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Leaf decomposition is the primary process in release of nutrients in the dynamic mangrove habitat, supporting the ecosystem food webs. On most environments, fungi are an essential part of this process. However, due to the peculiarities of mangrove forests, this group is currently neglected. Thus, this study tests the hypothesis that fungal communities display a specific succession pattern in different mangrove species and this due to differences in their ecological role. A molecular approach was employed to investigate the dynamics of the fungal community during the decomposition of three common plant species (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) from a mangrove habitat located at the southeast of Brazil. Plant material was the primary driver of fungi communities, but time also was marginally significant for the process, and evident changes in the fungal community during the decomposition process were observed. The five most abundant classes common to all the three plant species were Saccharomycetes, Sordariomycetes, Tremellomycetes, Eurotiomycetes, and Dothideomycetes, all belonging to the Phylum Ascomycota. Microbotryomycetes class were shared only by A. schaueriana and L. racemosa, while Agaricomycetes class were shared by L. racemosa and R. mangle. The class Glomeromycetes were shared by A. schaueriana and R. mangle. The analysis of the core microbiome showed that Saccharomycetes was the most abundant class. In the variable community, Sordariomycetes was the most abundant one, mainly in the Laguncularia racemosa plant. The results presented in this work shows a specialization of the fungal community regarding plant material during litter decomposition which might be related to the different chemical composition and rate of degradation.

Intensive agriculture requires large inputs of chemicals to avoid losses caused by pathogen infections. Exploring the rhizosphere of plants, which is an area with enormous abundance and diversity of microorganisms, represents a promising strategy to protect plants from pathogens in a sustainable way. Recent studies revealed the importance of soil microbiome in the process of natural plant defense and how current management practices can interfere in the dynamics of these microbial communities shaping a protective microbiome. This review emphasizes the main findings related to changes in rhizosphere microbiome composition and functions during plant infection by soilborne pathogens. Understanding plant-microbiome interactions in the rhizosphere is key to develop microbiome-based strategies for assembling beneficial protective resident microbial communities in production systems.

The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 mg ml-1 from phytate, 300 mg ml-1 from calcium phosphate, and 200 mg ml-1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha􀀀1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future. Made available in DSpace on 2021-08-12T18:00:25Z (GMT). No. of bitstreams: 1 Queiroz-Actinobacterium-strain-2021.pdf: 1861839 bytes, checksum: 1086e2f573058785947282cdc37c76b1 (MD5) Previous issue date: 2021

The success of a biological control programme depends on the isolation and selection of antagonists. There is an enormous diversity of culturable microbial species in the soil, rhizosphere, phylloplane, spermosphere and carposphere, which can be used in the isolation and selection of antagonists. The structures of fungal plant pathogens concerned with survival and infection may also be sources of antagonists. Although non-culturable microorganisms and microbiome-based strategies have great potential for development as commercial products in disease control, more knowledge is needed to understand the mechanisms involved in interactions between plants and complex microbial communities. Methods of isolation and selection of the most commercially exploited groups of antagonists and their advantages and disadvantages are discussed in this chapter as well as those of non-traditional antagonists. Finally, possible strategies for engineering the soil and host microbiome to actively promote plant protection against pathogens are discussed.

Acidic soils rapidly retain applied phosphorus fertilizers and consequently present low availability of this nutrient to plants. The use of phosphate-solubilizing microorganisms to help plant phosphorus (P) absorption is a promising sustainable strategy for managing P deficiencies in agricultural soils. Trichoderma strains have been one of the most studied filamentous fungi for improving the production and development of several crop species mainly due to their capability for symbiotic associations and their ability to control soil-borne plant diseases. Thus, this work sought to bioprospect Trichoderma strains from the Amazon rainforest capable of solubilizing/mineralizing soil phosphate and promoting soybean growth. Soybean plants inoculated with selected Trichoderma strains were cultivated in soil under greenhouse conditions and under a gradient of rock phosphate and triple superphosphate. As a result, 19.5% of the isolated Trichoderma strains were able to solubilize phosphate. In addition, those strains produced different organic acids during the solubilization process. Trichoderma spp. strains showed positive responses in the promotion of soybean growth—from 2.1% to 41.1%—as well as in the efficiency of P uptake-up to 141%. These results reveal the potential of Trichoderma spp. from the Amazon biome as promising biofertilizer agents.

