First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina

We report here on a high-quality draft genome sequence of Ochrobactrum haematophilum strain P6BS-III (DSM 106071), a Gram negative, non-sporulating bacterium isolated from a pastureland (Buenos Aires province, Argentina) which had been chronically exposed to the herbicide glyphosate. The genome of 5.25 Mb with a DNA G+C content of 56.63% size was estimated to contain 5,291 protein coding genes and 57 RNA genes. Genome analysis revealed the presence of the phn operon, which is involved in the phosphonate degradation pathway, and a class II 5-enolpyruvylshikimate-3-phosphate synthase (EPSP) that confers tolerance to glyphosate. Genes related to plant growth promotion traits are also present, and include genes for phosphorus metabolism, calcium phosphate and phytate solubilization, siderophore production, organic acid biosynthesis and indole acetic acid (IAA) production.Fil: Massot, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina. Hasselt University; BélgicaFil: Gkorezis, Panagiotis. Hasselt University; BélgicaFil: McAmmond, Breanne. Thompson Rivers University; CanadáFil: d´Haen, Jan. Hasselt University; BélgicaFil: Van Hamme, Jonathan. Thompson Rivers University; CanadáFil: Merini, Luciano Jose. Instituto Nacional de Tecnología Agropecuaria. Centro Regional La Pampa-San Luis. Estación Experimental Agropecuaria Anguil; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vangronsveld, Jaco. Hasselt University; BélgicaFil: Thijs, Sofie. Hasselt University; Bélgic

Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland)

Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up

Exploring the relationship between bacterial genera and lipid metabolism in bovine rumen

The rumen is characterised by a complex microbial ecosystem, which is particularly active in lipid metabolism. Several studies demonstrated a role of diet and breed on bacterial community profile, with the effect on metabolic pathways. Despite the knowledge achieved on metabolism and the bacterial profile, little is known about the relationship between individual bacteria and metabolic pathways. Therefore, a multivariate approach was used to search for possible relationships between bacteria and products of several pathways. The correlation between rumen bacterial community composition and rumen lipid metabolism was assessed in 40 beef steers (20 Maremmana and 20 Aubrac) reared with the same system and fed the same diet. A canonical discriminant analysis combined with a canonical correlation analysis (CCA) was performed to explore this correlation. The variables showing a Pearson correlation higher than 0.6 as absolute value and significant were retained for CCA considering the relationship of bacterial composition with several metabolic pathways. The results indicated that some bacterial genera could have significant impacts on the presence of several fatty acids. However, the relationship between genera and fatty acid changes according to the breed, demonstrating that the metabolic pathways change according to the host genetic background, related to breed evolution, although there is also an intra-breed genetic background which should not be ignored. In Maremmana, Succiniclasticum and Rikenellaceae_RC9_gut_group showed a high positive correlation with dimethylacetals (DMAs) DMAC13:0, DMAC14:0, DMAC14:0iso, DMAC15:0, DMAC15:0iso, and DMAC18:0. Prevotellaceae_UCG-003 correlates with C18:3c9c12c15 and C18:1t11, while Fibrobacter and Succiniclasticum correlate with C18:2c9t11 and Lachnospiraceae_NK3A20_group correlates with C18:1c12. Prevotellaceae_UCG-003, Ruminococcaceae_UCG-010, and Oribacterium showed a positive correlation with C13:0iso, and C17:0. Conversely, in Aubrac, Treponema_2 and Rikenellaceae_RC9_gut_group correlated with DMAC14:0iso, DMAC16:0iso, DMAC17:0iso, while Ruminococcaceae_UCG-010, Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group correlated with DMAC18:1t11, DMAC14:0, DMAC18:1c12. Acetitomaculum correlated with C18:2c9c12, C18:1c12, C18:1c13, C18:1t12 and Lachnospiraceae_NK3A20_group with C18:1t6-8 and C18:1t9. Saccharofermentas, Ruminococcaceae_UCG-010 and Rikenellaceae_RC9_gut_group correlated with C18:2c9t11 while, Prevotellaceae_UCG-001 and Ruminococcus_1 correlated with C14:0iso, C15:0, C15:0iso, C17:0. Saccharofermentans, Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Ruminococcaceae_UCG-010 correlated with C13:1c12 and C16:0iso. These results lead to hypothesise a possible association between several metabolic pathways and one or a few bacterial genera. If these associations are confirmed by further investigations that verify the causality of a bacterial genus with a particular metabolic process, it will be possible to deepen the knowledge on the activity of the rumen population in lipid metabolism. This approach appears to be a promising tool for uncovering the correlation between bacterial genera and products of rumen lipid metabolism

Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis