The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis.

The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.

Polyhydroxyalkanoates from organic waste streams using purple non-sulfur bacteria.

Many microorganisms can produce intracellular and extracellular biopolymers, such as polyhydroxyalkanoates (PHA). Despite PHA's benefits, their widespread at the industrial level has not occurred due mainly to high production costs. PHA production under a biorefinery scheme is proposed to improve its economic viability. In this context, purple non-sulfur bacteria (PNSB) are ideal candidates to produce PHA and other substances of economic interest. This review describes the PHA production by PNSB under different metabolic pathways, by using a wide range of wastes and under diverse operational conditions such as aerobic and anaerobic metabolism, irradiance level, light or dark conditions. Some strategies, such as controlling the feed regime, biofilm reactors, and open photobioreactors in outdoor conditions, were identified from the literature review as the approach needed to improve the process's economic viability when using mixed cultures of PNSB and wastes as substrates.

Effect of volatile fatty acids mixtures on the simultaneous photofermentative production of hydrogen and polyhydroxybutyrate.

Purple non-sulfur bacteria generate hydrogen and polyhydroxybutyrate (PHB) as a mechanism for disposing of reducing equivalents generated during substrate consumption. However, both pathways compete for the reducing equivalents released from bacteria growing under certain substrates, thus the formation of hydrogen or PHB is detrimental to the formation of each other. The effect of mixtures of acetic, propionic and butyric acids on the formation of H2 and PHB was evaluated using Box-Behnken design. A bacterial community mainly constituted by Rhodopseudomonas palustris was used as inoculum. It was observed that the three volatile fatty acids had a significant effect on the specific PHB production. However, only the propionic acid had a significant effect on the specific H2 production activity and the highest value was observed when acetate was the main component in the mixture. The maximum values for the specific PHB and hydrogen production rates were 16.4 mg-PHB/g-TSS/day and 391 mL-H2/g-TSS/day, respectively.

How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a "Candidatus Marithrix sp." Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico.

"Candidatus Marithrix" is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This genus of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, "Candidatus Marithrix" was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the "Candidatus Marithrix" genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98 and 100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes-the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or "intrasegmental sequence heterogeneity" (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

Photo-fermentational hydrogen production of Rhodobacter sp. KKU-PS1 isolated from an UASB reactor

Background In this study, the detection of nifH and nifD by a polymerase chain reaction assay was used to screen the potential photosynthetic bacteria capable of producing hydrogen from five different environmental sources. Efficiency of photo-hydrogen production is highly dependent on the culture conditions. Initial pH, temperature and illumination intensity were optimized for maximal hydrogen production using response surface methodology with central composite design. Results Rhodobacter sp. KKU-PS1 (GenBank Accession No. KC478552) was isolated from the methane fermentation broth of an UASB reactor. Malic acid was the favored carbon source while Na-glutamate was the best nitrogen source. The optimum conditions for simultaneously maximizing the cumulative hydrogen production (Hmax) and hydrogen production rate (Rm) from malic acid were an initial of pH 7.0, a temperature of 25.6°C, and an illumination intensity of 2500 lx. Hmax and Rm levels of 1264 ml H2/l and 6.8 ml H2/L-h were obtained, respectively. The optimum initial pH and temperature were further used to optimize the illumination intensity for hydrogen production. An illumination intensity of 7500 lx gave the highest values of Hmax (1339 ml H2/l) and Rm (12.0 ml H2/L-h) with a hydrogen yield and substrate conversion efficiency of 3.88 mol H2/mol malate and 64.7%, respectively. Conclusions KKU-PS1 can produce hydrogen from at least 8 types of organic acids. By optimizing pH and temperature, a maximal hydrogen production by this strain was obtained. Additionally, by optimizing the light intensity, Rm was increased by approximately two fold and the lag phase of hydrogen production was shortened.