Authors: Yinzhao Wang, Giorgio Casaburi, Wei Lin...

BACKGROUND

Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive.

RESULTS

We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages.

CONCLUSION

Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.

Topics: Bacterial Proteins; Biological Evolution; Genome, Bacterial; Genomics; Light; Magnetosomes; Phylogeny; Rhodospirillaceae

PubMed: 31117953
DOI: 10.1186/s12864-019-5751-9

Authors: Wenjing Xu, Zhi Chen, Lei Chen...

As a class of multifunctional biocatalysts, halohydrin dehalogenases are of great interest for the synthesis of chiral β-substituted alcohols and epoxides. There are less than 40 halohydrin dehalogenases with relatively clear catalytic functions, and most of them do not meet the requirements of scientific research and practical applications. Therefore, it is of great significance to excavate and identify more halohydrin dehalogenases. In the present study, a putative halohydrin dehalogenase (HHDH-Ra) from Rhodospirillaceae bacterium was expressed and its enzymatic properties were investigated. The HHDH-Ra gene was cloned into the expression host Escherichia coli BL21(DE3) and the target protein was shown to be soluble. Substrate specificity studies showed that HHDH-Ra possesses excellent specificity for 1,3-dichloro-2-propanol (1,3-DCP) and ethyl-4-chloro-3-hydroxybutyrate (CHBE). The optimum pH and temperature for HHDH-Ra with 1,3-DCP as the reaction substrate were 8.0 and 30 °C, respectively. HHDH-Ra was stable at pH 6.0-8.0 and maintained about 70% of its original activity after 100 h of treatment. The thermal stability results revealed that HHDH-Ra has a half-life of 60 h at 30 °C and 40 °C. When the temperature is increased to 50 °C, the enzyme still has a half-life of 20 h, which is much higher than that of the reported enzymes. To sum up, the novel halohydrin dehalogenase from Rhodospirillaceae bacterium possesses good temperature and pH stability as well as catalytic activity, and shows the potential to be used in the synthesis of chemical and pharmaceutical intermediates.

Topics: Escherichia coli; Hydrolases; Rhodospirillaceae; Substrate Specificity

PubMed: 33973443
DOI: 10.13345/j.cjb.200719

Authors: Yoshiaki Kawamura, Nagatoshi Fujiwara, Takashi Naka...

The genus Enhydrobacter, first reported as a member of the family Vibrionaceae, has been placed in the family Moraxellaceae, but as a genus incertae sedis in Bergey's Manual of Systematic Bacteriology 2nd edition. During our taxonomic investigation of Enhydrobacter-like organisms, we observed that the 16S rRNA sequences of E. aerosaccus-type strain versions NCIMB 12535(T) , ATCC 27094( T) and CCUG 58314(T) were very different from the accessible data (accession no. AJ550856). Phylogenetic analysis of our 16S rRNA sequence data revealed that these organisms were located within the family Rhodospirillaceae. The genera Inquilinus, Oceanibaculum, Skermanella and Nisaea were closely related (sequence similarities were 88.3~87.0%), but Enhydrobacter could be distinguished from these genera by growth characteristics, fatty acid profiles (C(19:0) cyclo ω8c; 38.4% C(18:1) ω7c; 32.2%, and C(16:0) ; 8.9% were major components), in being non-flagellated, and differing in enzymatic activities, including trypsin and β-glucosidase. From these data, we conclude that the genus Enhydrobacter should be recognized as an independent genus of the family Rhodospirillaceae within the class Alphaproteobacteria.

Topics: Alphaproteobacteria; Bacterial Typing Techniques; Enzyme Activation; Fatty Acids; Genes, rRNA; Moraxellaceae; Phenotype; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Rhodospirillaceae; Sequence Alignment; Species Specificity; Trypsin; beta-Glucosidase

PubMed: 22145860
DOI: 10.1111/j.1348-0421.2011.00401.x

Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to , Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism.

Authors: S Dubey, T E Meyer, J A Kyndt...

was reported to be a divergent member of the purple photosynthetic bacteria with limited ability to metabolize organic compounds. Whole-genome-based analysis shows that it is indeed only distantly related to freshwater species of Unexpectedly, the genome contains unique gene clusters for potential respiratory nitrate reduction and anaerobic glycerol metabolism.

PubMed: 33273003
DOI: 10.1128/MRA.01200-20

Authors: Hira Saleem, Qurat Ul Ain Kokab, Yasir Rehman...

