soja seleciona uma comunidade específica que habita sua rizosfera com base em atributos funcionais, os quais podem estar relacionados com benefícios à planta, como promoção do crescimento e nutrição. Esse processo de seleção segue a teoria de nicho, indicando o poder de seleção da planta e de outras variáveis ambientais em moldar as comunidades microbianas tanto de forma taxonômica quanto funcional. Esta tese destaca a importância de estudos em ecologia microbiana no contexto da Amazônia para uma melhor compreensão dos efeitos do desmatamento sobre os microrganismos e disponibiliza informações que podem ser futuramente utilizados para o desenvolvimento de metodologias mais sustentáveis para o uso do ecossistema

Since the dawn of classical microbiology, scientists have applied efforts to unravel the ecological patterns of occurrence, distribution and function of microorganisms in several ecosystems, including soil. In the last years, the famous Baas-Becking affirmation “Everything is everywhere, but, the environment selects”, have been largely used as central question, in microbial biogeographic studies and also in theoretical niche-based theories [1].

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (18% of sequences shared) than sites (25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations.

Tropical wetlands are the major natural source of methane released into the atmosphere, producing about 60% of all natural emissions. The great wetland areas of the Amazon basin are the largest source of methane in this region, contributing an estimated 5% of the total emissions from the world’s flooded areas. However, despite the important role that methanogenic archaea play in these environments, there have been few studies on the composition of their archaeal communities. In this survey, four 16S rRNA archaeal clone libraries from different depths were constructed to examine the archaeal community in an Amazon wetland soil. A total of 599 clones were used to perform diversity and phylogenetic analyses. A broad, diverse archaeal community was found at the site, with the diversity decreasing as the depth increased (Shannon index range: 2.40–1.94). Phylogenetic analysis revealed sequences belonging to two archaeal phyla, with 65% classified as Crenarchaeota and 35% classified as Euryarchaeota. Within the Euryarchaeota group, most sequences were clustered into the Methanococci and Methanomicrobia classes, two groups of methanogens. Based on the abundance of methanogenic organisms, culture–dependent isolation was used to isolate these organisms. To enhance the growth of methanogenic archaea, a modified atmosphere (H2:CO2 = 80:20) was established combined with an anoxic environment for 18 months. Among the isolates, the genera Methanosarcina and Methanobacterium were detected throughout the anaerobic in vitro cultivation, indicating a possible role for these organisms in methane production. In conclusion, these exploratory molecular and culture–dependent approaches enhance our understanding of the archaeal community and methanogenic archaea living in wetland soils of the eastern Amazon and their role in methane production.

Os manguezais tropicais são considerados um dos ecossistemas mais produtivos do mundo, sendo caracterizados pela alta taxa de ciclagem de matéria orgânica e nutrientes que ocorre entre os oceanos e os ambientes terrestres. Embora os manguezais sejam considerados áreas de proteção ambiental, a destruição desses ambientes é progressiva, devido a atividades industriais e portuárias nos estuários. Nos manguezais, a ciclagem de nutrientes está diretamente relacionada às atividades e a diversidade das comunidades microbianas presentes no solo. Este trabalho está inserido em um projeto mais amplo dentro do programa BIOTA/FAPESP, no que tange aos estudos da biodiversidade no Estado de São Paulo e utilização dessa biodiversidade de modo sustentável. O objetivo deste trabalho foi avaliar as estruturas e diversidade das comunidades de Bacteria, Archaea e Fungi presentes no solo de manguezal preservado da Ilha do Cardoso-SP. As amostras foram analisadas pelas técnicas de T-RFLP, ARISA, clonagem e seqüenciamento a fim de obter uma caracterização das estruturas das comunidades microbianas de uma área de manguezal preservado em comparação com os ambientes adjacentes de restinga e floresta e também a um manguezal antropizado. Os resultados permitiram concluir que o manguezal possui características exclusivas, com a presença de organismos distintos, revelando um possível potencial biotecnológico a ser explorado. Adicionalmente, os dados revelaram que a ação antrópica afetou as estruturas dessas comunidades de modo a ser notada uma sensível diminuição de diversidade no manguezal antropizado, evidenciando, dessa maneira, a importância da preservação desse ecossistema The tropical mangroves are considered one of the most productive ecosystems of the world, being characterized by the high tax of organic matter and recycling of nutrients, that happens between the oceans and the terrestrial habitats. Although the mangroves are considered areas of environmental protection, the destruction of those ecosystems is progressive, due to industrial and port activities in the estuaries. In mangroves, the recycling of nutrients is directly related to the activities and to the diversity of microbial communities present in the soil. This work is part of a wider project inside of the program BIOTA/FAPESP, with respect to the studies of the biodiversity in the State of São Paulo and use of that biodiversity in a maintainable way. The objective of this work was to evaluate the structures and diversity of communities of Bacteria, Archaea and Fungi present in the soil of preserved mangrove of Ilha do Cardoso-SP. The samples were analyzed by T-RFLP and ARISA techniques, cloning and sequencing in order to obtain a characterization of the microbial communities structure of preserved mangrove area in comparison with the adjacent environments of restinga (tropical moist forest) and forest and also to a degraded mangrove. The results allowed concluding that the mangroves present exclusive characteristics, with the presence of distinct organisms, revealing a possible biotechnological potential to be explored. Additionally, the data revealed that the human action affected the structures of those communities in a way to be noticed a sensitive diversity decrease in the degraded mangrove, evidencing, this way, the importance of the ecosystem preservation

The photochemical degradation of agrochemicals in aqueous solution by means of advanced oxidation processes (AOPs) was studied. The photo-Fenton process was evaluated in terms of the time evolution of dissolved organic carbon (COD) and chemical oxygen demand (DOC), their total removals, and increase in biodegradability of treated wastewater. Under the experimental conditions studied, the process showed to be superior to other AOPs, at any Fe(II) and H2O2 concentrations. The results pointed towards the use of solar irradiation and low cost commercial application.Neste trabalho, estuda-se a degradação fotoquímica de defensivos agrícolas presentes em efluentes aquosos, por meio de processos oxidativos avançados (POAs). Tais processos são baseados na ação do radical hidroxila (HO•), oxidante poderoso e não seletivo. Em particular, o processo foto-Fenton é avaliado quanto à redução da demanda química de oxigênio (DQO) e do teor de carbono orgânico dissolvido (COD), e ao aumento de biodegradabilidade dos efluentes. Os resultados abrem perspectivas para emprego de irradiação solar e aplicação em escala comercial a baixo custo.

Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.

Nhecolândia (MS), one important sub-region of the Pantanal, consists of 12,150 lakes among which approximately 600 lakes can be described as saline alkaline (soda lakes). Soda lakes present high concentrations of carbonates and sodium bicarbonates, resulting in high pH (above 9) and salinities (up to 35 mS cm-1). Even under hostile conditions, this ecosystem hosts a rich biodiversity of microorganisms. In this study, an approach that included molecular and chemical analyses was used to evaluate the composition (taxonomic and functional) and lifestyle of bacterial communities in the surface water of this environment. Through ordination analysis using limnological and metagenomic data, it was possible to group the soda lakes into three distinct profiles: eutrophic turbid (ET), oligotrophic turbid (OT) and clear vegetated oligotrophic (CVO). Seasonality was a crucial factor in the dynamics of the bacterial community. During the dry season, the water level reduced drastically due to intense evaporation periods, leading to an increase in salinity, pH and nutrient concentration, which in turn enhanced the diversity and relative abundance of microorganisms. This scenario led to the predominance of cyanobacterial blooms in ET lakes, mainly associated with Artrospira platensis or Anabaenopsis elenkinii. This predominance could be justified by the investment in mechanisms of nutrient acquisition by these organisms. In the OT and CVO lakes, there was a predominance of Actinobacteria, Alphaproteobacteria and Betaproteobacteria and these organisms possibly adopted strategies associated with nutrient uptake. It is interesting to note that nutrient acquisition genes were predominant in ET lakes, with high relative abundance of genes associated with biological fixation of CO2, N2, alkaline phosphatase and sulfate reduction. In OT and CVO lakes, we observed a higher abundance of low frequent processes such as nitrification and methanogenesis while genes associated with nitrate and nitrite reduction, and denitrification were more abundant. Moreover, the OT and CVO lakes presented prevalence of genes related to phosphate transport, phosphorus regulation as well as oxidation of sulfide and thiosulfate. Altogether, this study illustrates the taxonomic and functional diversity in tropical soda lakes, as well as how microorganisms behave under distinct environmental conditions. Moreover, the dataset obtained in this study may provide guidelines for management practices and conservation of the Pantanal\'s biodiversity A Nhecolândia (MS), uma importante sub-região do Pantanal, é composta por 12.150 mil lagoas dentre as quais aproximadamente 600 lagoas podem ser descritas como salino alcalinas (soda lakes). As lagoas salino alcalinas apresentam altas concentrações de carbonatos e bicarbonatos de sódio, resultando em altos valores de pH (acima de 9) e salinidade (até 35 mS cm-1). Mesmo apresentando condições consideradas extremas, este ecossistema possui uma rica biodiversidade de microrganismos. Neste trabalho, foram adotadas estratégias que combinaram análises moleculares e químicas com o objetivo de avaliar a composição (taxonômica e funcional) e o estilo de vida das comunidades bacterianas nas águas superficiais deste ambiente. Por meio de análises de ordenação utilizando dados limnológicos e metagenômicos, foi possível agrupar as lagoas salino alcalinas avaliadas em três perfis distintos: túrbidas eutróficas (ET), túrbidas oligotróficas (OT) e cristalinas oligotróficas vegetadas (CVO). Um fator preponderante na dinâmica da comunidade bacteriana foi a sazonalidade. Durante a estação seca, o nível da água reduziu consideravelmente devido a intensos períodos de evaporação, levando a um aumento nos níveis de salinidade, pH e concentração de nutrientes, o que por sua vez aumentou a diversidade e a abundância relativa dos microrganismos. Esse cenário propiciou a ocorrência de florações de cianobactérias nas lagoas ET, principalmente associadas aos táxons Arthrospira platensis ou Anabaenopsis elenkinii. Essa predominância pode ser justificada pelo investimento por mecanismos de aquisição de nutrientes por esses organismos. Nas lagoas OT e CVO houve uma predominância de Actinobacteria, Alphaproteobacteria e Betaproteobacteria e esses organismos possivelmente adotaram estratégias associadas a captação de nutrientes. É interessante observar que os genes de aquisição de nutrientes foram predominantes nas lagoas ET, com elevada abundância relativa de genes associados a fixação biológica de CO2, N2, fosfatase alcalina e redução de sulfato. Em lagoas OT e CVO, observamos uma baixa ocorrência de genes associados a nitrificação e metanogênese enquanto genes associados a redução de nitratos e nitritos, e a desnitrificação foram mais abundantes. Em condições oligotróficas genes relacionados com o transporte de fosfato, a regulação de fósforo como também a oxidação de sulfeto e tiossulfato foram abundantes. Ao todo, este estudo desvenda a diversidade taxonômica e funcional em lagoas salino alcalinas tropicais, como também explora como os microrganismos se comportam em condições ambientais distintas. Além disso, este estudo servirá como ponto de partida para as práticas de manejo e medidas de conservação da biodiversidade do Pantanal

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Made available in DSpace on 2022-05-19T18:12:54Z (GMT). No. of bitstreams: 1 GeneticallyRelatedGenotypesCowpeaSR12.2022.pdf: 3969211 bytes, checksum: e6aa59f5e56a237a0a51c50fc3548f5f (MD5) Previous issue date: 2022

The exponential increase of world population has raised the demand for energy and food resources. In order to achieve it, alternative practices are required to improve agricultural production using fewer natural resources. It is essential, among other factors, to achieve a better soil quality for sustainable production, which turns fundamental to keep soil permanently covered by crop residues or cover crops. Soil coverage acts as a physical barrier to soil losses and increases soil organic matter, enhancing the aggregate structure and nutritional availability. However, little is known about soil coverage\'s influence on the microbial community. Here, we studied the effect of soil coverage on bacterial communities in coffee and sugarcane plantations. Coffee was evaluated comparing conventional and intercropping systems, while sugarcane was studied in four levels of straw maintained in soil surface [total remove (TR), high remove (HR), low remove (LR), and no remove (NR)]. We assessed bacterial community from 0 - 15 cm, divided into four layers in coffee, and 0 - 20 cm, along with five layers in sugarcane crop. We evaluated β-glucosidase and acid-phosphatase activities, biological nitrogen fixation and phosphorus solubilization functional genes abundance (nifH and phoD, respectively), and bacterial community by 16S rRNA sequencing. Further, we performed network co-occurrence analysis and topological