The classical view on plant diseases represented by a triangle where the host, the pathogen, and the environment interact with each other resulting in disease or not is recently challenged by a more complex holistic view including the presence of complex microbial communities in the pathosystem. The plant and soil microbiomes are closely connected with all three causal factors of the classical “disease triangle.” The environment, especially the soil characteristics, determines the source of microbes recruited by plant roots, which in turn directly affect the success of given pathogen to cause disease. In the plant, the microbiome impacts host development and health and its assembling and functioning is to some extend controlled by the host genetic traits. The pathogen, as member of the soil microbiome, also interacts and competes with a complex microbial community striving to invade the rhizosphere microbiome and reach the root system to infect and cause disease. Here, we discuss the interactions on the rhizosphere microbiome in the context of soil-borne diseases, highlighting the microbiome as a key player in pathosystems, acting as first line of defense in the rhizosphere. We also discuss strategies to identify plant genetic traits involved in recruitment of beneficial microorganisms and the potential to explore it in the breeding programs to promote plant health and productivity.

Background Phosphorus (P) availability is the main nutritional factor that limits crops yields in tropical soils due to edaphic processes that lead to P immobilization after mineral fertilization. Considering the potential of the rhizosphere microbiome to transform insoluble P into forms readily available for plant uptake, in this study is proposed that plants with contrasting P uptake efficiency, growing under depleted amounts of P are able to shape distinct bacterial communities in the rhizosphere enriching taxa specialized in P mobilization. Methods We selected two common bean genotypes contrasting in P efficiency uptake and grew them in a soil with a gradient of two different sources of P, triple superphosphate (TSP) or rock phosphate Bayovar (RPB). The rhizosphere bacterial community was assessed by 16S rRNA amplicon sequencing. Data analyses focused in describing the structure of the bacterial communities, identification of OTUs differentially enriched in different treatments, functional metagenomic prediction and cooccurrence network. Results P sources and levels resulted in different rhizosphere bacterial community structure. A high number of differentially enriched OTUs were observed under P depleted conditions in the P-inefficient genotype, mainly belonging to Actinobacteria phylum. The P-inefficient genotype did not show significant differences in the rhizosphere bacterial community assembly growing in different P sources. Predicted metagenome profiles showed the enrichment of bacterial functions involved in P mobilization, in the rhizosphere of the P inefficient genotype cultivated in P depleted conditions. The network analysis revealed that in the rhizosphere of the P-inefficient genotype under P depleted conditions the bacterial community has a higher number of nodes and edges, higher average degree and clustering coeficient when compared to the treatment with optimal P level. Conclusion Our data showed that the uptake of exogenous input resulted in the assembly of a P-competent microbiome in the P-inefficient genotype compared to the efficient one, supporting the hypothesis that the selective pressure for the P uptake engages P-inefficient genotypes in symbiotic relationships with the soil microbiome. These results will pave the way for future experimentation aiming at explore the contribution of this P-competent microbiome to plant growth and development in a range of soil type.

Crop yield decrease is the main concern when a pathogen or plague is identified in an agriculture field. Thus, part of this issue can be attributed to plant-parasitic nematodes (PPNs), such as Meloidogyne species, due to, most of the time, the hard diagnosis, and non-specific symptoms. Its management is mainly based on chemical pesticides, followed by a few potential biological control agents, and the management system. Therefore, this study aimed to evaluate the effects of biological agents in Meloidogyne incognita control in different soil systems. For that, two biological products were chosen, Trichoderma asperellum BV10 and Bacillus amyloliquefaciens BV03, and soils were sampled from three different managements systems: (i) soybean no-tilled system at Goiás state, Brazil; (ii) forest soil at Goiás state, Brazil, and (iii) soybean conventional managed system at Mato Grosso do Sul state, Brazil. Biocontrol and growth promotion effects, volatile organic compounds (VOCs) and soil respiration were determined in vegetation house and laboratory, respectively. As a result, both BV10 and BV03 had significant nematode control activity, comparing to control treatment, in all the three soils systems. Plus, the number of immobile nematodes by potential VOCs had significant increase when BV03 was applied, while the application of BV10 agent raised the soil respiration rate. In conclusion, both biocontrol agents presented great efficiency in control M. incognita, with better performance of BV03. Lastly, more studies must be done to elucidate how the resident soil microbiome can influence on biocontrol agent establishment and performance, as well as the consequence of the application of biological products on soil microbiome network.

The current population growth will demand a higher productive agriculture to full the food requirement. To supply this need and preserve the environment, many resources are applied to promote sustainable agriculture. Phosphorus depletion is the main factor that limits crops yields in tropical soils, where the pH and clay content rapid fixate this nutrient. Plant breeders aim to solve this issue by changing the plant requirements for phosphorus and adapting them to low P availability. However, with these approaches the demand for phosphorus fertilizers will continue and so the depletion of the natural deposits. In this study is proposed that plants with contrasting phosphorus uptake efficiency, i.e. P-efficient and P-inefficient, recruits distinct rhizosphere microbiome specialized in phosphorus mobilization. This hypothesis was tested growing plants in a gradient of two sources of P, triple superphosphate or rock phosphate Bayovar. Thebean rhizosphere microbiome was assessed with culture dependent and independent approaches, enzymatic assays, predictive metagenomics and networks analysis. A differential enrichment of several OTUs in the rhizosphere of the P-inefficient common bean genotype, and the enrichment of bacterial chemotaxis functions and functions involved in phosphorus mobilization suggest that this genotype has superior communication with the rhizosphere microbiome and is highly dependent on it for phosphorus mobilization. As a proof of concept, the P-efficientefficient genotype was sown in soil previously cultivated with P-inefficientinefficient genotype. The results showed that P-efficientefficient genotype positively responded to the modified rhizosphere in early stages, that is, the microbiome selected and enriched by the P-inefficient genotype improved the P uptake in the genotype cultivated afterwards in the same soil. Taken collectively, these results suggest that plants partly rely on the rhizosphere microbiome for P uptake and that the exploration of these interactions during plant breeding would allow the selection of even more efficient genotypes, leading to a sustainable agriculture by exploring soil residual P. O atual aumento populacional irá demandar uma maior produção agrícola para completar a necessidade de alimento. Para suprir essa necessidade e preservar o meio ambiente, muitos recursos serão aplicados para promover a agricultura sustentável. A depleção de fósforo é um dos principais fatores que limita a produção agrícola em solos tropicais, onde o pH e o conteúdo de argila fixam rapidamente esse nutriente. Os melhoristas de plantas visam solucionar esse problema alterando a necessidade de fósforo das plantas e adaptando-as as baixas disponibilidade de fósforo. No entanto, com essas estratégias a demanda por fertilizantes fosfatados irá continuar assim como a exploração das reservas naturais de fósforo. Nesse estudo foi proposto que as plantas contrastantes em relação a eficiência na absorção de fósforo, i.e. P-eficiente e P-ineficiente, recrutariam um microbioma rizosférico distinto em relação a mobilização de fósforo. Essa hipótese foi testada cultivando plantas em um gradiente usando duas fontes distintas de P, triplo fosfato ou fosfato de rocha Bayovar. O microbioma da rizosfera de feijão foi então avaliado por técnicas dependentes e independentes de cultivo, análise enzimática, predição metagenômica e análises de network. Um enriquecimento diferencial de várias OTUs observado na rizosfera do genótipo de feijão P-ineficiente, e o enriquecimento de funções de quimiotaxia bacteriana e envolvidas na mobilização de fósforo sugerem que esse genótipo tem uma maior comunicação com o microbioma rizosférico e é altamente dependente deste para a mobilização de fósforo. Como prova de conceito, o genótipo P-eficiente foi plantado em solo previamente cultivadocom o genótipo P-ineficiente. Os resultados mostraram que o genótipo P-eficiente responde positivamente à rizosfera modificada nos estádios iniciais de crescimento, ou seja, o microbioma selecionado e enriquecido pelo genótipo P-ineficiente melhorou a absorção de fósforo no genótipo cultivado posteriormente no mesmo solo. Coletivamente, esses resultados sugerem que as plantas dependem parcialmente do microbioma da rizosfera para a absorção de P e que a exploraçãodestas interações durante o melhoramento vegetal permitiria a seleção de genótipos muito mais eficientes, conduzindo à uma agricultura sustentável explorando o fósforo residual do solo.

Ruminants are important as suppliers of dairy products for human consumption and are responsible by a large portion of global greenhouse gas emissions. The rumen microbial colonization is a complex process and occurs simultaneously with animal development and maturation of the host immune system. Ruminal microorganisms are responsible for converting energy stored in plant biomass into volatile fatty acid, which are subsequently metabolized and absorbed by the animal. In this chapter, we briefly describe the rumen compartment and the coevolution between ruminants and microorganisms. Further, we discuss the rumen microbiome composition, including the structure of bacterial and archaeal communities and the role of Protozoa, anaerobic fungi, and bacteriophages in the rumen. Finally, we discuss how the use of molecular tools on rumen microbiome studies has impacted on biotechnological exploitation of this ecosystem.

Knowledge of the vastness of microbial diversity associated with plants is still limited. Plant microbiome structure and functions are shaped by several factors, including host genotype and developmental stage, the presence or absence of diseases, and environmental conditions. These factors may lead to distinct microbial communities in the rhizosphere, endosphere, and phyllosphere. Studies directed to microbial interactions in plant compartments are fundamental for understanding the microbial ecology of phytobiomes, enabling the development of microbiome-based technologies in the search for sustainable agriculture. In this chapter, we describe plant compartments, i.e., the rhizosphere, phyllosphere and endosphere, and the more common bacterial composition of each compartment. We also discuss manipulation of the plant microbiome toward improved plant health. Advances in this field will lead to strategies where the manipulation of the plant microbiome will allow the reduction of pesticide and fertilizer use in field crops, paving the way to a more sustainable agriculture.

Knowing the bacterial community, as well as understanding how it changes during a hydrological pulse, is very important to understand nutrient cycles in floodplain systems. The bacterial community structure was analyzed in the 12 sites of upper Paraná River floodplain, and its changes during a flood pulse were described. In order to understand how high and low water phases change bacterial community by changing abiotical variables, the bacterial community distribution was determined in superficial water of 12 different sampling stations, every 3 months, from December 2010 to September 2011. The bacterial community structure and diversity was analyzed by fluorescent in situ hybridization, considering the main domains Bacteria and Archaea and the subdivisions of the phylum Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and the Cytophaga-Flavobacterium cluster. Smaller densities were observed on ebb and low water periods and the highest density was observed in March 2011. The high water period caused a decrease in diversity because of the lost of equitability. The highest values of Shannon-Wiener index were found on December 2010 and September 2011. The nutrients runoff to the aquatic environments of the floodplain promoted an increase in the total bacterial density during the high water phase as well as changes in bacterial community composition. The bacterial community presented both spatial and temporal differences. Yet, temporal changes in limnological characteristics of the floodplain were the most important predictor of bacterial community and also influenced its diversity.

Ilha Grande National Park is an important conservation unit localized in the Southern part of the upper Parana river floodplain (Brazil) that includes diverse aquatic environments. Oligochaeta (Annelida) is a large group of invertebrates, with several small specimens inhabiting almost every possible niche at most freshwater ecosystem. The goal of the present study was to examine the spatial variation of Oligochaeta community in five floodplain lakes from the Ilha Grande National Park and relate the distribution with abiotic variables. Samples were taken at five sampling stations using a modified Petersen grab. Thirteen species of Oligochaeta belonging to two families Naididae and Tubificidae were recorded. Different patterns of richness and abiotic factors were identified among the lakes located in the island and at the margin of Parana river. The different patterns of granulometric texture affected directly the distribution of the Oligochaeta assemblage of theses environments. The results of this study permit to infer that the Oligochaeta assemblage, in preserved areas, present a higher richness in relation to long term studies with more frequent samplings. We concluded that Ilha Grande National Park contributes for the preservation of benthic invertebrates.

A bacterial community has a central role in nutrient cycle in aquatic habitats. Therefore, it is important to analyze how this community is distributed throughout different locations. Thirty-six different sites in the upper Paraná River floodplain were surveyed to determine the influence of environmental variable in bacterial community composition. The sites are classified as rivers, channels, and floodplain lakes connected or unconnected to the main river channel. The bacterial community structure was analyzed by fluorescent in situ hybridization (FISH) technique, based on frequency of the main domains Bacteria and Archaea, and subdivisions of the phylum Proteobacteria (Alpha-proteobacteria, Beta-proteobacteria, Gamma-proteobacteria) and the Cytophaga-Flavobacterium cluster. It has been demonstrated that the bacterial community differed in density and frequency of the studied groups. And these differences responded to distinct characteristics of the three main rivers of the floodplain as well as to the classification of the environments found in this floodplain. We conclude that dissimilarities in the bacterial community structure are related to environmental heterogeneity, and the limnological variables that most predicted bacterial communities in the upper Paraná River floodplain was total and ammoniacal nitrogen, orthophosphate and chlorophyll-a.

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.

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations\' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface. Made available in DSpace on 2022-03-14T19:00:41Z (GMT). No. of bitstreams: 1 Melo-Unexplored-bacterial-2021.pdf: 1374343 bytes, checksum: e21b8a0b619e4fcada9dc130c88c9117 (MD5) Previous issue date: 2020