Bacteria

From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.

@article{doi101126science1483667186,
    author = "Gray, Clarke T. and Gest, Howard",
    title = "Biological Formation of Molecular Hydrogen",
    year = "1965",
    journal = "Science",
    abstract = "From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.",
    url = "https://doi.org/10.1126/science.148.3667.186",
    doi = "10.1126/science.148.3667.186",
    openalex = "W1618573139",
    references = "doi101016000398616190073x"
}

Purple photosynthetic bacteria produce H2 from organic compounds by an anaerobic light-dependent electron transfer process in which nitrogenase functions as the terminal catalyst. It has been established that the H2-evolving function of nitrogenase is inhibited by N2 and ammonium salts, and is maximally expressed in cells growing photoheterotrophically with certain amino acids as sources of nitrogen. In the present studies with Rhodopseudomonas capsulata, nutritional factors affecting the rate and magnitude of H2 photoproduction in cultures growing with amino acid nitrogen sources were examined. The highest H2 yields and rates of formation were observed with the organic acids: lactate, pyruvate, malate, and succinate in media containing glutamate as the N source; under optimal conditions with excess lactate, H2 was produced at rates of ca. 130 ml/h per g(dry weight) of cells. Hydrogen production is significantly influenced by the N/C ratio in the growth substrates; when this ratio exceeds a critical value, free ammonia appears in the medium and H2 is not evolved. In the "standard" lactate + glutamate system, both H2 production and growth are "saturated" at a light intesity of ca. 600 ft-c (6,500 lux). Evolution of H2, however, occurs during growth at lithe intensities as low as 50 to 100 ft-c (540 to 1,080 lux), i.e., under conditions of energy limitation. In circumstances in which energy conversion rate and supplies of reducing power exceed the capacity of the biosynthetic machinery, energy-dependent H2 production presumably represents a regulatory device that facilitates "energy-idling." It appears that even when light intensity (energy) is limiting, a significant fraction of the available reducing power and adenosine 5'-triphosphate is diverted to nitrogenase, resulting in H2 formation and a bioenergetic burden to the cell.

@article{doi101128jb12927247311977,
    author = "Hillmer, P. and Gest, Howard",
    title = "H2 metabolism in the photosynthetic bacterium Rhodopseudomonas capsulata: H2 production by growing cultures",
    year = "1977",
    journal = "Journal of Bacteriology",
    abstract = {Purple photosynthetic bacteria produce H2 from organic compounds by an anaerobic light-dependent electron transfer process in which nitrogenase functions as the terminal catalyst. It has been established that the H2-evolving function of nitrogenase is inhibited by N2 and ammonium salts, and is maximally expressed in cells growing photoheterotrophically with certain amino acids as sources of nitrogen. In the present studies with Rhodopseudomonas capsulata, nutritional factors affecting the rate and magnitude of H2 photoproduction in cultures growing with amino acid nitrogen sources were examined. The highest H2 yields and rates of formation were observed with the organic acids: lactate, pyruvate, malate, and succinate in media containing glutamate as the N source; under optimal conditions with excess lactate, H2 was produced at rates of ca. 130 ml/h per g(dry weight) of cells. Hydrogen production is significantly influenced by the N/C ratio in the growth substrates; when this ratio exceeds a critical value, free ammonia appears in the medium and H2 is not evolved. In the "standard" lactate + glutamate system, both H2 production and growth are "saturated" at a light intesity of ca. 600 ft-c (6,500 lux). Evolution of H2, however, occurs during growth at lithe intensities as low as 50 to 100 ft-c (540 to 1,080 lux), i.e., under conditions of energy limitation. In circumstances in which energy conversion rate and supplies of reducing power exceed the capacity of the biosynthetic machinery, energy-dependent H2 production presumably represents a regulatory device that facilitates "energy-idling." It appears that even when light intensity (energy) is limiting, a significant fraction of the available reducing power and adenosine 5'-triphosphate is diverted to nitrogenase, resulting in H2 formation and a bioenergetic burden to the cell.},
    url = "https://doi.org/10.1128/jb.129.2.724-731.1977",
    doi = "10.1128/jb.129.2.724-731.1977",
    openalex = "W1566208906",
    references = "doi101007bf00447139, doi101007bf00447140, doi101016000398616190073x, doi101016b978012395630950058x, doi101016s0021925818565376, doi101073pnas713971, doi101126science1092840558, doi101128jb12927327391977, doi101128jb5822392451949, doi101128mmbr26151661962"
}

@article{baltscheffsky1981stepwise,
    author = "Baltscheffsky, Herrick",
    title = "Stepwise molecular evolution of bacterial photosynthetic energy conversion",
    year = "1981",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/0303-2647(81)90021-6",
    doi = "10.1016/0303-2647(81)90021-6",
    number = "1",
    openalex = "W1969033454",
    pages = "49-56",
    volume = "14",
    references = "doi101007bf00420631, doi101007bf00439699, doi1010160307441279900542, doi101038287248a0, doi101038289095a0, doi101111j143210331980tb04969x, doi101111j174966321957tb49665x, doi101126science15337401120, doi101126science6771870, doi101126science7466396"
}

@misc{baltscheffsky1981stepwise1,
    author = "Baltscheffsky, H",
    title = "Stepwise molecular evolution of bacterial photosynthetic energy conversion",
    year = "1981",
    howpublished = "BioSystems, v. 14, p. 49-56",
    note = "talkorigins\_source = {true}; raw\_reference = {Baltscheffsky, H., 1981, Stepwise molecular evolution of bacterial photosynthetic energy conversion: BioSystems, v. 14, p. 49-56.}"
}

@article{crossref1984gram,
    title = "Gram positive bacteria, Negative bacteria",
    year = "1984",
    journal = "NIPPON SHOKUHIN KOGYO GAKKAISHI",
    url = "https://doi.org/10.3136/nskkk1962.31.11\_759",
    doi = "10.3136/nskkk1962.31.11\_759",
    number = "11",
    pages = "759-760",
    volume = "31"
}

@incollection{babenzien1985bacteria,
    author = "Babenzien, H.-D. and Babenzien, Christina",
    title = "Bacteria",
    year = "1985",
    booktitle = "Monographiae Biologicae",
    url = "https://doi.org/10.1007/978-94-009-5506-6\_6",
    doi = "10.1007/978-94-009-5506-6\_6",
    pages = "197-211"
}

@article{cocchi1987bacteria,
    author = "Cocchi, Pietro",
    title = "BACTERIA VS. BACTERIA",
    year = "1987",
    journal = "The Pediatric Infectious Disease Journal",
    url = "https://doi.org/10.1097/00006454-198706000-00028",
    doi = "10.1097/00006454-198706000-00028",
    number = "6",
    pages = "583",
    volume = "6"
}

@article{doi101128mmbr5122212711987,
    author = "Woese, C R",
    title = "Bacterial evolution.",
    year = "1987",
    journal = "Microbiological Reviews",
    url = "https://doi.org/10.1128/mmbr.51.2.221-271.1987",
    doi = "10.1128/mmbr.51.2.221-271.1987",
    openalex = "W4246548745"
}

Article de synthese sur les methodes d'obtention de phylogenese a partir de sequences moleculaires, tests statistiques des phylogeneses et simulations sur ordinateur

@article{doi101146annurevge22120188002513,
    author = "Felsenstein, Joseph",
    title = "PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY",
    year = "1988",
    journal = "Annual Review of Genetics",
    abstract = "Article de synthese sur les methodes d'obtention de phylogenese a partir de sequences moleculaires, tests statistiques des phylogeneses et simulations sur ordinateur",
    url = "https://doi.org/10.1146/annurev.ge.22.120188.002513",
    doi = "10.1146/annurev.ge.22.120188.002513",
    openalex = "W2154284350"
}

@incollection{bailey1991bacteria,
    author = "Bailey, L. and Ball, B.V.",
    title = "BACTERIA",
    year = "1991",
    booktitle = "Honey Bee Pathology",
    url = "https://doi.org/10.1016/b978-0-12-073481-8.50008-4",
    doi = "10.1016/b978-0-12-073481-8.50008-4",
    pages = "35-52"
}

Perspective can be defined as the relationships or relative importance of facts or matters from any special point of view. Thus, my Personal perspective reflects the threads I followed in a 50-year journey of research in the complex tapestry of bioenergetics and various aspects of microbial metabolism. An early interest in biochemical and microbial evolution led to the fertile hunting grounds of anoxygenic photosynthetic bacteria. Viewed as a physiological class, these organisms show remarkable metabolic versatility in that certain individual species are capable of using all the known major types of energy conversion (photosynthetic, respiratory, and fermentative) to support growth. Since such anoxyphototrophs are readily amenable to molecular genetic/biological manipulation, it can be expected that they will eventually provide important clues for unraveling the evolutionary relationships of the several kinds of energy conversion. I gradually came to believe that understanding the evolution of phototrophs would require detailed knowledge not only of how light is converted to chemical energy, but also of a) pathways of monomer production from extracellular sources of carbon and nitrogen and b) mechanisms cells use for integrating ATP regeneration with the energy-requiring biosyntheses of biological macromolecules. Serendipic observation of photoproduction of H2 from organic compounds by Rhodospirillum rubrum in 1949 led to discovery of N2 fixation by anoxyphototrophs, and this capacity was later exploited for the isolation of hitherto unknown species of photosynthetic prokaryotes, including the heliobacteria. Recent studies on the reaction centers of the heliobacteria suggest the possibility that these bacteria are descendents of early phototrophs that gave rise to oxygenic photosynthetic organisms.

@article{doi101007bf00019331,
    author = "Gest, H",
    title = "A microbiologist's odyssey: Bacterial viruses to photosynthetic bacteria.",
    year = "1994",
    journal = "Photosynthesis research",
    abstract = "Perspective can be defined as the relationships or relative importance of facts or matters from any special point of view. Thus, my Personal perspective reflects the threads I followed in a 50-year journey of research in the complex tapestry of bioenergetics and various aspects of microbial metabolism. An early interest in biochemical and microbial evolution led to the fertile hunting grounds of anoxygenic photosynthetic bacteria. Viewed as a physiological class, these organisms show remarkable metabolic versatility in that certain individual species are capable of using all the known major types of energy conversion (photosynthetic, respiratory, and fermentative) to support growth. Since such anoxyphototrophs are readily amenable to molecular genetic/biological manipulation, it can be expected that they will eventually provide important clues for unraveling the evolutionary relationships of the several kinds of energy conversion. I gradually came to believe that understanding the evolution of phototrophs would require detailed knowledge not only of how light is converted to chemical energy, but also of a) pathways of monomer production from extracellular sources of carbon and nitrogen and b) mechanisms cells use for integrating ATP regeneration with the energy-requiring biosyntheses of biological macromolecules. Serendipic observation of photoproduction of H2 from organic compounds by Rhodospirillum rubrum in 1949 led to discovery of N2 fixation by anoxyphototrophs, and this capacity was later exploited for the isolation of hitherto unknown species of photosynthetic prokaryotes, including the heliobacteria. Recent studies on the reaction centers of the heliobacteria suggest the possibility that these bacteria are descendents of early phototrophs that gave rise to oxygenic photosynthetic organisms.",
    url = "https://pubmed.ncbi.nlm.nih.gov/24311283/",
    doi = "10.1007/BF00019331",
    openalex = "W1975871978",
    pmid = "24311283",
    references = "doi101007bf00032643, doi101007bf00039173, doi101007bf00415602, doi101007bf00447139, doi101016000398616190073x, doi101016s0021925818642103, doi101016s0021925818959569, doi101021bi00851a033, doi101073pnas713971, doi101128jb12927247311977"
}

The aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. Although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthetically under anaerobic conditions. Aerobic anoxygenic phototrophic bacteria are classified in two marine (Erythrobacter and Roseobacter) and six freshwater (Acidiphilium, Erythromicrobium, Erythromonas, Porphyrobacter, Roseococcus, and Sandaracinobacter) genera, which phylogenetically belong to the alpha-1, alpha-3, and alpha-4 subclasses of the class Proteobacteria. Despite this phylogenetic information, the evolution and ancestry of their photosynthetic properties are unclear. We discuss several current proposals for the evolutionary origin of aerobic phototrophic bacteria. The closest phylogenetic relatives of aerobic phototrophic bacteria include facultatively anaerobic purple nonsulfur phototrophic bacteria. Since these two bacterial groups share many properties, yet have significant differences, we compare and contrast their physiology, with an emphasis on morphology and photosynthetic and other metabolic processes.

@article{doi101128mmbr6236957241998,
    author = "Yurkov, Vladimir V. and Beatty, J. Thomas",
    title = "Aerobic Anoxygenic Phototrophic Bacteria",
    year = "1998",
    journal = "Microbiology and Molecular Biology Reviews",
    abstract = "The aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. Although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthetically under anaerobic conditions. Aerobic anoxygenic phototrophic bacteria are classified in two marine (Erythrobacter and Roseobacter) and six freshwater (Acidiphilium, Erythromicrobium, Erythromonas, Porphyrobacter, Roseococcus, and Sandaracinobacter) genera, which phylogenetically belong to the alpha-1, alpha-3, and alpha-4 subclasses of the class Proteobacteria. Despite this phylogenetic information, the evolution and ancestry of their photosynthetic properties are unclear. We discuss several current proposals for the evolutionary origin of aerobic phototrophic bacteria. The closest phylogenetic relatives of aerobic phototrophic bacteria include facultatively anaerobic purple nonsulfur phototrophic bacteria. Since these two bacterial groups share many properties, yet have significant differences, we compare and contrast their physiology, with an emphasis on morphology and photosynthetic and other metabolic processes.",
    url = "https://doi.org/10.1128/mmbr.62.3.695-724.1998",
    doi = "10.1128/mmbr.62.3.695-724.1998",
    openalex = "W2163539745",
    references = "doi101007bf00039173"
}

The origin and evolution of photosynthesis have long remained enigmatic due to a lack of sequence information of photosynthesis genes across the entire photosynthetic domain. To probe early evolutionary history of photosynthesis, we obtained new sequence information of a number of photosynthesis genes from the green sulfur bacterium Chlorobium tepidum and the green nonsulfur bacterium Chloroflexus aurantiacus. A total of 31 open reading frames that encode enzymes involved in bacteriochlorophyll/porphyrin biosynthesis, carotenoid biosynthesis, and photosynthetic electron transfer were identified in about 100 kilobase pairs of genomic sequence. Phylogenetic analyses of multiple magnesium-tetrapyrrole biosynthesis genes using a combination of distance, maximum parsimony, and maximum likelihood methods indicate that heliobacteria are closest to the last common ancestor of all oxygenic photosynthetic lineages and that green sulfur bacteria and green nonsulfur bacteria are each other's closest relatives. Parsimony and distance analyses further identify purple bacteria as the earliest emerging photosynthetic lineage. These results challenge previous conclusions based on 16S ribosomal RNA and Hsp60/Hsp70 analyses that green nonsulfur bacteria or heliobacteria are the earliest phototrophs. The overall consensus of our phylogenetic analysis, that bacteriochlorophyll biosynthesis evolved before chlorophyll biosynthesis, also argues against the long-held Granick hypothesis.

@article{doi101126science28954851724,
    author = "Xiong, Jin and Fischer, Will and Inoue, Kazuhito and Nakahara, Masaaki and Bauer, Carl E.",
    title = "Molecular Evidence for the Early Evolution of Photosynthesis",
    year = "2000",
    journal = "Science",
    abstract = "The origin and evolution of photosynthesis have long remained enigmatic due to a lack of sequence information of photosynthesis genes across the entire photosynthetic domain. To probe early evolutionary history of photosynthesis, we obtained new sequence information of a number of photosynthesis genes from the green sulfur bacterium Chlorobium tepidum and the green nonsulfur bacterium Chloroflexus aurantiacus. A total of 31 open reading frames that encode enzymes involved in bacteriochlorophyll/porphyrin biosynthesis, carotenoid biosynthesis, and photosynthetic electron transfer were identified in about 100 kilobase pairs of genomic sequence. Phylogenetic analyses of multiple magnesium-tetrapyrrole biosynthesis genes using a combination of distance, maximum parsimony, and maximum likelihood methods indicate that heliobacteria are closest to the last common ancestor of all oxygenic photosynthetic lineages and that green sulfur bacteria and green nonsulfur bacteria are each other's closest relatives. Parsimony and distance analyses further identify purple bacteria as the earliest emerging photosynthetic lineage. These results challenge previous conclusions based on 16S ribosomal RNA and Hsp60/Hsp70 analyses that green nonsulfur bacteria or heliobacteria are the earliest phototrophs. The overall consensus of our phylogenetic analysis, that bacteriochlorophyll biosynthesis evolved before chlorophyll biosynthesis, also argues against the long-held Granick hypothesis.",
    url = "https://doi.org/10.1126/science.289.5485.1724",
    doi = "10.1126/science.289.5485.1724",
    openalex = "W2092553727",
    references = "doi101007bf00039173"
}

1. Light and Energy. 2. Organization and Structure of Photosynthetic Systems. 3. History and Development of Photosynthesis. 4. Photosynthetic Pigments-Structure and Spectroscopy. 5. Antenna Complexes and Energy Transfer Processes. 6. Reaction Center Complexes. 7. Electron Transfer Pathways and Components. 8. Chemiosmotic Coupling and ATP Synthesis. 9. Carbon Metabolism. 10. Genetics, Assembly and Regulation of Photosynthetic. Systems. 11. Origin and Evolution of Photosynthesis. Appendix 1. Light, Energy and Kinetics

@book{doi1010029780470758472,
    author = "Blankenship, Robert E.",
    title = "Molecular Mechanisms of Photosynthesis",
    year = "2002",
    abstract = "1. Light and Energy. 2. Organization and Structure of Photosynthetic Systems. 3. History and Development of Photosynthesis. 4. Photosynthetic Pigments-Structure and Spectroscopy. 5. Antenna Complexes and Energy Transfer Processes. 6. Reaction Center Complexes. 7. Electron Transfer Pathways and Components. 8. Chemiosmotic Coupling and ATP Synthesis. 9. Carbon Metabolism. 10. Genetics, Assembly and Regulation of Photosynthetic. Systems. 11. Origin and Evolution of Photosynthesis. Appendix 1. Light, Energy and Kinetics",
    url = "https://doi.org/10.1002/9780470758472",
    doi = "10.1002/9780470758472",
    openalex = "W1531102271"
}

@incollection{crossref2008entomophagous,
    title = "Entomophagous Bacteria (entomopathogenic bacteria)",
    year = "2008",
    booktitle = "Encyclopedia of Genetics, Genomics, Proteomics and Informatics",
    url = "https://doi.org/10.1007/978-1-4020-6754-9\_5377",
    doi = "10.1007/978-1-4020-6754-9\_5377",
    pages = "612-612"
}

@article{crossref2012bacteria,
    title = "Bacteria beaten by bacteria",
    year = "2012",
    journal = "Nature",
    url = "https://doi.org/10.1038/491010c",
    doi = "10.1038/491010c",
    number = "7422",
    pages = "10-10",
    volume = "491"
}

Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization.

@article{doi101074jbcm111326447,
    author = "Faries, Kaitlyn M and Kressel, Lucas L and Wander, Marc J and Holten, Dewey and Laible, Philip D and Kirmaier, Christine and Hanson, Deborah K",
    title = "High throughput engineering to revitalize a vestigial electron transfer pathway in bacterial photosynthetic reaction centers.",
    year = "2012",
    journal = "The Journal of biological chemistry",
    abstract = "Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100\% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC3318735/",
    doi = "10.1074/jbc.M111.326447",
    openalex = "W2073629509",
    pmcid = "PMC3318735",
    pmid = "22247556",
    references = "doi1010079789401139533, doi101007bf00447139, doi1010160378111995005841, doi101016s0969212694000948, doi101038318618a0, doi101073pnas081078898, doi101073pnas84165730, doi101128mmbr6933733922005, doi101146annurevbiophys37032807125832"
}

Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.

@article{doi101073pnas1400295111,
    author = "Zeng, Yonghui and Feng, Fuying and Medová, Hana and Dean, Jason and Koblížek, Michal",
    title = "Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes",
    year = "2014",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.",
    url = "https://doi.org/10.1073/pnas.1400295111",
    doi = "10.1073/pnas.1400295111",
    openalex = "W2107679249",
    references = "doi101007bf00415602, doi101023bpres000003044824695ec, doi101073pnas713971"
}

In all photosynthetic organisms, chlorophylls function as light-absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen-sensitive dark-operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen-insensitive but light-dependent PORs (LPORs). Based on this observation it was suggested that light-dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α-proteobacterium Dinoroseobacter shibae DFL12(T). In vitro and in vivo functional assays unequivocally prove light-dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence-based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light-dependent enzyme of D. shibae DFL12(T) might have been obtained from cyanobacteria by horizontal gene transfer.