parameters to evaluate bacterial assembly and interactions. Our results propose that soil coverage provides a more stable environment for bacterial communities\' development, functioning, and structuring. Our findings indicate that bacterial communities interplay with soil coverage, and its outcomes may boost bacterial benefits for crop performance. The resulting communities observed in both systems under soil coverage can protect the plant from pathogen invasion and benefit the plant by nutritional supply and efficient use of soil resources. Overall, this study contributed to better understand bacterial communities in agricultural soils, which is essential to future design better practices for a more sustainable agricultural system. O aumento exponencial da população mundial aumentou a demanda por recursos energéticos e alimentares. Com isso, práticas alternativas são necessárias a fim de aumentar a produção agrícola e mitigar o uso de recursos naturais cada vez mais escassos. É necessário promover a qualidade do solo para uma produção mais sustentável, onde sua cobertura permanente, seja por resíduos ou culturas de cobertura, se torna fundamental. A cobertura do solo atua como uma barreira física à erosão, e aumenta a matéria orgânica do solo, melhorando a agregação de partículas de solo e a disponibilidade nutricional. No entanto, pouco se sabe sobre a influência da cobertura do solo na comunidade microbiana. Neste trabalho, estudamos o efeito da cobertura do solo nas comunidades microbianas nas plantações de café e cana-de-açúcar. O café foi avaliado comparando-se os sistemas convencional e consorciado, enquanto a cana-de-açúcar foi estudada em quatro níveis de palha mantida na superfície do solo [remoção total (TR), alta remoção (HR), baixa remoção (LR) e nenhuma remoção (NR)]. Avaliamos a comunidade bacteriana de 0 a 15 cm, dividida em quatro camadas no café, e de 0 a 20 cm, em cinco camadas na cultura da cana-de-açúcar. Neste medimos as atividades das enzimas β-glucosidase e fosfatase ácida, a abundância de genes funcionais de fixação biológica de nitrogênio e solubilização de fósforo (nifH e phoD, respectivamente) e a comunidade microbiana por sequenciamento de 16S rRNA. Além disso, realizamos análise de co-ocorrência de rede e calculamos os parâmetros topológicos para avaliar as relações e as interações microbianas. Nossos resultados propõem que a cobertura do solo fornece um ambiente mais estável para o desenvolvimento, funcionamento e estruturação das comunidades microbianas. Estes indicam que as comunidades microbianas interagem com a cobertura do solo, e seus resultados podem aumentar os benefícios microbianos para o desempenho da cultura. As comunidades bacterianas observadas em ambos os sistemas sob cobertura de solo podem proteger a planta da invasão de patógenos e beneficiá-la pelo fornecimento nutricional e uso eficiente dos recursos do solo. No geral, este estudo contribuiu para entender melhor as comunidades microbianas em solos agrícolas, o que é essencial para o futuro design de melhores práticas para um sistema agrícola mais sustentável.

O uso de resíduos agropecuários junto com fertilizantes minerais é uma prática que busca aumentar a eficiência e reduzir a dependência pelos insumos externos. Porém, ainda restam dúvidas sobre as vantagens de se realizar o processo de compostagem nesses resíduos, principalmente em termos de aumento de produtividade das plantas e da qualidade do solo. Por isso, esse trabalho visou avaliar as vantagens do processo de compostagem nos principais resíduos agropecuários gerados e utilizados na agricultura brasileira, como a torta de filtro, a cama de frango e o esterco de poedeiras, para serem utilizados como suplemento da adubação mineral. Esses benefícios foram avaliados através das propriedades físico-químicas dos resíduos agropecuários nas formas \"in natura\" e compostado, e dos resultados obtidos no sistema solo-planta, tais como disponibilização e efeitos residuais dos nutrientes para as plantas e acúmulo de carbono no solo. Também foram avaliadas as mudanças no microbioma do solo associados às plantas de milho, tais como diversidade e riqueza de espécies, composição e estruturação da comunidade microbiana do solo e das correlações com os dados ambientais do solo, como carbono total, pH e teores de macro e micronutrientes no solo. Os resultados do processo de compostagem levaram a redução dos teores de matéria orgânica, carbono e de macronutrientes nos resíduos. Porém, os resíduos compostados apresentaram maior eficiência para o uso dos nutrientes pelas plantas e acumularam mais carbono no solo, proporcionalmente. Por outro lado, os resíduos \"in natura\" apresentam maiores resultados para produção de biomassa aérea e acumularam mais macronutrientes nas plantas. Todavia, apresentaram poucas diferenças em relação ao acúmulo de micronutrientes, e não apresentaram diferenças nos teores de carbono e nitrogênio do solo. Em contrapartida, os resíduos compostados apresentaram melhores respostas microbiológicas em termos de aumento da diversidade, riqueza e estruturação da comunidade de bacteriana, tanto nos resíduos como no solo. Assim, foi possível concluir que os resíduos \"in natura\" podem oferecer melhores resultados a curto prazo devido a presença de maiores teores de nutrientes. Porém, podem levar a um desequilíbrio da qualidade do solo, uma vez que apresentam menor diversidade e riqueza de microbiana nos resíduos e no solo, além de poder causar riscos ambientais devido ao excesso de nutrientes, principalmente N e P. Já os resíduos compostados, oferecem maior segurança ambiental e estimulam o aumento da diversidade e riqueza da comunidade microbiana do solo, podendo oferecer melhores resultados a longo prazo. The use of agricultural wastes along with mineral fertilizers is a practice that seeks to increase efficiency and reduce dependence on external inputs, however, there are still concerns about the advantages of performing the composting process in these wastes, especially in terms of increased plant productivity and soil quality. Therefore, this work aimed to evaluate the advantages of the composting process in the main agricultural wastes generated and used in Brazilian agriculture, such as sugarcane filter cake, poultry litter, and chicken manure, as to be used as a supplement to mineral fertilization. These benefits were evaluated through the physicochemical properties of the agricultural wastes \"in natura\" and composted forms, and the results obtained in the soil-plant system, such as availability and residual effects of the nutrients for plants and carbon accumulation in the soil. Changes in the soil microbiome associated with maize plants were also evaluated, such as diversity and richness of species, soil microbial community composition and structure, and the correlations with soil environmental data, such as total carbon, pH, and macro and micronutrients contents in the soil. The composting process results led to a reduction in the contents of organic matter, carbon, and macronutrients in the wastes. However, the composted residues showed greater efficiency for the use of the nutrients by plants and accumulated more carbon in the soil, proportionally. On the other hand, \"in natura\" wastes present greater results for aerial biomass production and accumulated more macronutrients in plants. However, they showed few differences concerning micronutrient accumulation and did not show differences in soil carbon and nitrogen contents. In contrast, the composted residues presented better microbiological responses in terms of increasing the diversity, richness, and structuring of the bacterial community, both in the residues and in the soil. Thus, it was possible to conclude that \"in natura\" wastes can offer better results in the short term due to the presence of higher nutrient levels. However, they can lead to an imbalance in soil quality, since they present lower microbial diversity and richness in waste and soil, in addition to causing environmental risks due to excess nutrients, especially N and P. On the other hand, composted wastes offer greater environmental safety, stimulate the increase of the diversity and richness of the soil microbial community, and can offer better results in the long term.

Cianobactérias podem estabelecer associações ecológicas com muitos organismos, como fungos, animais e plantas. Embora cianobactérias possam também interagir com outras bactérias, essas associações são puco estudadas. As cianobactérias da ordem Nostocales são capazes de fixar nitrogênio atmosférico, sendo que todos utilizam a mesma estratégia para conseguir realizar esse metabolismo. Logo, tornam-se um modelo adequado para o estudo da interação bactéria-cianobactérias. Os avanços das técnicas de sequenciamento e da bioinformática vêm, nos últimos anos, permitindo que essas interações seja estudadas em maior detalhe. Dessa forma, neste trabalho, tivemos o objeto de caracterizar os genomas das bactérias da cianosfera de cinco linhagens de cianobactérias da ordem Nostocales analisando o potencial metabólico do consórcio. Para isso, os dados resultantes do sequenciamento em plataforma Illumina MiSeq dos cultivos unicianobacterianos das linhagens Sphaerospermopsis torques-reginae ITEP-024, Nostoc sp. CENA67, Fischerella sp. CENA161 e Cylindrospermopsis raciborskii CENA302 e CENA303 foram analisados, pré-processados e montados, e os genomas das cianobactérias e das bactérias da cianosfera foram reconstruídos, levando em conta a abundância e da proporção de conteúdo GC. Os genomas foram taxonomicamente classificados e funcionalmente anotados. A diversidade da comunidade foi acessada por meio da recuperação de sequências do gene 16S RNAr. Os dados brutos do sequenciamento também foram analisados para taxonomia e função no servidor MG-RAST. No total, 33 genomas de alta qualidade foram recuperados e identificados como pertendentes às classe Actinobacteria (1), Alphaproteobacteria (23), Bacteroidetes (2), Betaproteobacteria (4), Deltaproteobacteria (1) e Gammaproteobacteria (3). As análises de diversidade baseadas no gene 16S RNAr identificaram 41 gêneros de bactérias associadas às cianobactérias, distribuídos em 5 filos diferentes, revelando estrutura e composição distintas para cada consórcio. A análise funcional do consórcio revelou o potencial de produção de muitos metabólitos secundário pelas bactérias da cianosfera que podem atuar no estabelecimento e manutenção de sua associação com as cianobactérias. Os dados revelam ainda que a cianobactéria é a única fornecedora de nitrogênio para os organismos do consórcio, uma vez que é a única capaz de realizar o processo de fixação de nitrogênio. Por sua vez, as cianobactérias apresentam maior capacidade de utilização de fósforo inorgânico, enquanto que as bactérias da ciansfera têm genes para consumo de fontes de fósforo orgânico. Esses dados sugerem que as bactérias da cianosfera são dependentes do hospedeiro tanto em estrutura, como em função. Cyanobacteria may establish ecological associations with several organisms like fungi, animals and plants. Although cyanobacteria may also interact with other bacteria, these associations are little studied. Cyanobacteria from Nostocales order can fix atmospheric nitrogen, using the same strategy to perform the metabolism. Thus, they are an adequate model for study of bacteria- cyanobacteria interactions. The advantages of sequencing and bioinformatic techniques in the last years, allow a deeper study of these association. Then, this work aimed to characterize the genomes of cyanosphere bacteria of five Nostocalean cyanobacterial strains as in vitro consortia, analyzing the metabolic potential of the consortia. To achieve these goals, the MiSeq Illumina data sequencing from the unicyanobacterial strains Sphaerospermopsis torques-reginae ITEP-024, Nostoc sp. CENA67, Fischerella sp. CENA161 and Cylindrospermopsis raciborskii CENA302 and CENA303 were analyzed, pre-processed and assembled for subsequent genomes separation of the cyanobacterium and its cyanosphere bacteria, in function of abundance and GC content. The genomes were classified and functionally annotated. Consortia diversity was inferred by retrieving 16S rRNA gene sequences from metagenome. The raw data sequencing were also analyzed to taxonomy and function on MG-RAST server. A total of 33 high-quality genomes were recovered and identified on the classes Actinobacteria (1), Alphaproteobacteria (23), Bacteroidetes (2), Betaproteobacteria (4), Deltaproteobacteria (1) e Gammaproteobacteria (3). The diversity analysis based on 16S RNAr identified 41 genus of cyanosphere bacteria, distributed into five distinct phyla, revealing different structure and composition to each consortium. Functional analysis showed the potential production of many secundary metabolities by cyanosphere bacteria that can act in establishing and maintaining their association with cyanobacteria. Furthermore, the data reveal the cyanobacteria as the only nitrogen provider, since it is the only one capable of performing the nitrogen fixation process. On the other hand, cyanobacteria have a high capacity for using inorganic phosphorus, while associated bacteria have genes for consumption of organic sources of phosphorus. These results suggest that the cyanosphere bacteria are dependent on host in structure and function.

A Amazônia hospeda a maior floresta tropical do planeta, considerada um \"hotspot\" de biodiversidade. O aumento das ações antropogênicas nas ultimas décadas (desmatamento e queimadas) tem ocasionado perdas irreparáveis na diversidade biológica, contribuindo significativamente nas mudanças climáticas por meio de alterações dos fluxos hidrológicos e emissão excessiva de gases relacionados ao efeito estufa, dentre os quais o metano. Assim, na busca de uma melhor compreensão dessas alterações é de fundamental importância o estudo das comunidades microbianas associadas ao consumo do metano. Este trabalho teve como objetivo avaliar o impacto das alterações no uso da terra sobre a estrutura genômica e das comunidades bacterianas associadas a oxidação do metano presentes no solo, buscando a combinação de análises independentes (de comunidades) e dependentes de cultivo (enriquecimento e cultivo), juntamente com o acesso aos genomas montados de bactérias metanotróficas. Amostras provenientes de diferentes usos do solo e regiões da floresta amazônica foram coletadas, em sistemas de florestas primárias, florestas secundárias e pastagens na região de Santarém (PA), e florestas primárias e pastagens em Ariquemes (RO). Os solos coletados foram adicionados ao meio enriquecido com