Phototrophic Bacteria 2.0

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 16092

Special Issue Editor


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Guest Editor
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
Interests: thermophilic; phototrophic bacteria; extreme environments; microbial ecology

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Phototrophic Bacteria

This Special Issue focuses on the functional group of phototrophic bacteria, including both anoxygenic and oxygenic forms. Research on these bacteria has greatly advanced our understanding of the basic principles that underlie the light capture and energy storage that takes place in all types of photosynthetic organisms, including both bacterial and eukaryotic forms. Types of papers that will be considered are original scientific research articles, comprehensive (mini)-reviews, comments, or perspectives. Topics of interest include but are not restricted to microbial physiology, microbial ecology, microbial genetics and genomics, evolutionary microbiology, systems microbiology, agricultural microbiology, microbial biotechnology, and environmental microbiology, all as related to phototrophic bacteria. All manuscripts will be peer-reviewed.

Dr. Vera Thiel
Guest Editor

Manuscript Submission Information

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Keywords

  • phototrophic bacteria
  • oxygenic photosynthesis
  • anoxygenic photosynthesis
  • light-harvesting
  • reaction center
  • chlorophyll
  • bacteriochlorophyll

Published Papers (10 papers)

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Research

Jump to: Review

10 pages, 1400 KiB  
Communication
Evaluation of Holmium(III), Erbium(III), and Gadolinium(III) Accumulation by Cyanobacteria Arthrospira platensis Using Neutron Activation Analysis and Elements’ Effects on Biomass Quantity and Biochemical Composition
by Inga Zinicovscaia, Liliana Cepoi, Ludmila Rudi, Tatiana Chiriac and Dmitrii Grozdov
Microorganisms 2024, 12(1), 122; https://doi.org/10.3390/microorganisms12010122 - 07 Jan 2024
Viewed by 923
Abstract
Rare-earth elements are released into the aquatic environment as a result of their extensive use in industry and agriculture, and they can be harmful for living organisms. The effects of holmium(III), erbium(III), and gadolinium(III) when added to a growth medium in concentrations ranging [...] Read more.
Rare-earth elements are released into the aquatic environment as a result of their extensive use in industry and agriculture, and they can be harmful for living organisms. The effects of holmium(III), erbium(III), and gadolinium(III) when added to a growth medium in concentrations ranging from 10 to 30 mg/L on the accumulation ability and biochemical composition of Arthrospira platensis were studied. According to the results of a neutron activation analysis, the uptake of elements by cyanobacteria occurred in a dose-dependent manner. The addition of gadolinium(III) to the growth medium did not significantly affect the amount of biomass, whereas erbium(III) and holmium(III) reduced it up to 22% compared to the control. The effects of rare-earth elements on the content of proteins, carbohydrates, phycobiliproteins, lipids, β carotene, and chlorophyll a were evaluated. The studied elements had different effects on the primary biomolecule content, suggesting that holmium(III) and erbium(III) were more toxic than Gd(III) for Arthrospira platensis. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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30 pages, 6087 KiB  
Article
Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities
by Donna L. Bedard, Greta Van Slyke, Ulrich Nübel, Mary M. Bateson, Sue Brumfield, Yong Jun An, Eric D. Becraft, Jason M. Wood, Vera Thiel and David M. Ward
Microorganisms 2023, 11(12), 2921; https://doi.org/10.3390/microorganisms11122921 - 04 Dec 2023
Viewed by 1423
Abstract
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) [...] Read more.
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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18 pages, 4065 KiB  
Article
Loss of Biliverdin Reductase Increases Oxidative Stress in the Cyanobacterium Synechococcus sp. PCC 7002
by Wendy M. Schluchter, Courtney H. Babin, Xindi Liu, Amori Bieller, Gaozhong Shen, Richard M. Alvey and Donald A. Bryant
Microorganisms 2023, 11(10), 2593; https://doi.org/10.3390/microorganisms11102593 - 20 Oct 2023
Viewed by 1286
Abstract
Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread [...] Read more.
Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread in mammals but is also found in many cyanobacteria. We show that a previously described bvdR mutant of Synechocystis sp. PCC 6803 contained a secondary deletion mutation in the cpcB gene. The bvdR gene from Synechococcus sp. PCC 7002 was expressed in Escherichia coli, and recombinant BvdR was purified and shown to reduce biliverdin to bilirubin. The bvdR gene was successfully inactivated in Synechococcus sp. PCC 7002, a strain that is naturally much more tolerant of high light and ROS than Synechocystis sp. PCC 6803. The bvdR mutant strain, BR2, had lower total phycobiliprotein and chlorophyll levels than wild-type cells. As determined using whole-cell fluorescence at 77 K, the photosystem I levels were also lower than those in wild-type cells. The BR2 mutant had significantly higher ROS levels compared to wild-type cells after exposure to high light for 30 min. Together, these results suggest that bilirubin plays an important role as a scavenger for ROS in Synechococcus sp. PCC 7002. The oxidation of bilirubin by ROS could convert bilirubin to biliverdin IXα, and thus BvdR might be important for regenerating bilirubin. These results further suggest that BvdR is a key component of a scavenging cycle by which cyanobacteria protect themselves from the toxic ROS byproducts generated during oxygenic photosynthesis. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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20 pages, 2265 KiB  
Article
Thiorhodovibrio frisius and Trv. litoralis spp. nov., Two Novel Members from a Clade of Fastidious Purple Sulfur Bacteria That Exhibit Unique Red-Shifted Light-Harvesting Capabilities
by Anika Methner, Steven B. Kuzyk, Jörn Petersen, Sabine Bauer, Henner Brinkmann, Katja Sichau, Gerhard Wanner, Jacqueline Wolf, Meina Neumann-Schaal, Petra Henke, Marcus Tank, Cathrin Spröer, Boyke Bunk and Jörg Overmann
Microorganisms 2023, 11(10), 2394; https://doi.org/10.3390/microorganisms11102394 - 25 Sep 2023
Cited by 3 | Viewed by 1097
Abstract
In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption [...] Read more.
In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963–966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800–870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777T) as Thiorhodovibrio frisius sp. nov. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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18 pages, 15511 KiB  
Article
Modeling the Characteristic Residues of Chlorophyll f Synthase (ChlF) from Halomicronema hongdechloris to Determine Its Reaction Mechanism
by Min Chen, Artur Sawicki and Fanyue Wang
Microorganisms 2023, 11(9), 2305; https://doi.org/10.3390/microorganisms11092305 - 13 Sep 2023
Viewed by 819
Abstract
Photosystem II (PSII) is a quinone-utilizing photosynthetic system that converts light energy into chemical energy and catalyzes water splitting. PsbA (D1) and PsbD (D2) are the core subunits of the reaction center that provide most of the ligands to redox-active cofactors and exhibit [...] Read more.
Photosystem II (PSII) is a quinone-utilizing photosynthetic system that converts light energy into chemical energy and catalyzes water splitting. PsbA (D1) and PsbD (D2) are the core subunits of the reaction center that provide most of the ligands to redox-active cofactors and exhibit photooxidoreductase activities that convert quinone and water into quinol and dioxygen. The performed analysis explored the putative uncoupled electron transfer pathways surrounding P680+ induced by far-red light (FRL) based on photosystem II (PSII) complexes containing substituted D1 subunits in Halomicronema hongdechloris. Chlorophyll f-synthase (ChlF) is a D1 protein paralog. Modeling PSII-ChlF complexes determined several key protein motifs of ChlF. The PSII complexes included a dysfunctional Mn4CaO5 cluster where ChlF replaced the D1 protein. We propose the mechanism of chlorophyll f synthesis from chlorophyll a via free radical chemistry in an oxygenated environment created by over-excited pheophytin a and an inactive water splitting reaction owing to an uncoupled Mn4CaO5 cluster in PSII-ChlF complexes. The role of ChlF in the formation of an inactive PSII reaction center is under debate, and putative mechanisms of chlorophyll f biosynthesis are discussed. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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13 pages, 2451 KiB  
Article
Fluorescence Microscopy Study of the Intracellular Sulfur Globule Protein SgpD in the Purple Sulfur Bacterium Allochromatium vinosum
by Carolin Kümpel, Fabian Grein and Christiane Dahl
Microorganisms 2023, 11(7), 1792; https://doi.org/10.3390/microorganisms11071792 - 12 Jul 2023
Cited by 1 | Viewed by 1133
Abstract
When oxidizing reduced sulfur compounds, the phototrophic sulfur bacterium Allochromatium vinosum forms spectacular sulfur globules as obligatory intracellular–but extracytoplasmic–intermediates. The globule envelope consists of three extremely hydrophobic proteins: SgpA and SgpB, which are very similar and can functionally replace each other, and SgpC [...] Read more.
