Draft genome sequences of 13 putatively novel Haemophilus species and strains assembled from human saliva.

We present the draft metagenome-assembled genomes (MAGs) of 13 Haemophilus representatives from human saliva. MAGs were reconstructed by a streamlined pre-assembly mapping approach performed against 9 clinically relevant reference genomes. Overall, genomes belonging to 2 potentially novel Haemophilus species and 11 strains were recovered, as determined by genome-wide ANI analysis.

Organic matter decay and bacterial community succession in mangroves under simulated climate change scenarios.

Mangroves are coastal environments that provide resources for adjacent ecosystems due to their high productivity, organic matter decomposition, and carbon cycling by microbial communities in sediments. Since the industrial revolution, the increase of Greenhouse Gases (GHG) released due to fossil fuel burning led to many environmental abnormalities such as an increase in average temperature and ocean acidification. Based on the hypothesis that climate change modifies the microbial diversity associated with decaying organic matter in mangrove sediments, this study aimed to evaluate the microbial diversity under simulated climate change conditions during the litter decomposition process and the emission of GHG. Thus, microcosms containing organic matter from the three main plant species found in mangroves throughout the State of São Paulo, Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were incubated simulating climate changes (increase in temperature and pH). The decay rate was higher in the first seven days of incubation, but the differences between the simulated treatments were minor. GHG fluxes were higher in the first ten days and higher in samples under increased temperature. The variation in time resulted in substantial impacts on α-diversity and community composition, initially with a greater abundance of Gammaproteobacteria for all plant species despite the climate conditions variations. The PCoA analysis reveals the chronological sequence in ß-diversity, indicating the increase of Deltaproteobacteria at the end of the process. The GHG emission varied in function of the organic matter source with an increase due to the elevated temperature, concurrent with the rise in the Deltaproteobacteria population. Thus, these results indicate that under the expected climate change scenario for the end of the century, the decomposition rate and GHG emissions will be potentially higher, leading to a harmful feedback loop of GHG production. This process can happen independently of an impact on the bacterial community structure due to these changes.

Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths.

The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.

The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Bacterial genomes recovered from litter's metagenomes in Amazonian Dark Earths.

Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).

Concentration, characterization and application of lipases from Sporidiobolus pararoseus strain

Lipases produced by a newly isolated Sporidiobolus pararoseus strain have potential catalytic ability for esterification reactions. After production, the enzymatic extracts (conventional crude and precipitated, 'CC' and 'CP', and industrial crude and precipitated, 'IC' e 'IP') were partially characterized. The enzymes presented, in general, higher specificity for short chain alcohols and fatty acids. The precipitated extract showed a good thermal stability, higher than that for crude enzymatic extracts. The 'CC' and 'CP' enzymes presented high activities after exposure to pH 6.5 and 40 ºC. On the other hand, the 'IC' and 'IP' extracts kept their activities in a wide range of pH memory but presented preference for higher reaction temperatures. Preliminary studies of application of the crude lipase extract in the enzymatic production of geranyl propionate using geraniol and propionic acid as substrates in solvent-free system led to a reaction conversion of 42 ± 1.5%.

'Synthetic lipase' production from a newly isolated Sporidiobolus pararoseus strain by submerged fermentation

The lipase produced by a newly isolate Sporidiobolus pararoseus strain has potential catalysis ability for esterification reactions. In order to improve its synthetic activity, this work aimed at optimizing 'synthetic lipase' production by submerged fermentation of a conventional media based on peptone, yeast extract, NaCl and olive oil using experimental design technique. According to the results obtained in the first experimental design (2(4-1)), yeast extract and NaCl concentrations were tested to further optimization by response surface methodology. The maximum 'synthetic lipase' activity obtained was 26.9 U/mL in the optimized media (5.0, 6.8, 7.0 and 1.0% (wt/v) of peptone, yeast extract, NaCl and olive oil, respectively), representing a 6.36-fold increase compared to the initial medium. The time course of 'synthetic lipase' production in the optimized condition was evaluated in terms of synthetic activity, protease activity, biomass and total carbon and the maximum synthetic activity was observed during the stationary phase of growth.

16s-23S rDNA: polymorphisms and their use for detection and identification of Xylella fastidiosa strains

Strains of Xylella fastidiosa from several hosts (coffee, citrus, grape, almond, oleander, peach, plum, etc.) were characterized by analyzing the content of the nucleotide sequences of 16S-23S rDNA (coding for a small subunit ribosomal RNA) spacer region (ITS). Current methods for sequencing the ITS region yields partial sequences that do not contribute with significant information. According to this fact, new primers have been designed in order to obtain a complete sequence and facilitate the sequencing. The complete 16S-23S sequences from 08 strains were amplified through PCR using the primers designed in our lab. The 16S-23S sequences obtained were compared with 52 others sequences entries in GenBank database. The results revealed a higher level of variation than that found in 16S gene sequences, with similarity values ranging from 0.79-1.00. The dendogram based on similarity data revealed 5 main groups. This spacer sequence contains two genes for tRNA (tRNAala and tRNAile). The sequence analysis of the tRNA content showed a conserved region with a few differences in the nucleotide composition.