metano para estimular o metabolismo das bacterias metanotróficas. Tanto nas amostras originais como nas oriundas dos enriquecimentos, foram realizadas quantificações do gene pmoA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade total (bactérias e arquéias) e metanotróficas por meio do sequênciamento da região V4-V5 do gene 16S rRNA. Foram também realizadas análises de network e isolamentos de bactérias, na busca de uma maior compreensão sobre as correlações e associações microbianas das amostras. Por fim, o acesso ao metagenoma de amostras enriquecidas e montagens de genomas por metagenoma (MAG - Metagenome Assembled Genome), permitiu comparar a estrutura genômica do operon pmoCAB oriunda de diferentes solos. Os resultados mostraram que estrutura da comunidade total e metanotrófica se alteram com a conversão do solo florestal em pastagem, de maneiras distintas nas áreas amostradas, e com comportamento diferenciado ao longo dos enriquecimentos. O filo Acidobacteria mostrou-se característico de solos florestais, enquanto Actinobacteria, Firmicutes e Bacteoidetes de pastagens, ao passo que a abundância relativa e a riqueza de metanotróficos foi mais elevada em solos de pastagens. Também ocorrem alterações nas interações microbianas, mostrando que florestas possuem correlações mais estáveis que solos de pastagem, porém diferentes entre as áreas estudadas. Estas correlações também são notadas na associação de bactérias metanotróficas com outros grupos, como os gêneros Burkholderia, Pseudomonas, Flavisobacter e Cupriavidus. Em resumo, observa-se que há diferenciação no enriquecimento de bactérias metanotróficas nos diferentes solos e áreas, e os genomas montados indicam a possibilidade de metabolismos distintos. Estes dados contribuem para a compreensão das alterações, em diferentes níveis, da comunidade microbiana nos ambientes de conversão do uso do solo. The Amazon hosts the largest rainforest on the planet, considered a biodiversity \"hotspot\". The increase in anthropogenic actions in the last decades (deforestation and burning) has caused irreparable losses in biological diversity, contributing significantly to climate change through changes in hydrological flows and excessive emissions of greenhouse gases, including methane. Thus, in the search for the best understanding of these changes, it is of fundamental importance to study the microbial communities associated with methane consumption. This work aimed to evaluate the impact of changes in land use on the genomic structure and bacterial communities associated with the oxidation of methane in the soil, seeking the combination of independent (community) and dependent analyzes (enrichment and growth), along with access to the genomes assembled from methanotrophic bacteria. Samples from different soil uses and regions of the Amazon rainforest were collected, such as primary forests, secondary forests and pastures in the Santarém region (PA) and primary forests and pastures in Ariquemes (RO). The collected soils were added to the methane-enriched medium to stimulate the metabolism of the methanotrophic bacteria. In both the original and the enriched samples, were performed quantifications of the pmoA gene by the quantitative PCR technique (qPCR) and characterization of the total community (bacteria and archaea) and methanotrophic by the sequencing of the V4-V5 region of the 16S rRNA gene. Network analyzes and bacterial isolations were also carried out in order to obtain a better understanding of the microbial correlations and associations of the samples. Finally, the access to the metagenome of enriched samples and genome assemblies by metagenome (MAG - Metagenome Assembled Genome) allowed comparing the genomic structure of the pmoCAB operon from different soils. The results showed that the structure of the total and methanotrophic community analyzed changes with the conversion of the forest soil to pasture, in different ways in the sampled areas and in enriched soils. The phyla Acidobacteria showed to be characteristic of forest soils, while Actinobacteria, Firmicutes, and Bacteroides of pastures and the relative abundance and richness of methanotrophic are higher in pastures soils. The changes were observed for microbial interactions, showing that forests have more stable correlations than pasture soils, but different between the areas studied. These correlations are also noted in the association of methanotrophic bacteria with other groups, such as the genera Burkholderia, Pseudomonas, Flavisobacter and Cupriavidus. In summary, it was observed differentiation in the enrichment of methanotrophic bacteria in the different soils and areas, and the assembled genomes indicate the possibility of different metabolisms. These data contribute to the understanding of the changes, at different levels, of the microbial community in the land use conversion environments.

The Earth\'s atmosphere is warming due to a combination of natural effects and anthropic activities, which are directly related to the increment of greenhouse gas (GHG) emissions by burning fossil fuel. Brazil stands out in the world economic scenario as the main producer of ethanol, from sugar cane, considered a source of clean, renewable and economically viable energy. The expansion of this crop into pasture areas, in the Center-South region of Brazil, and the intensification in the production of this biofuel to supply the market have raised concerns about its sustainability. The agricultural is one of the main sectors responsible for the emission of GHG into the atmosphere, therefore, more studies are needed about how land use change (LUC) and production intensification, mainly due to the application of agricultural inputs rich in carbon and nitrogen, can affect GHG emissions. In the Center-South region of Brazil, the main LUC is composed of the succession native vegetation areas to pasture, and in sequence to sugarcane. Therefore, two studies were carried out aiming to determine soil GHG emissions under different land uses in the Center-South region of Brazil (Valparaíso-SP), as well as to characterize the emission factor of the main agricultural inputs in either sugarcane planting or ratoon areas. In the first study, three different land use areas were evaluated, composed of native vegetation, pasture and sugarcane. Among the land uses evaluated in this study, the soil under pasture exhibited the highest emission of carbon equivalents (CO2-eq), which was 41-fold higher than under native vegetation and 5.6-fold higher than under sugarcane. In the second study, two experiments were set up to determine the soil GHG emission fluxes after the application of sources of carbon and nitrogen during sugarcane cultivation. Experiment I: set up in a sugarcane planting area with application of ammonium nitrate, limestone and filter cake, in addition to a control treatment without application of any input. Experiment II: set up in a sugarcane ratoon area with application of vinasse and urea in the first year, and vinasse in the second year. In the first experiment, the soil tillage during the planting process produced a larger increase of soil GHG emissions when compared to the sugarcane ratoon area. Among the inputs applied to the cane plant, filter cake or ammonium nitrate produced the highest GHG emissions from the soil. On the other hand, in the area of sugarcane ratoon, the highest emissions were observed with the application of a combination of organic and mineral fertilizers (vinasse and urea), but with the application of only vinasse, the emission increment was less intense. The emission factors for C-CO2 and N-N2O reported by the IPCC are higher than those observed in this study, in the Center-South region of Brazil. The highest emission factor was observed for ammonium nitrate, with 0.13% for N-N2O in the rainy season. Thus, the expansion of sugarcane planted areas plays an important role in GHG emission. New studies on this contribution to GHG emissions are urgently needed in different regions around the world, in order to define measures to limit emissions and aiming at maintaining the sustainability of this biofuel O aquecimento da Terra decorrente de atividades antrópicas, está diretamente relacionado ao aumento das emissões de gases de efeito estufa (GEE) por queima de combustíveis fósseis. O Brasil se destaca no cenário econômico mundial como o principal produtor de etanol, de cana-de-açúcar, considerado uma fonte de energia limpa, renovável e economicamente viável. A expansão desta cultura sobre áreas de pastagem, na região Centro-Sul do Brasil, e a intensificação da produção deste biocombustível, necessárias para suprir o mercado têm levantado preocupações sobre a sua sustentabilidade. O setor agrícola é uma das principais fases relacionadas à emissão de GEE na atmosfera, sendo necessário maior entendimento sobre como as mudanças de uso da terra (MUT) e intensificação de produção podem afetar as emissões GEE, principalmente após a aplicação no solo de insumos agrícolas ricos em carbono e nitrogênio. Na região Centro-Sul do Brasil, a principal MUT é composta pela sucessão de áreas de vegetação nativa- pastagem- cana-de-açúcar. Foram realizados dois estudos com o objetivo de determinar as emissões de GEE do solo em diferentes usos da terra em Valparaíso-SP, bem como caracterizar o fator de emissão dos principais insumos agrícolas utilizados em áreas de cana planta e cana soca. No primeiro estudo, foram avaliadas três áreas de uso da terra, compostas por vegetação nativa, pastagem e cana-de-açúcar. Entre os sistemas de usos da terra avaliados neste estudo, a pastagem apresentou a maior emissão de carbono equivalente (CO2-eq), no qual representou cerca de 41 vezes maior do que a vegetação nativa e 5,6 vezes maior do que a cana-de-açúcar. No segundo estudo, dois experimentos foram conduzidos simultaneamente para determinar os fluxos de emissões de gases do solo após a aplicação de fontes de carbono e nitrogênio durante diferentes fases do ciclo da cana-de-açúcar. Experimento I: realizado em uma área de plantio de cana-de-açúcar com aplicação de nitrato de amônio, calcário e torta de filtro, além de um tratamento controle sem aplicação de nenhum insumo. Experimento II: área de cana soca com aplicação de vinhaça e ureia no primeiro ano, e vinhaça no segundo ano. No primeiro experimento o revolvimento do solo no processo de plantio proporcionou as maiores emissões de GEE quando comparada a área de cana soca. Dentre os insumos aplicados na cana planta, a torta de filtro ou nitrato de amônio proporcionaram as maiores emissões de GEE do solo. Por outro lado, na área de cana soca, as maiores emissões foram verificadas quando houve a combinação de fertilizante orgânico e mineral (vinhaça e ureia), sendo que com a aplicação somente de vinhaça, o aumento das emissões foi menos intenso. Os fatores de emissão para C-CO2 e N-N2O relatados pelo IPCC ainda são maiores do que os observados neste estudo, realizado na região Centro-Sul do Brasil, no qual o maior fator de emissão foi observado para nitrato de amônio, com 0,13% para N-N2O, na estação chuvosa. A expansão das áreas plantadas de cana de açúcar tem importante papel na emissão de GEE, sendo necessários novos estudos sobre essa contribuição em distintas regiões de produção em todo o mundo, na busca de medidas menos emissoras, visando a sustentabilidade deste biocombustível