Two arsenic-resistant purple non-sulphur bacteria (PNSB), Q3B and Q3C, were isolated (from industrial contaminated site and paddy fields) and identified by SSU rRNA gene sequencing as Rhodospirillum and Rhodospirillaceae species, respectively. Maximum arsenic reduction by these PNSB was observed in anaerobic conditions. Rhodospirillum sp. Q3B showed 74.92% (v/v) arsenic reduction while Rhodospirillaceae sp. Q3C reduced arsenic up to 76.67% (v/v) in anaerobic conditions. Rhodospirillaceae sp. Q3C was found to contain highest carotenoid content up to 5.6mg·g. Under anaerobic conditions, the isolates were able to respire arsenic in the presence of lactate, citrate, and oxalate. Rhodospirillum sp. Q3B and Rhodospirillaceae sp. Q3C were also found to produce hydrogen gas. Such diverse bacteria can be useful tools for bioremediation purposes. These bacteria can be further exploited and optimized to treat wastewater containing arsenic along with bio-hydrogen production.

Topics: Arsenic; Bacteria; Biodegradation, Environmental; Rhodospirillaceae; Waste Water

PubMed: 30905576
DOI: 10.1016/j.crvi.2019.02.001

Authors: A Marchese, L Santoriello, G Riccio...

Topics: Aged; Anti-Bacterial Agents; Bacteriological Techniques; Gram-Negative Bacterial Infections; Humans; Male; Mastoiditis; Molecular Diagnostic Techniques; RNA, Ribosomal, 16S; Rhodospirillaceae; Seawater; Treatment Outcome

PubMed: 31170455
DOI: 10.1016/j.cmi.2019.05.023

Authors: Juanjuan Guo, Longtao Zhang, Xu Lu...

Effective degradation of κ-carrageenan by isolated sp. fjfst-332 is reported for the first time in this paper. It was identified by 16S rDNA sequencing and morphological observation using Transmission Electron Microscopy (TEM). Based on a Plackett-Burman design for significant variables, Box-Behnken experimental design and response surface methodology were used to optimize the culture conditions. Through statistical optimization, the optimum medium components were determined as follows: 2.0 g/L κ-carrageenan, 1.0 g/L yeast extract, 1.0 g/L FOS, 20.0 g/L NaCl, 2.0 g/L NaNO₃, 0.5 g/L MgSO₄·7H₂O, 0.1 g/L K₂HPO₄, and 0.1 g/L CaCl₂. The highest activity exhibited by sp. fjfst-332 was 267 U/mL, which makes it the most vigorous wild bacterium for κ-carrageenan production. In order to guide scaled-up production, two empirical models-the logistic equation and Luedeking-Piretequation-were proposed to predict the strain growth and enzyme production, respectively. Furthermore, we report the fermentation kinetics and every empirical equation of the coefficients (α, β, ₀, and μ) for the two models, which could be used to design and optimize industrial processes.

Topics: Bacterial Proteins; Carrageenan; Culture Media; DNA, Bacterial; DNA, Ribosomal; Fermentation; Glycoside Hydrolases; Kinetics; Logistic Models; Microscopy, Electron, Transmission; Models, Chemical; RNA, Ribosomal, 16S; Rhodospirillaceae; Sequence Analysis, DNA

PubMed: 27827964
DOI: 10.3390/molecules21111479

Authors: Sang Taek Heo, Ki Tae Kwon, Jeong Rae Yoo...

Topics: Aged; Anti-Bacterial Agents; Diagnosis, Differential; Fasciitis, Necrotizing; Gram-Negative Bacterial Infections; Humans; Male; Phylogeny; RNA, Ribosomal, 16S; Rhodospirillaceae; Sepsis; Sequence Analysis, DNA

PubMed: 30027706
DOI: 10.3343/alm.2018.38.6.604

Authors: Gregory Hovan, Andrew Hollinger

A clinical case study involving a man (35-49 years of age) with wounds to his lower right extremity. An isolate was sent to the Delaware Public Health Laboratory for confirmatory testing by genetic analysis of the 16S gene. Testing identified the isolate as a novel genus and species, Haematospirillum jordaniae.

Topics: Adult; Anti-Bacterial Agents; Bacteriological Techniques; Gram-Negative Bacterial Infections; Humans; Male; Middle Aged; RNA, Ribosomal, 16S; Rhodospirillaceae; Treatment Outcome; Wound Infection

PubMed: 30226180
DOI: 10.3201/eid2410.180548

Comparative Study

Authors: Nanako Kanno, Katsumi Matsuura, Shin Haruta...

Survivability under carbon-starvation conditions was investigated in four species of purple phototrophic bacteria: Rhodopseudomonas palustris, Rhodobacter sphaeroides, Rhodospirillum rubrum, and Rubrivivax gelatinosus. All these test organisms survived longer in the light than in the dark. ATP levels in the cultures were maintained in the light, which indicated that survivability was supported by photosynthesis. Survivability and tolerance against hypertonic stress in the dark was higher in Rhodopseudomonas palustris, which is widely distributed in natural environments including soils, than in the three other species.

Topics: Light; Microbial Viability; Photosynthesis; Rhodospirillaceae; Species Specificity

PubMed: 24941957
DOI: 10.1264/jsme2.me14013