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Michal Kobližek - One of the best experts on this subject based on the ideXlab platform.

  • genomic analysis of the evolution of phototrophy among haloalkaliphilic rhodobacterales
    Genome Biology and Evolution, 2017
    Co-Authors: K Kopejtka, Jürgen Tomasch, Yonghui Zeng, Dimitry Y. Sorokin, Martin Tichy, Michal Kobližek
    Abstract:

    : A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.

  • ecology of aerobic anoxygenic phototrophs in aquatic environments
    Fems Microbiology Reviews, 2015
    Co-Authors: Michal Kobližek
    Abstract:

    Recognition of the environmental role of photoheterotrophic bacteria has been one of the main themes of aquatic microbiology over the last 15 years. Aside from cyanobacteria and proteorhodopsin-containing bacteria, aerobic anoxygenic phototrophic (AAP) bacteria are the third most numerous group of phototrophic prokaryotes in the ocean. This functional group represents a diverse assembly of species which taxonomically belong to various subgroups of Alpha-, Beta- and Gammaproteobacteria. AAP bacteria are facultative Photoheterotrophs which use bacteriochlorophyll-containing reaction centers to harvest light energy. The light-derived energy increases their bacterial growth efficiency, which provides a competitive advantage over heterotrophic species. Thanks to their enzymatic machinery AAP bacteria are active, rapidly growing organisms which contribute significantly to the recycling of organic matter. This chapter summarizes the current knowledge of the ecology of AAP bacteria in aquatic environments, implying their specific role in the microbial loop.

  • genome sequences and photosynthesis gene cluster composition of a freshwater aerobic anoxygenic phototroph sandarakinorhabdus sp strain aap62 isolated from the shahu lake in ningxia china
    Genome Announcements, 2013
    Co-Authors: Yonghui Zeng, Fuying Feng, Yapeng Liu, Michal Kobližek
    Abstract:

    We report the first genome sequence from the recently established alpha-4 proteobacterial genus Sandarakinorhabdus. The genome of the Sandarakinorhabdus sp. strain AAP62 contains a photosynthesis gene cluster carrying major genes for bacterial reaction centers. The presence of genes related to aerobic respiratory electron transport confirms the lifestyle of this organism as an aerobic anoxygenic photoheterotroph.

  • genome sequence of the marine photoheterotrophic bacterium erythrobacter sp strain nap1
    Journal of Bacteriology, 2011
    Co-Authors: Michal Kobližek, Justin Johnson, Jan Janouskovec, Miroslav Obornik, Steven Ferriera, Paul G Falkowski
    Abstract:

    Here we report the full genome sequence of marine phototrophic bacterium Erythrobacter sp. strain NAP1. The 3.3-Mb genome contains a full set of photosynthetic genes organized in one 38.9-kb cluster; however, it does not contain genes for CO2 or N2 fixation, thereby confirming that the organism is a photoheterotroph.

  • Isolation and characterization of Erythrobacter sp. strains from the upper ocean
    Archives of Microbiology, 2003
    Co-Authors: Michal Kobližek, Paul G Falkowski, Oded Béjà, Robert R. Bidigare, Stephanie Christensen, Bryan Benitez-nelson, Costantino Vetriani, Marcin K. Kolber, Zbigniew S. Kolber
    Abstract:

    Seven strains of marine aerobic anoxygenic phototrophs belonging to the genus Erythrobacter were isolated. The strains were characterized regarding their physiological and biochemical properties, 16S rDNA and pufM gene sequences, morphological features, substrate preference, as well as pigment and lipid composition. All strains had functional type-2 reaction centers containing bacteriochlorophyll, served by small, light-harvesting complex 1, and were photosynthetically competent. In addition, large pools of carotenoids were found, but only some of the accessory pigments transfer energy to the reaction centers. All of the isolates were facultative Photoheterotrophs. They required an organic carbon substrate for growth; however, they are able to supplement a significant fraction of their metabolic requirements with photosynthetically derived energy.

David L Kirchman - One of the best experts on this subject based on the ideXlab platform.

  • single cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production
    The ISME Journal, 2016
    Co-Authors: Maria Carolina Garciachaves, Matthew T Cottrell, David L Kirchman, Clara Ruizgonzalez, Paul A Del Giorgio
    Abstract:

    Aerobic anoxygenic phototrophic (AAP) bacteria are Photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these Photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

  • patterns in abundance cell size and pigment content of aerobic anoxygenic phototrophic bacteria along environmental gradients in northern lakes
    PLOS ONE, 2015
    Co-Authors: Lisa Fauteux, Matthew T Cottrell, David L Kirchman, Maria Carolina Garciachaves, Carles M Borrego, Paul A Del Giorgio
    Abstract:

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Quebec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

  • Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary
    The ISME Journal, 2010
    Co-Authors: Matthew T Cottrell, Josephine Ras, David L Kirchman
    Abstract:

    Photoheterotrophic microbes use organic substrates and light energy to satisfy their demand for carbon and energy and seem to be well adapted to eutrophic estuarine and oligotrophic oceanic environments. One type of photoheterotroph, aerobic anoxygenic phototrophic (AAP) bacteria, is especially abundant in particle-rich, turbid estuaries. To explore questions regarding the controls of these photoheterotrophic bacteria, we examined their abundance by epifluorescence microscopy, concentrations of the light-harvesting pigment, bacteriochlorophyll a (BChl a ) and the diversity of pufM and 16S ribosomal RNA (rRNA) genes in the Chesapeake Bay. Concentrations of BChl a varied substantially, much more so than AAP bacterial abundance, along the estuarine salinity gradient. The BChl a concentration was correlated with turbidity only when oceanic and estuarine waters were considered together. Concentrations of BChl a and BChl a quotas were higher in particle-associated than in free-living AAP bacterial communities and appear to reflect physiological adaptation, not different AAP bacterial communities; pufM genes did not differ between particle-associated and free-living communities. In contrast, particle-associated and free-living bacterial communities were significantly different, on the basis of the analysis of 16S rRNA genes. The BChl a quota of AAP bacteria was not correlated with turbidity, suggesting that pigment synthesis varies in direct response to particles, not light attenuation. The AAP bacteria seem to synthesize more BChl a when dissolved and particulate substrates are available than when only dissolved materials are accessible, which has implications for understanding the impact of substrates on the level of photoheterotrophy compared with heterotrophy in AAP bacteria.

