1
|
Koblížek M, Ferrera I, Kolářová E, Duhamel S, Popendorf KJ, Gasol JM, Van Mooy BAS. Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre. Appl Environ Microbiol 2024; 90:e0003224. [PMID: 38551354 PMCID: PMC11022572 DOI: 10.1128/aem.00032-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.
Collapse
Affiliation(s)
- Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Eva Kolářová
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Solange Duhamel
- Department of Cellular and Molecular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kimberly J. Popendorf
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, Florida, USA
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Benjamin A. S. Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| |
Collapse
|
2
|
Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 2024; 9:e0131123. [PMID: 38376261 PMCID: PMC10949492 DOI: 10.1128/msystems.01311-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
Collapse
Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Bílý
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Alastair T. Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department Chemistry, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| |
Collapse
|
3
|
Ma ZX, Feng CX, Song YZ, Sun J, Shao Y, Song SZ, Wan B, Zhang C, Fan H, Bao K, Yang S. Engineering photo-methylotrophic Methylobacterium for enhanced 3-hydroxypropionic acid production during non-growth stage fermentation. BIORESOURCE TECHNOLOGY 2024; 393:130104. [PMID: 38008225 DOI: 10.1016/j.biortech.2023.130104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
This study explored the potential of methanol as a sustainable feedstock for biomanufacturing, focusing on Methylobacterium extorquens, a well-established representative of methylotrophic cell factories. Despite this bacterium's long history, its untapped photosynthetic capabilities for production enhancement have remained unreported. Using genome-scale flux balance analysis, it was hypothesized that introducing photon fluxes could boost the yield of 3-hydroxypropionic acid (3-HP), an energy- and reducing equivalent-consuming chemicals. To realize this, M. extorquens was genetically modified by eliminating the negative regulator of photosynthesis, leading to improved ATP levels and metabolic activity in non-growth cells during a two-stage fermentation process. This modification resulted in a remarkable 3.0-fold increase in 3-HP titer and a 2.1-fold increase in its yield during stage (II). Transcriptomics revealed that enhanced light-driven methanol oxidation, NADH transhydrogenation, ATP generation, and fatty acid degradation were key factors. This development of photo-methylotrophy as a platform technology introduced novel opportunities for future production enhancements.
Collapse
Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Chen-Xi Feng
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Ya-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Jing Sun
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Yi Shao
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Shu-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Bin Wan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Huan Fan
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan 430062, Hubei, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People's Republic of China.
| |
Collapse
|
4
|
Gardiner AT, Mujakić I, Bína D, Gardian Z, Kopejtka K, Nupur, Qian P, Koblížek M. Characterisation of the photosynthetic complexes from the marine gammaproteobacterium Congregibacter litoralis KT71. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148946. [PMID: 36455648 DOI: 10.1016/j.bbabio.2022.148946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Possibly the most abundant group of anoxygenic phototrophs are marine photoheterotrophic Gammaproteobacteria belonging to the NOR5/OM60 clade. As little is known about their photosynthetic apparatus, the photosynthetic complexes from the marine phototrophic bacterium Congregibacter litoralis KT71 were purified and spectroscopically characterised. The intra-cytoplasmic membranes contain a smaller amount of photosynthetic complexes when compared with anaerobic purple bacteria. Moreover, the intra-cytoplasmic membranes contain only a minimum amount of peripheral LH2 complexes. The complexes are populated by bacteriochlorophyll a, spirilloxanthin and two novel ketocarotenoids, with biophysical and biochemical properties similar to previously characterised complexes from purple bacteria. The organization of the RC-LH1 complex has been further characterised using cryo-electron microscopy. The overall organisation is similar to the complex from the gammaproteobacterium Thermochromatium tepidum, with the type-II reaction centre surrounded by a slightly elliptical LH1 antenna ring composed of 16 αβ-subunits with no discernible gap or pore. The RC-LH1 and LH2 apoproteins are phylogenetically related to other halophilic species but LH2 also to some alphaproteobacterial species. It seems that the reduction of light-harvesting apparatus and acquisition of novel ketocarotenoids in Congregibacter litoralis KT71 represent specific adaptations for operating the anoxygenic photosynthesis under aerobic conditions at sea.