Linhagens de Xylella fastidiosa de diferentes hospedeiros (café, uva, amêndoa, ameixa, etc.) foram caracterizados analisando as sequências de nucleotídeos do espaço intergênico 16S-23S (ITS). Os métodos atuais para o sequenciamento da região ITS produzem fragmentos parciais das sequências que não contribuem com informações significantes. Em vista disso, novos primers foram desenhados a fim de obter uma sequência completa e facilitar o sequenciamento. A sequencia completa da região ITS de 08 linhagens de X. Fastidiosa foram amplificadas via PCR, sequenciadas e comparadas com outras 52 sequencias depositadas no GenBank. Os resultados revelaram um alto nível de variação sendo maior que os níveis encontrados quando se utiliza o gene 16S para este tipo de análise, com valores variando entre 0.79 a 1.00. O dendograma baseado em dados de similaridade agrupou as linhagens de X. fastidiosa em 5 grupos principais. Duas sequencias codificadoras de tRNA's foram encontradas (tRNAala e tRNAile) e mostram-se conservadas entre as linhagens analisadas com pouca diferença entre a composição nucleotídica.

Identification of citrus expressed sequence tags (ESTs) encoding pleiotropic drug resistance (PDR)-like proteins

Pleiotropic drug resistance (PDR) proteins, a subfamily of the ATP-binding cassette (ABC) transporters, have been recently shown to play a role in plant defense against biotic and abiotic stresses. However, nothing is known about their expression in citrus. To investigate the occurrence of PDR homologues in citrus species, we have surveyed EST sequences from different tissues and conditions of the Citrus Expressed Sequence Tags (CitEST) database, through sequence similarity search analyses and inspections for characteristic PDR domains. Multiple sequence alignments, prediction of transmembrane topology and phylogenetic analysis of PDR-like proteins were additionally performed. This study allowed the identification of nine putative proteins showing characteristic PDR features in citrus species under various conditions, which may indicate a potential correlation between PDRs and stress and metabolism of citrus plants. Moreover, a tissue-specific putative PDR-like protein was found in sweet orange fruits. To our knowledge, this is the first report regarding the identification of citrus ESTs encoding PDR-like proteins as well as the first to identify a putative full ABC transporter with specific expression in fruits.

Specific amplification of iron receptor genes in Xylella fastidiosa strains from different hosts

Bacterial production of siderophores may involve specific genes related to nonribosomal peptide and polyketide biosynthesis, which have not been fully identified in the genome of Xylella fastidiosa strain 9a5c. However, a search for siderophore-related genes in strain 9a5c indicated five membrane receptors, including siderophore, ferrichrome-iron and hemin receptors. All these biomolecules are thought to be associated with iron transport and utilization. Eighty isolates obtained from citrus orchards containing trees that developed citrus variegated chlorosis (CVC) were screened for siderophore production. The results demonstrated that only 10 of the isolates did not produce siderophores. Additional strains obtained from coffee, almond, mulberry, elm, ragweed, periwinkle and grape also infected by X. fastidiosa were also shown by the chromeazurol bioassay to produce siderophores. In order to correlate siderophore production with the presence of siderophore-related genes, a polymerase chain reaction (PCR) was developed using specific primers for the catechol-type ferric enterobactin receptor (pfeA) and the hydroxamate-type ferrisiderophore receptor (fiuA) genes of strain 9a5c. The PCR results confirmed our hypothesis by demonstrating that amplification products were detected in all strains except for those isolates that did not produce siderophores.