  • aerobic anoxygenic phototrophic bacteria attached to particles in turbid waters of the delaware and chesapeake estuaries
    Applied and Environmental Microbiology, 2007
    Co-Authors: Lisa A Waidner, David L Kirchman
    Abstract:

    Aerobic anoxygenic phototrophic (AAP) bacteria are Photoheterotrophs that, if abundant, may be biogeochemically important in the oceans. We used epifluorescence microscopy and quantitative PCR (qPCR) to examine the abundance of these bacteria by enumerating cells with bacteriochlorophyll a (bChl a) and the light-reaction center gene pufM, respectively. In the surface waters of the Delaware estuary, AAP bacteria were abundant, comprising up to 34% of prokaryotes, although the percentage varied greatly with location and season. On average, AAP bacteria made up 12% of the community as measured by microscopy and 17% by qPCR. In the surface waters of the Chesapeake, AAP bacteria were less abundant, averaging 6% of prokaryotes. AAP bacterial abundance was significantly correlated with light attenuation (r = 0.50) and ammonium (r = 0.42) and nitrate (r = 0.71) concentrations. Often, bChl a-containing bacteria were mostly attached to particles (31 to 94% of total AAP bacteria), while usually 20% or less of total prokaryotes were associated with particles. Of the cells containing pufM, up to 87% were associated with particles, but the overall average of particle-attached cells was 15%. These data suggest that AAP bacteria are particularly competitive in these two estuaries, in part due to attachment to particles.

Bernhard M Fuchs - One of the best experts on this subject based on the ideXlab platform.

  • taxonomy and evolution of bacteriochlorophyll a containing members of the om60 nor5 clade of marine gammaproteobacteria description of luminiphilus syltensis gen nov sp nov reclassification of haliea rubra as pseudohaliea rubra gen nov comb nov and e
    BMC Microbiology, 2013
    Co-Authors: Stefan Spring, Jens Harder, Thomas Riedel, Cathrin Sproer, Shiqiang Yan, Bernhard M Fuchs
    Abstract:

    Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Within this group a close relationship between aerobic anoxygenic Photoheterotrophs and non-phototrophic members has been found.

  • comparable light stimulation of organic nutrient uptake by sar11 and prochlorococcus in the north atlantic subtropical gyre
    The ISME Journal, 2013
    Co-Authors: Paola R Gomezpereira, Manuela Hartmann, David J. Scanlan, Bernhard M Fuchs, Carolina Grob, Glen A Tarran, Adrian Martin, Mikhail V. Zubkov
    Abstract:

    Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic, that is, potentially enhance uptake of scarce organic molecules using the available solar radiation to energise appropriate transport systems. Here, we assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions using 33P-ATP, 3H-ATP and 35S-methionine tracers. Light-stimulated uptake of these substrates was assessed in two dominant bacterioplankton groups discriminated by flow cytometric sorting of tracer-labelled cells and identified using catalysed reporter deposition fluorescence in situ hybridisation. One group of cells, encompassing 48% of all bacterioplankton, were identified as members of the SAR11 clade, whereas the other group (24% of all bacterioplankton) was Prochlorococcus. When exposed to light, SAR11 cells took 31% more ATP and 32% more methionine, whereas the Prochlorococcus cells took 33% more ATP and 34% more methionine. Other bacterioplankton did not demonstrate light stimulation. Thus, the SAR11 and Prochlorococcus groups, with distinctly different light-harvesting mechanisms, used light equally to enhance, by approximately one-third, the uptake of different types of organic molecules. Our findings indicate the significance of light-driven uptake of essential organic nutrients by the dominant bacterioplankton groups in the surface waters of one of the less productive, vast regions of the world’s oceans—the oligotrophic North Atlantic subtropical gyre.

Stefan Spring - One of the best experts on this subject based on the ideXlab platform.

  • taxonomy and evolution of bacteriochlorophyll a containing members of the om60 nor5 clade of marine gammaproteobacteria description of luminiphilus syltensis gen nov sp nov reclassification of haliea rubra as pseudohaliea rubra gen nov comb nov and e
    BMC Microbiology, 2013
    Co-Authors: Stefan Spring, Jens Harder, Thomas Riedel, Cathrin Sproer, Shiqiang Yan, Bernhard M Fuchs
    Abstract:

    Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Within this group a close relationship between aerobic anoxygenic Photoheterotrophs and non-phototrophic members has been found.

  • genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin like protein
    PLOS ONE, 2013
    Co-Authors: Thomas Riedel, Jürgen Tomasch, Stefan Spring, Jose M Gonzalez, Thorsten Brinkhoff, Laura Gomezconsarnau, Madeleine Martin, Michael Jarek, Meike Rohlfs, Heribert Cypionka
    Abstract:

    Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.

Shiqiang Yan - One of the best experts on this subject based on the ideXlab platform.