Collapse
Affiliation(s)
- Alastair T Gardiner
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Izabela Mujakić
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Karel Kopejtka
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Nupur
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Michal Koblížek
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic.
| |
Collapse
|
5
|
Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park. Microorganisms 2022; 10:microorganisms10061169. [PMID: 35744687 PMCID: PMC9231093 DOI: 10.3390/microorganisms10061169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Rhodobacter consists of purple nonsulfur photosynthetic alphaproteobacteria known for their diverse metabolic capabilities. Here, we report the genome sequence and initial characterization of a novel Rhodobacter species, strain M37P, isolated from Mushroom hot spring runoff in Yellowstone National Park at 37 °C. Genome-based analyses and initial growth characteristics helped to define the differentiating characteristics of this species and identified it as an aerobic anoxygenic phototroph (AAP). This is the first AAP identified in the genus Rhodobacter. Strain M37P has a pinkish-red pigmentation that is present under aerobic dark conditions but disappears under light incubation. Whole genome-based analysis and average nucleotide identity (ANI) comparison indicate that strain M37P belongs to a specific clade of recently identified species that are genetically and physiologically unique from other representative Rhodobacter species. The genome encodes a unique xanthorhodopsin, not found in any other Rhodobacter species, which may be responsible for the pinkish-red pigmentation. These analyses indicates that strain M37P is a unique species that is well-adapted to optimized growth in the Yellowstone hot spring runoff, for which we propose the name Rhodobacter calidifons sp. nov.
Collapse
|
6
|
Piwosz K, Villena-Alemany C, Mujakić I. Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake. THE ISME JOURNAL 2022; 16:1046-1054. [PMID: 34802055 PMCID: PMC8941148 DOI: 10.1038/s41396-021-01142-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023]
Abstract
Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO2 to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO2 from respiration unbalanced by net primary production was by 3.69 × 109 g CO2 lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.
Collapse
Affiliation(s)
- Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981, Třeboň, Czechia. .,National Marine Fisheries Research Institute, 81-332, Gdynia, Poland.
| | - Cristian Villena-Alemany
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Izabela Mujakić
- grid.418095.10000 0001 1015 3316Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia ,grid.14509.390000 0001 2166 4904Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| |
Collapse
|
7
|
Paix B, Potin P, Schires G, Le Poupon C, Misson B, Leblanc C, Culioli G, Briand JF. Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study. Environ Microbiol 2021; 23:6777-6797. [PMID: 34490980 DOI: 10.1111/1462-2920.15758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/29/2022]
Abstract
In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.
Collapse
Affiliation(s)
- Benoit Paix
- Université de Toulon, Laboratoire MAPIEM, La Garde, EA 4323, France
| | - Philippe Potin
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), UMR 8227, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gaëtan Schires
- Sorbonne Université, CNRS, Center for Biological Marine Resources (CRBM), FR 2424, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM110, La Garde, France
| | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM110, La Garde, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), UMR 8227, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, La Garde, EA 4323, France
| | | |
Collapse
|
8
|
Koblížek M, Dachev M, Bína D, Nupur, Piwosz K, Kaftan D. Utilization of light energy in phototrophic Gemmatimonadetes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 213:112085. [PMID: 33220599 DOI: 10.1016/j.jphotobiol.2020.112085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/30/2020] [Accepted: 11/11/2020] [Indexed: 02/03/2023]
Abstract
Gemmatimonas phototrophica is, so far, the only described phototrophic species of the bacterial phylum Gemmatimonadetes. Its cells contain a unique type of photosynthetic complex with the reaction center surrounded by a double ring antenna, however they can also grow in the dark using organic carbon substrates. Its photosynthesis genes were received via horizontal gene transfer from Proteobacteria. This raises two questions; how the horizontally transferred photosynthesis apparatus has integrated into the cellular machinery, and how much light-derived energy actually contributes to the cellular metabolism? To address these points, the photosynthetic reactions were studied on several levels, from photophysics of the reaction center to cellular growth. Flash photolysis measurements and bacteriochlorophyll fluorescence kinetic measurements documented the presence of fully functional type-2 reaction centers with a large light harvesting antenna. When illuminated, the bacterial cells reduced their respiration rate by 58 ± 5%, revealing that oxidative phosphorylation was replaced by photophosphorylation. Moreover, illumination also more than doubled the assimilation rates of glucose, a sugar that is mostly used for respiration. Finally, light increased the growth rates of Gemmatimonas phototrophica colonies on agar plates. All the presented data provide evidence that photosynthetic complexes are fully integrated into cellular metabolism of Gemmatimonas phototrophica, and are able to provide a substantial amount of energy for its metabolism and growth.