@article{doi101111mmi12719,
    author = "Kaschner, Marco and Loeschcke, Anita and Krause, Judith and Minh, Bui Quang and Heck, Achim and Endres, Stephan and Svensson, Vera and Wirtz, Astrid and von Haeseler, Arndt and Jaeger, Karl-Erich and Drepper, Thomas and Krauss, Ulrich",
    title = "Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria.",
    year = "2014",
    journal = "Molecular microbiology",
    abstract = "In all photosynthetic organisms, chlorophylls function as light-absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen-sensitive dark-operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen-insensitive but light-dependent PORs (LPORs). Based on this observation it was suggested that light-dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α-proteobacterium Dinoroseobacter shibae DFL12(T). In vitro and in vivo functional assays unequivocally prove light-dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence-based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light-dependent enzyme of D. shibae DFL12(T) might have been obtained from cyanobacteria by horizontal gene transfer.",
    url = "https://pubmed.ncbi.nlm.nih.gov/25039543/",
    doi = "10.1111/mmi.12719",
    openalex = "W2139716118",
    pmid = "25039543",
    references = "doi101007bf00160154, doi1010160378111984900593, doi10108010635150802429642, doi101093bioinformaticsbtm404, doi101093molbevmsn067, doi101093molbevmst010, doi101093molbevmst024, doi101146annurevarplant042110103811, openalexw163498145"
}

@incollection{moratadeambrosini2014bacteria,
    author = "Morata de Ambrosini, V.I. and Martín, M.C. and Merín, M.G.",
    title = "BACTERIA | Classification of the Bacteria",
    year = "2014",
    booktitle = "Encyclopedia of Food Microbiology",
    url = "https://doi.org/10.1016/b978-0-12-384730-0.00027-6",
    doi = "10.1016/b978-0-12-384730-0.00027-6",
    pages = "169-173"
}

@incollection{mehlhorn2016bacteria,
    author = "Mehlhorn, Heinz",
    title = "Bacteria",
    year = "2016",
    booktitle = "Encyclopedia of Parasitology",
    url = "https://doi.org/10.1007/978-3-662-43978-4\_348",
    doi = "10.1007/978-3-662-43978-4\_348",
    pages = "290-290"
}

Systematic control over molecular driving forces is essential for understanding the natural electron transfer processes as well as for improving the efficiency of the artificial mimics of energy converting enzymes. Oxygen producing photosynthesis uniquely employs manganese ions as rapid electron donors. Introducing this attribute to anoxygenic photosynthesis may identify evolutionary intermediates and provide insights to the energetics of biological water oxidation. This work presents effective environmental methods that substantially and simultaneously tune the redox potentials of manganese ions and the cofactors of a photosynthetic enzyme from native anoxygenic bacteria without the necessity of genetic modification or synthesis. A spontaneous coordination with bis-tris propane lowered the redox potential of the manganese (II) to manganese (III) transition to an unusually low value (\textasciitilde 400 mV) at pH 9.4 and allowed its binding to the bacterial reaction center. Binding to a novel buried binding site elevated the redox potential of the primary electron donor, a dimer of bacteriochlorophylls, by up to 92 mV also at pH 9.4 and facilitated the electron transfer that is able to compete with the wasteful charge recombination. These events impaired the function of the natural electron donor and made BTP-coordinated manganese a viable model for an evolutionary alternative.

@article{doi101016jbbabio201801002,
    author = "Deshmukh, Sasmit S and Protheroe, Charles and Ivanescu, Matei-Alexandru and Lag, Sarah and Kálmán, László",
    title = "Low potential manganese ions as efficient electron donors in native anoxygenic bacteria.",
    year = "2018",
    journal = "Biochimica et biophysica acta. Bioenergetics",
    abstract = "Systematic control over molecular driving forces is essential for understanding the natural electron transfer processes as well as for improving the efficiency of the artificial mimics of energy converting enzymes. Oxygen producing photosynthesis uniquely employs manganese ions as rapid electron donors. Introducing this attribute to anoxygenic photosynthesis may identify evolutionary intermediates and provide insights to the energetics of biological water oxidation. This work presents effective environmental methods that substantially and simultaneously tune the redox potentials of manganese ions and the cofactors of a photosynthetic enzyme from native anoxygenic bacteria without the necessity of genetic modification or synthesis. A spontaneous coordination with bis-tris propane lowered the redox potential of the manganese (II) to manganese (III) transition to an unusually low value (\textasciitilde 400 mV) at pH 9.4 and allowed its binding to the bacterial reaction center. Binding to a novel buried binding site elevated the redox potential of the primary electron donor, a dimer of bacteriochlorophylls, by up to 92 mV also at pH 9.4 and facilitated the electron transfer that is able to compete with the wasteful charge recombination. These events impaired the function of the natural electron donor and made BTP-coordinated manganese a viable model for an evolutionary alternative.",
    url = "https://pubmed.ncbi.nlm.nih.gov/29355486/",
    doi = "10.1016/j.bbabio.2018.01.002",
    openalex = "W2788846398",
    pmid = "29355486",
    references = "doi101016jfebslet201110048, doi101016s0969212694000948, doi101021cr4004874, doi101038416076a, doi101038nature09913, doi101073pnas061514798, doi101093bioinformaticsbti315, doi101126science28954851703, doi101126science28954851724, doi101146annurevarplant042110103811"
}

Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.

@article{doi101146annurevarplant042817040500,
    author = "Thiel, Vera and Tank, Marcus and Bryant, Donald A.",
    title = "Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era",
    year = "2018",
    journal = "Annual Review of Plant Biology",
    abstract = "Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.",
    url = "https://doi.org/10.1146/annurev-arplant-042817-040500",
    doi = "10.1146/annurev-arplant-042817-040500",
    openalex = "W2793926271",
    references = "doi101111mmi12719"
}

@incollection{berman2019bacteria,
    author = "Berman, Jules J.",
    title = "Bacteria",
    year = "2019",
    booktitle = "Taxonomic Guide to Infectious Diseases",
    url = "https://doi.org/10.1016/b978-0-12-817576-7.00003-1",
    doi = "10.1016/b978-0-12-817576-7.00003-1",
    pages = "39-119"
}

Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.

@article{doi103389fmicb201901658,
    author = "Ward, Lewis M. and Cardona, Tanai and Holland‐Moritz, Hannah",
    title = "Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2)",
    year = "2019",
    journal = "Frontiers in Microbiology",
    abstract = {Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.},
    url = "https://doi.org/10.3389/fmicb.2019.01658",
    doi = "10.3389/fmicb.2019.01658",
    openalex = "W2954781791",
    references = "doi10100714020332496, doi101023bpres000003044824695ec"
}

The production and use of antibiotics are becoming increasingly common worldwide, and the problem of antibiotic resistance is increasing alarmingly. Drug-resistant infections threaten human life and health and impose a heavy burden on the global economy. The origin and molecular basis of bacterial resistance is the presence of antibiotic resistance genes (ARGs). Investigations on ARGs mostly focus on the environments in which antibiotics are frequently used, such as hospitals and farms. This literature review summarizes the current knowledge of the occurrence of antibiotic-resistant bacteria in nonclinical environments, such as air, aircraft wastewater, migratory bird feces, and sea areas in-depth, which have rarely been involved in previous studies. Furthermore, the mechanism of action of plasmid and phage during horizontal gene transfer was analyzed, and the transmission mechanism of ARGs was summarized. This review highlights the new mechanisms that enhance antibiotic resistance and the evolutionary background of multidrug resistance; in addition, some promising points for controlling or reducing the occurrence and spread of antimicrobial resistance are also proposed.

@article{doi101002jobm202100201,
    author = "Jian, Zonghui and Zeng, Li and Xu, Taojie and Sun, Shuai and Yan, Shixiong and Yang, Lan and Huang, Ying and Jia, Junjing and Dou, Tengfei",
    title = "Antibiotic resistance genes in bacteria: Occurrence, spread, and control",
    year = "2021",
    journal = "Journal of Basic Microbiology",
    abstract = "The production and use of antibiotics are becoming increasingly common worldwide, and the problem of antibiotic resistance is increasing alarmingly. Drug-resistant infections threaten human life and health and impose a heavy burden on the global economy. The origin and molecular basis of bacterial resistance is the presence of antibiotic resistance genes (ARGs). Investigations on ARGs mostly focus on the environments in which antibiotics are frequently used, such as hospitals and farms. This literature review summarizes the current knowledge of the occurrence of antibiotic-resistant bacteria in nonclinical environments, such as air, aircraft wastewater, migratory bird feces, and sea areas in-depth, which have rarely been involved in previous studies. Furthermore, the mechanism of action of plasmid and phage during horizontal gene transfer was analyzed, and the transmission mechanism of ARGs was summarized. This review highlights the new mechanisms that enhance antibiotic resistance and the evolutionary background of multidrug resistance; in addition, some promising points for controlling or reducing the occurrence and spread of antimicrobial resistance are also proposed.",
    url = "https://doi.org/10.1002/jobm.202100201",
    doi = "10.1002/jobm.202100201",
    openalex = "W3205657162",
    references = "doi101073pnas713971"
}

Photosynthetic microorganisms including the green alga Chlamydomonas reinhardtii are essential to terrestrial habitats as they start the carbon cycle by conversion of CO2 to energy-rich organic carbohydrates. Terrestrial habitats are densely populated, and hence, microbial interactions mediated by natural products are inevitable. We previously discovered such an interaction between Streptomyces iranensis releasing the marginolactone azalomycin F in the presence of C. reinhardtii Whether the alga senses and reacts to azalomycin F remained unknown. Here, we report that sublethal concentrations of azalomycin F trigger the formation of a protective multicellular structure by C. reinhardtii, which we named gloeocapsoid. Gloeocapsoids contain several cells which share multiple cell membranes and cell walls and are surrounded by a spacious matrix consisting of acidic polysaccharides. After azalomycin F removal, gloeocapsoid aggregates readily disassemble, and single cells are released. The presence of marginolactone biosynthesis gene clusters in numerous streptomycetes, their ubiquity in soil, and our observation that other marginolactones such as desertomycin A and monazomycin also trigger the formation of gloeocapsoids suggests a cross-kingdom competition with ecological relevance. Furthermore, gloeocapsoids allow for the survival of C. reinhardtii at alkaline pH and otherwise lethal concentrations of azalomycin F. Their structure and polysaccharide matrix may be ancestral to the complex mucilage formed by multicellular members of the Chlamydomonadales such as Eudorina and Volvox Our finding suggests that multicellularity may have evolved to endure the presence of harmful competing bacteria. Additionally, it underlines the importance of natural products as microbial cues, which initiate interesting ecological scenarios of attack and counter defense.

@article{doi101073pnas2100892118,
    author = "Krespach, Mario K C and Stroe, Maria C and Flak, Michal and Komor, Anna J and Nietzsche, Sandor and Sasso, Severin and Hertweck, Christian and Brakhage, Axel A",
    title = "Bacterial marginolactones trigger formation of algal gloeocapsoids, protective aggregates on the verge of multicellularity.",
    year = "2021",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    abstract = "Photosynthetic microorganisms including the green alga Chlamydomonas reinhardtii are essential to terrestrial habitats as they start the carbon cycle by conversion of CO2 to energy-rich organic carbohydrates. Terrestrial habitats are densely populated, and hence, microbial interactions mediated by natural products are inevitable. We previously discovered such an interaction between Streptomyces iranensis releasing the marginolactone azalomycin F in the presence of C. reinhardtii Whether the alga senses and reacts to azalomycin F remained unknown. Here, we report that sublethal concentrations of azalomycin F trigger the formation of a protective multicellular structure by C. reinhardtii, which we named gloeocapsoid. Gloeocapsoids contain several cells which share multiple cell membranes and cell walls and are surrounded by a spacious matrix consisting of acidic polysaccharides. After azalomycin F removal, gloeocapsoid aggregates readily disassemble, and single cells are released. The presence of marginolactone biosynthesis gene clusters in numerous streptomycetes, their ubiquity in soil, and our observation that other marginolactones such as desertomycin A and monazomycin also trigger the formation of gloeocapsoids suggests a cross-kingdom competition with ecological relevance. Furthermore, gloeocapsoids allow for the survival of C. reinhardtii at alkaline pH and otherwise lethal concentrations of azalomycin F. Their structure and polysaccharide matrix may be ancestral to the complex mucilage formed by multicellular members of the Chlamydomonadales such as Eudorina and Volvox Our finding suggests that multicellularity may have evolved to endure the presence of harmful competing bacteria. Additionally, it underlines the importance of natural products as microbial cues, which initiate interesting ecological scenarios of attack and counter defense.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC8609452/",
    doi = "10.1073/pnas.2100892118",
    openalex = "W3209632396",
    pmcid = "PMC8609452",
    pmid = "34740967",
    references = "doi101038nature20139, doi101038nrmicro2916, doi101073pnas0608949103, doi101073pnas0901870106, doi101073pnas5461665, doi101074jbcra117001068, doi101093nargkz310, doi101126science1143609, doi101126science1188800, doi105860choice272713"
}