When oxidizing reduced sulfur compounds, the phototrophic sulfur bacterium Allochromatium vinosum forms spectacular sulfur globules as obligatory intracellular–but extracytoplasmic–intermediates. The globule envelope consists of three extremely hydrophobic proteins: SgpA and SgpB, which are very similar and can functionally replace each other, and SgpC which is involved in the expansion of the sulfur globules. The presence of a fourth protein, SgpD, was suggested by comparative transcriptomics and proteomics of purified sulfur globules. Here, we investigated the in vivo function of SgpD by coupling its carboxy-terminus to mCherry. This fluorescent protein requires oxygen for chromophore maturation, but we were able to use it in anaerobically growing A. vinosum provided the cells were exposed to oxygen for one hour prior to imaging. While mCherry lacking a signal peptide resulted in low fluorescence evenly distributed throughout the cell, fusion with SgpD carrying its original Sec-dependent signal peptide targeted mCherry to the periplasm and co-localized it exactly with the highly light-refractive sulfur deposits seen in sulfide-fed A. vinosum cells. Insertional inactivation of the sgpD gene showed that the protein is not essential for the formation and degradation of sulfur globules. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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12 pages, 4516 KiB  
Article
Ectothiorhodospira lacustris sp. nov., a New Purple Sulfur Bacterium from Low-Mineralized Soda Lakes That Contains a Unique Pathway for Nitric Oxide Reduction
by Irina A. Bryantseva, John A. Kyndt, Vladimir M. Gorlenko and Johannes F. Imhoff
Microorganisms 2023, 11(5), 1336; https://doi.org/10.3390/microorganisms11051336 - 19 May 2023
Cited by 2 | Viewed by 1600
Abstract
Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the [...] Read more.
Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the major photosynthetic pigment. The strains were found to grow at 25–35 °C, pH 7.5–10.2 (optimum, pH 9.0), and with 0–8% (w/v) NaCl (optimum, 0%). In the presence of sulfide and bicarbonate, acetate, butyrate, yeast extract, lactate, malate, pyruvate, succinate, and fumarate promoted growth. The DNA G + C content was 62.9–63.0 mol%. While the 16S rRNA gene sequences confirmed that the new strains belonged to the genus Ectothiorhodospira of the Ectothiorhodospiraceae, comparison of the genome nucleotide sequences of strains B14B, A-7R, and A-7Y revealed that the new isolates were remote from all described Ectothiorhodospira species both in dDDH (19.7–38.8%) and in ANI (75.0–89.4%). The new strains are also genetically differentiated by the presence of a nitric oxide reduction pathway that is lacking from all other Ectiothiorhodospiraceae. We propose to assign the isolates to the new species, Ectothiorhodospira lacustris sp. nov., with the type strain B14BT (=DSM 116064T = KCTC 25542T = UQM 41491T). Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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15 pages, 3025 KiB  
Article
The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica
by Sahana Shivaramu, Jürgen Tomasch, Karel Kopejtka, Nupur, Mohit Kumar Saini, Syed Nadeem Hussain Bokhari, Hendrik Küpper and Michal Koblížek
Microorganisms 2023, 11(1), 27; https://doi.org/10.3390/microorganisms11010027 - 22 Dec 2022
Cited by 2 | Viewed by 2389
Abstract
The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, [...] Read more.
The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L−1. When grown at a lower concentration of calcium (2 mg CaCl2 L−1) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L−1 to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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15 pages, 2167 KiB  
Article
Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)
by Christine E. Humphrey, Nicole Burnett, Shivangi Dubey and John A. Kyndt
Microorganisms 2022, 10(10), 2024; https://doi.org/10.3390/microorganisms10102024 - 13 Oct 2022
Viewed by 1771
Abstract
The genus Rhodopseudomonas is known for its versatile metabolic capabilities and has been proposed to be used in a wide variety of innovative applications, ranging from biohydrogen and electricity production, bioremediation and as biostimulant in agriculture. Here, we report the isolation, characterization and [...] Read more.
The genus Rhodopseudomonas is known for its versatile metabolic capabilities and has been proposed to be used in a wide variety of innovative applications, ranging from biohydrogen and electricity production, bioremediation and as biostimulant in agriculture. Here, we report the isolation, characterization and genome sequence analysis of a novel Rhodopseudomonas species, strain HC1, isolated from the Hell Creek urban native restoration area. Whole genome-based analysis, average nucleotide identity (ANI) comparison, and growth characteristics identified this isolate as a new species of the Rhodopseudomonas genus, for which we propose the name Rhodopseudomonas infernalis sp. nov. Besides containing several nitrogenases for nitrogen fixation and hydrogen production, the HC1 genome encodes a unique gene cluster, not found in any other Rhodopseudomonas species, which encodes genes for the degradation of yet-unidentified aromatic PCB-type chemicals with potentially interesting biotechnological applications. The genomic features of Rps. infernalis HC1 indicate that it plays a positive role in the degradation of anthropogenic substances and aids the restoration of the Hell Creek watershed by contributing to N2 and carbon fixation and plant growth; however, the genome also contains several antibiotic resistance genes, indicating a broad range of antibiotic resistance in this environmental isolate. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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Review

Jump to: Research

35 pages, 1108 KiB  
Review
Co-Occurrence of Taste and Odor Compounds and Cyanotoxins in Cyanobacterial Blooms: Emerging Risks to Human Health?
by Maura Manganelli, Emanuela Testai, Zakaria Tazart, Simona Scardala and Geoffrey A. Codd
Microorganisms 2023, 11(4), 872; https://doi.org/10.3390/microorganisms11040872 - 28 Mar 2023
Cited by 6 | Viewed by 2281
Abstract
Cyanobacteria commonly form large blooms in waterbodies; they can produce cyanotoxins, with toxic effects on humans and animals, and volatile compounds, causing bad tastes and odors (T&O) at naturally occurring low concentrations. Notwithstanding the large amount of literature on either cyanotoxins or T&O, [...] Read more.
Cyanobacteria commonly form large blooms in waterbodies; they can produce cyanotoxins, with toxic effects on humans and animals, and volatile compounds, causing bad tastes and odors (T&O) at naturally occurring low concentrations. Notwithstanding the large amount of literature on either cyanotoxins or T&O, no review has focused on them at the same time. The present review critically evaluates the recent literature on cyanotoxins and T&O compounds (geosmin, 2-methylisoborneol, β-ionone and β-cyclocitral) to identify research gaps on harmful exposure of humans and animals to both metabolite classes. T&O and cyanotoxins production can be due to the same or common to different cyanobacterial species/strains, with the additional possibility of T&O production by non-cyanobacterial species. The few environmental studies on the co-occurrence of these two groups of metabolites are not sufficient to understand if and how they can co-vary, or influence each other, perhaps stimulating cyanotoxin production. Therefore, T&Os cannot reliably serve as early warning surrogates for cyanotoxins. The scarce data on T&O toxicity seem to indicate a low health risk (but the inhalation of β-cyclocitral deserves more study). However, no data are available on the effects of combined exposure to mixtures of cyanotoxins and T&O compounds and to combinations of T&O compounds; therefore, whether the co-occurrence of cyanotoxins and T&O compounds is a health issue remains an open question. Full article
(This article belongs to the Special Issue Phototrophic Bacteria 2.0)
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