Collapse
Affiliation(s)
- Michal Koblížek
- Center Algatech, Institute of Microbiology, Czech Acad Sci, 37981 Třeboň, Czechia.
| | - Marko Dachev
- Center Algatech, Institute of Microbiology, Czech Acad Sci, 37981 Třeboň, Czechia
| | - David Bína
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czechia; Institute of Plant Molecular Biology, Biology Centre, Czech Acad Sci, Branišovská 1760, 370 05 České Budějovice, Czechia
| | - Nupur
- Center Algatech, Institute of Microbiology, Czech Acad Sci, 37981 Třeboň, Czechia
| | - Kasia Piwosz
- Center Algatech, Institute of Microbiology, Czech Acad Sci, 37981 Třeboň, Czechia
| | - David Kaftan
- Center Algatech, Institute of Microbiology, Czech Acad Sci, 37981 Třeboň, Czechia; University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czechia
| |
Collapse
|
9
|
Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria. Sci Rep 2019; 9:18766. [PMID: 31822744 PMCID: PMC6904477 DOI: 10.1038/s41598-019-55210-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/25/2019] [Indexed: 01/21/2023] Open
Abstract
The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.
Collapse
|
10
|
Dachev M, Bína D, Sobotka R, Moravcová L, Gardian Z, Kaftan D, Šlouf V, Fuciman M, Polívka T, Koblížek M. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PLoS Biol 2017; 15:e2003943. [PMID: 29253871 PMCID: PMC5749889 DOI: 10.1371/journal.pbio.2003943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/02/2018] [Accepted: 11/22/2017] [Indexed: 11/29/2022] Open
Abstract
The majority of life on Earth depends directly or indirectly on the sun as a source of energy. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers (RCs). Here, we analyzed the organization of photosynthetic (PS) complexes in the bacterium G. phototrophica, which so far is the only phototrophic representative of the bacterial phylum Gemmatimonadetes. The isolated complex has a molecular weight of about 800 ± 100 kDa, which is approximately 2 times larger than the core complex of Rhodospirillum rubrum. The complex contains 62.4 ± 4.7 bacteriochlorophyll (BChl) a molecules absorbing in 2 distinct infrared absorption bands with maxima at 816 and 868 nm. Using femtosecond transient absorption spectroscopy, we determined the energy transfer time between these spectral bands as 2 ps. Single particle analyses of the purified complexes showed that they were circular structures with an outer diameter of approximately 18 nm and a thickness of 7 nm. Based on the obtained, we propose that the light-harvesting complexes in G. phototrophica form 2 concentric rings surrounding the type 2 RC. The inner ring (corresponding to the B868 absorption band) is composed of 15 subunits and is analogous to the inner light-harvesting complex 1 (LH1) in purple bacteria. The outer ring is composed of 15 more distant BChl dimers with no or slow energy transfer between them, resulting in the B816 absorption band. This completely unique and elegant organization offers good structural stability, as well as high efficiency of light harvesting. Our results reveal that while the PS apparatus of Gemmatimonadetes was acquired via horizontal gene transfer from purple bacteria, it later evolved along its own pathway, devising a new arrangement of its light harvesting complexes. The majority of life on Earth depends directly or indirectly on the sun as a source of energy. Phototrophic organisms use energy from light to power various cellular and metabolic processes. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers where it is used to power proton gradients or to form new chemical bonds. Here, we analyzed photosynthetic complexes in Gemmatimonas phototrophica, the only known phototrophic representative of the bacterial phylum Gemmatimonadetes. Using a combination of biochemical and spectroscopic techniques, we show that the light-harvesting complexes of G. phototrophica are organized in 2 concentric rings around the reaction center. This organization is unique among anoxygenic phototrophs. It offers both structural stability and high efficiency of light harvesting. The structural unit of both antenna rings is a dimer of photosynthetic pigments called bacteriochlorophyll. The inner ring is populated by more densely packed dimers, while the outer ring contains more distant dimers with a minimal excitation exchange. Such an arrangement modifies the spectral properties of bacteriochlorophylls in the complex and ensures efficient capture of light in the near-infrared part of the solar spectrum.