In silico characterization of microsatellites in Eucalyptus spp: abundance, length variation and transposon associations

This study assessed the abundance of microsatellites, or simple sequence repeats (SSR), in 19 Eucalyptus EST libraries from FORESTs, containing cDNA sequences from five species: E. grandis, E. globulus, E. saligna, E. urophylla and E. camaldulensis. Overall, a total of 11,534 SSRs and 8,447 SSR-containing sequences (25.5% of total ESTs) were identified, with an average of 1 SSR/2.5 kb when considering all motifs and 1 SSR/3.1 kb when mononucleotides were not included. Dimeric repeats were the most abundant (41.03%), followed by trimerics (36.11%) and monomerics (19.59%). The most frequent motifs were A/T (87.24%) for monomerics, AG/CT (94.44%) for dimerics, CCG/CGG (37.87%) for trimerics, AAGG/CCTT (18.75%) for tetramerics, AGAGG/CCTCT (14.04%) for pentamerics and ACGGCG/CGCCGT (6.30%) for hexamerics. According to sequence length, Class II or potentially variable markers were the most commonly found, followed by Class III. Two sequences presented high similarity to previously published Eucalyptus sequences from the NCBI database, EMBRA_72 and EMBRA_122. Local blastn search for transposons did not reveal the presence of any transposable elements with a cut-off value of 10-50. The large number of microsatellites identified will contribute to the refinement of marker-assisted mapping and to the discovery of novel markers for virtually all genes of economic interest

Efeito da temperatura sobre a produção de enterotoxina estafilocócica em leite / Effect of temperature on production of staphylococcal enterotoxin in milk

Muitos estudos têm investigado as condições nas quais Staphylococcus aureus está apto para produzir enteroxinas. As necessidades nutricionais (presença ou ausência de aminoácidos e glicose), bem como variações de pH e temperatura, podem resultar na produção de enterotoxinas capazes de causar doenças. Neste estudo foram usadas cepas de S. aureus produtoras de enterotoxinas A e C2 (respectivamente FRI 722 e FRI 361) e um isolado no qual foi detectada a presença concomitante dos genes de enterotoxina A e da Síndrome do Choque Tóxico (TSST-1) em estudo anterior. As cepas foram inoculadas em leite UHT e as amostras submetidas a diferentes situações de estresse térmico (tempo e temperatura). Em nosso trabalho, houve produção das enterotoxinas A e C2 e de TSST-1 quando o leite UHT foi exposto a temperaturas elevadas, na faixa de 37 a 42ºC e/ou quando o leite foi exposto a temperaturas oscilantes. Os resultados obtidos neste estudo parecem alertar para os métodos de conservação do leite, uma vez que o mesmo pode ser responsável por intoxicações alimentares causadas pela presença de S. aureus e suas enterotoxinas se não houver correta manipulação do produto, em todas as fases de produção.

Aplicação da técnica de REP – PCR no rastreamento de Staphylococcus aureus em sala de ordenha, para o monitoramento da qualidade do leite / Using the REP-PCR technic in the tracking of Staphylococcus aureus in milking room, for milk quality production

A identificação e classificação bacteriana são de suma importância no ambiente, na indústria, na medicina veterinária, na microbiologia e na ecologia microbiana. Um número de diferentes métodos genotípicos e fenotípicos estão sendo empregados para identificação e classificação microbiana. A técnica de REP-PCR é baseada no uso de primers sintetizados a partir de sequências repetidas de DNA, chamadas depalindrômicas extragênicas repetidas (REP), e têm sido descrita como um método o qual gera impressões digitais (fingerprints) de DNA que podem diferenciar bactérias entre gêneros e espécies. Neste estudo, o método de fingerprint foi usado para Staphylococcus aureus com o objetivo de avaliar a higiene de ordenha em duas fazendas leiteiras.Foram obtidos vários fingerprints de todos os isolados coletados das diferentes fontes estudadas (mãos de ordenhadores, tetos das vacas,leite e ordenhadeira), e foram obtidos comportamentos muito similares das bandas indicando que os isolados podem ser relatados como clones epidemiológicos. Em nosso estudo, a técnica mostrou ser eficiente para a análise da similaridade entre indivíduos da mesma espécie, no caso, o Staphylococcus aureus, mostrando ser uma ferramenta útil para investigação de falhas no manejo e, em um controle mais eficiente para evitar e/ou diminuir a disseminação de microrganismos causadores de sérias enfermidades em humanos e em animais, que podem ser transmitidas através de produtos como o leite e seus derivados.

The identification and classification of bacteria are of crucial importance in environmental, industrial, veterinary, microbiology and microbial ecology. A number of different phenotypic and genotypic methods are presently being employed for microbial identification and classification. Repetitive-element PCR (Rep-PCR) with primers basedon repetitive extragenic palindromic (REP) repeated DNA sequencesis a recently described method which generates DNA fingerprints that descriminate between bacterial species and strains. In this study, this method was used for genomic fingerprinting of Staphylococcus aureus in control of hygiene in milk line production on two farms. Complex fingerprinting patterns were obtained for all isolates from different sources (milking handlers, cows teats, milk and milk machine) were very similar, and the data indicated that the isolated were closely related.In our study, this technic shows to be usefull for investigation in fails on milk line production and for more efficient control for patogenic microrganisms that cause serious illness in humans and animals.