Bactérias amonificantes e nitrificantes e teores de amônio e nitrato afetados por plantas de cobertura e fertilizantes nitrogenados.

O objetivo do trabalho foi avaliar o efeito das plantas de cobertura e da fonte de N nas bactérias nitrificantes e amonificantes do solo, bem como nos teores de nitrato e amônio. O experimento foi conduzido em um latossolo vermelho distrófico sobre sistema plantio direto (SPD) por seis anos. O delineamento experimental foi em blocos casualizados, no esquema de parcelas subdivididas, com quatro repetições. As parcelas foram constituídas por seis espécies de plantas de cobertura do solo (Brachiaria brizantha, Brachiaria decumbens, Brachiaria humidicola, Brachiaria ruziziensis, Pennisetum americanum e Crotalaria spectabilis) e as subparcelas pelo controle e três fontes de N (1- controle, sem aplicação de N, 2- nitrato de cálcio, 3- sulfato de amônio e 4-sulfato de amônio + dicianodiamida (DCD)) aplicadas imediatamente após a emergência do arroz na dose de 40 kg ha-1 de N. Foram avaliadas a atividade das bactérias e os teores de nitrato e amônio no solo aos 15 DAE. As plantas de cobertura milheto (Pennisetum americanum), crotalaria (Crotalaria spectabilis); Brachiaria brizantha, B. decumbens; e B. humidicola proporcionaram os maiores teores de amônio no solo; O uso do inibidor de nitrificação (dicianodiamida-DCD) inibiu parte das bactérias nitrificantes e proporcionou os maiores teores de amônio no solo. A atividade das bactérias amonificantes e nitrificantes foi maior nas parcelas cultivadas com braquiárias. Plantas de cobertura aliada ao uso de DCD pode ser uma estratégia para aumentar os teores de amônio do solo cultivado sobre SPD

Bacterial community and chemical composition of mixed fresh cactus forage and buffel grass hay during aerobic exposure.

The chemical composition of cactus forage becomes a favorable culture medium for accelerated microbial activity when exposed to air, as it contains high content of non-fiber carbohydratesand water. Thus, the aim of this study was to evaluate the bacterial community dynamics of different mixtures, using fresh forage of cactus and buffel grass hay as a function of the period of exposure to air. The experimental design used was a 5 × 5 factorial completely randomized (five levels of cactus forage × five times of exposure to air), with five replications. The peak of Escherichia coli population growth was after 16.06 h of exposure to air, observed in treatments of 90% and 100% cactus forage. There was an increase in microbial richness and uniformity of all treatments after six hours. The most abundant genera were Weissella, Lactobacillus, Bacteroides, Pseudomonas, Sphingobacterium, and Sphingomonas. The diet with 100% cactus forage showed a predominance of Weissella, Lactobacillus, and Leuconostoc. With 20% cactus forage, there was a greater apparent abundance of Pseudomonas, Sphingomonas, and Sphingobacterium. Aerobic exposure of mixtures of cactus forage with buffel grass hay increases the proliferation of microorganisms with pathogenic potential in the diet. Aerobic exposure of mixtures of cactus forage with buffel grass hay increases the proliferation of microorganisms with pathogenic potential in the diet. Therefore, an exposure period of fewer than six hours with 20% cactus forage is recommended to minimize levels of E. coli. Avoiding negative effects of the multiplication of pathogenic microorganisms on animal and human healt

Exploring interactions of plant microbiomes

A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. In this review, we first summarize features of microbial communities that compose the plant microbiome and further present a series of studies describing the underpinning factors that shape the phylogenetic and functional plant-associated communities. We advocate the idea that understanding the mechanisms by which plants select and interact with their microbiomes may have a direct effect on plant development and health, and further lead to the establishment of novel microbiome-driven strategies, that can cope with the development of a more sustainable agriculture

Xylella fastidiosa gene expression analysis by DNA microarrays

Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation

Background: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees. Results: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere. Conclusion: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas

Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment

Background: Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. Results: The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. Conclusion: This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas