Metabolic and physiological adaptations of microalgal growth-promoting bacterium Azospirillum brasilense growing under biogas atmosphere: a microarray-based transcriptome analysis

Using microalgal growth-promoting bacteria (MGPB) to improve the cultured microalga metabolism during biotechnological processes is one of the most promising strategies to enhance their benefits. Nonetheless, the culture condition effect used during the biotechnological process on MGPB growth and metabolism is key to ensure the expected positive bacterium growth and metabolism of microalgae. In this sense, the present research study investigated the effect of the synthetic biogas atmosphere (75% CH4-25% CO2) on metabolic and physiological adaptations of the MGPB Azospirillum brasilense by a microarray-based transcriptome approach. A total of 394 A. brasilense differentially expressed genes (DEGs) were found: 201 DEGs (34 upregulated and 167 downregulated) at 24 h and 193 DEGs (140 upregulated and 53 downregulated) under the same conditions at 72 h. The results showed a series of A. brasilense genes regulating processes that could be essential for its adaptation to the early stressful condition generated by biogas. Evidence of energy production is shown by nitrate/nitrite reduction and activation of the hypothetical first steps of hydrogenotrophic methanogenesis; signal molecule modulation is observed: indole-3-acetic acid (IAA), riboflavin, and vitamin B6, activation of Type VI secretion system responding to IAA exposure, as well as polyhydroxybutyrate (PHB) biosynthesis and accumulation. Moreover, an overexpression of ipdC, ribB, and phaC genes, encoding the key enzymes for the production of the signal molecule IAA, vitamin riboflavin, and PHB production of 2, 1.5 and 11 folds, respectively, was observed at the first 24 h of incubation under biogas atmosphere Overall, the ability of A. brasilense to metabolically adapt to a biogas atmosphere is demonstrated, which allows its implementation for generating biogas with high calorific values and the use of renewable energies through microalga biotechnologies.

Effect of the oil from the fatty tissues of Crocodylus siamensis on gut microbiome diversity and metabolism in mice

Dietary fat can alter host metabolism and gut microbial composition. Crocodile oil (CO) was extracted from the fatty tissues of Crocodylus siamensis. CO, rich in monounsaturated- and polyunsaturated fatty acids, has been reported to reduce inflammation, counter toxification, and improve energy metabolism. The aim of this study was to investigate the effect of CO on gut microbiota (GM) in laboratory mice as well as the accompanying metabolic changes in the animals. Forty-five C57BL/6 male mice were randomly divided into five groups and orally administrated either sterile water (control [C]); 1 or 3% (v/w) CO (CO-low [CO-L] and CO-high [CO-H], respectively); or 1 or 3% (v/w) palm oil (PO-low and PO-high, respectively) for 11 weeks. Body weight gain, food intake, energy intake, blood glucose levels, and blood lipid profiles were determined. Samples from colon tissue were collected and the 16S rRNA genes were pyrosequenced to clarify GM analyses. The results showed that there were no differences in body weight and blood glucose levels. Food intake by the mice in the CO-L and CO-H groups was statistically significantly less when compared to that by the animals in the C group. However, neither CO treatment had a statistically significant effect on calorie intake when compared to the controls. The CO-H exhibited a significant increase in serum total cholesterol and low-density lipoprotein but showed a downward trend in triglyceride levels compared to the control. The GM analyses revealed that both CO treatments have no significant influence on bacterial diversity and relative abundance at the phylum level, whereas increases of Choa1 and abundance-based coverage estimator indexes, distinct β-diversity, and Proteobacteria abundance were observed in the PO-high group compared with the C group. Furthermore, the abundance of Azospirillum thiophilum and Romboutsia ilealis was significantly higher in the CO-L and CO-H groups which could be associated with energy metabolic activity. Thus, CO may be an alternative fat source for preserving host metabolism and gut flora.

Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.

Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats

Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N₂. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N₂ fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.

Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST

Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy involves direct oxidation of thiosulfate (S₂O₃^2-) to sulfate (SO₄^2-) without any free intermediate. This pathway mediated by SoxXAYZBCD is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate(S₄O₆^2-)-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process of Paracoccus pantotrophus. Our results reveal a unique case where an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation converting ∼10% of the thiosulfate supplied, whilst ∼90% of the substrate is oxidized via a pathway that produces tetrathionate as an intermediate. Sulfur oxidation kinetics of a deletion mutant showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which in turn is also less efficient than the P. pantotrophus Sox. Deletion of soxB abolished sulfate-formation from thiosulfate/tetrathionate, while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the insertional mutation of a thiol dehydrotransferase (thdT) homolog, together with the absence of sulfite as an intermediate, indicated that SST tetrathionate oxidation is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. The present findings highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.

Azospirillum brasilense: Laboratory Maintenance and Genetic Manipulation

Bacteria of the genus Azospirillum, including the most comprehensively studied Azospirillum brasilense, are non-pathogenic soil bacteria that promote the growth of diverse plants, making them an attractive model to understand non-symbiotic, beneficial plant-bacteria associations. Research into the physiology and genetics of these organisms spans decades and a range of molecular tools and protocols have been developed for allelic exchange mutagenesis, in trans expression of genes, and fusions to reporter genes. © 2017 by John Wiley & Sons, Inc.