Collapse
Affiliation(s)
- Marko Dachev
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Roman Sobotka
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Lenka Moravcová
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - David Kaftan
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Václav Šlouf
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Marcel Fuciman
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Polívka
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Center of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
| |
Collapse
|
11
|
Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans. Appl Environ Microbiol 2017; 84:AEM.02116-17. [PMID: 29030444 DOI: 10.1128/aem.02116-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
The genus Limnohabitans (Comamonadaceae, Betaproteobacteria) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization.IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans, indicating that they may have a novel role in freshwater habitats.
Collapse
|
12
|
Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacteriumDinoroseobacter shibae. Environ Microbiol 2017; 20:724-733. [DOI: 10.1111/1462-2920.14003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Kasia Piwosz
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - David Kaftan
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jason Dean
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jiří Šetlík
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Michal Koblížek
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| |
Collapse
|
13
|
Muzziotti D, Adessi A, Faraloni C, Torzillo G, De Philippis R. Acclimation strategy of Rhodopseudomonas palustris to high light irradiance. Microbiol Res 2017; 197:49-55. [PMID: 28219525 DOI: 10.1016/j.micres.2017.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/02/2017] [Accepted: 01/23/2017] [Indexed: 12/30/2022]
Abstract
The ability of Rhodopseudomonas palustris cells to rapidly acclimate to high light irradiance is an essential issue when cells are grown under sunlight. The aim of this study was to investigate the photo-acclimation process in Rhodopseudomonas palustris 42OL under different culturing conditions: (i) anaerobic (AnG), (ii) aerobic (AG), and (iii) under H2-producing (HP) conditions both at low (LL) and high light (HL) irradiances. The results obtained clearly showed that the photosynthetic unit was significantly affected by the light irradiance at which Rp. palustris 42OL was grown. The synthesis of carotenoids was affected by both illumination and culturing conditions. At LL, lycopene was the main carotenoid synthetized under all conditions tested, while at HL under HP conditions, it resulted the predominant carotenoid. Oppositely, under AnG and AG at HL, rhodovibrin was the major carotenoid detected. The increase in light intensity produced a deeper variation in light-harvesting complexes (LHC) ratio. These findings are important for understanding the ecological distribution of PNSB in natural environments, mostly characterized by high light intensities, and for its growth outdoors.
Collapse
Affiliation(s)
- Dayana Muzziotti
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144, Florence, Italy.
| | - Alessandra Adessi
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144, Florence, Italy; Institute of Chemistry of Organometallic Compounds (ICCOM), CNR, Via Madonna del Piano, 10-50019 Sesto Fiorentino, Florence, Italy.
| | - Cecilia Faraloni
- Institute of Ecosystem Study (ISE), CNR, Via Madonna del Piano, 10-50019 Sesto Fiorentino, Florence, Italy.
| | - Giuseppe Torzillo
- Institute of Ecosystem Study (ISE), CNR, Via Madonna del Piano, 10-50019 Sesto Fiorentino, Florence, Italy.
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental Sciences, University of Florence, via Maragliano 77, 50144, Florence, Italy; Institute of Chemistry of Organometallic Compounds (ICCOM), CNR, Via Madonna del Piano, 10-50019 Sesto Fiorentino, Florence, Italy.
| |
Collapse
|