1
|
Chlorobaculum tepidum Modulates Amino Acid Composition in Response to Energy Availability, as Revealed by a Systematic Exploration of the Energy Landscape of Phototrophic Sulfur Oxidation. Appl Environ Microbiol 2016; 82:6431-6439. [PMID: 27565613 DOI: 10.1128/aem.02111-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/17/2016] [Indexed: 12/26/2022] Open
Abstract
Microbial sulfur metabolism, particularly the formation and consumption of insoluble elemental sulfur (S0), is an important biogeochemical engine that has been harnessed for applications ranging from bioleaching and biomining to remediation of waste streams. Chlorobaculum tepidum, a low-light-adapted photoautolithotrophic sulfur-oxidizing bacterium, oxidizes multiple sulfur species and displays a preference for more reduced electron donors: sulfide > S0 > thiosulfate. To understand this preference in the context of light energy availability, an "energy landscape" of phototrophic sulfur oxidation was constructed by varying electron donor identity, light flux, and culture duration. Biomass and cellular parameters of C. tepidum cultures grown across this landscape were analyzed. From these data, a correction factor for colorimetric protein assays was developed, enabling more accurate biomass measurements for C. tepidum, as well as other organisms. C. tepidum's bulk amino acid composition correlated with energy landscape parameters, including a tendency toward less energetically expensive amino acids under reduced light flux. This correlation, paired with an observation of increased cell size and storage carbon production under electron-rich growth conditions, suggests that C. tepidum has evolved to cope with changing energy availability by tuning its proteome for energetic efficiency and storing compounds for leaner times. IMPORTANCE How microbes cope with and adapt to varying energy availability is an important factor in understanding microbial ecology and in designing efficient biotechnological processes. We explored the response of a model phototrophic organism, Chlorobaculum tepidum, across a factorial experimental design that enabled simultaneous variation and analysis of multiple growth conditions, what we term the "energy landscape." C. tepidum biomass composition shifted toward less energetically expensive amino acids at low light levels. This observation provides experimental evidence for evolved efficiencies in microbial proteomes and emphasizes the role that energy flux may play in the adaptive responses of organisms. From a practical standpoint, our data suggest that bulk biomass amino acid composition could provide a simple proxy to monitor and identify energy stress in microbial systems.
Collapse
|
2
|
Marnocha CL, Levy AT, Powell DH, Hanson TE, Chan CS. Mechanisms of extracellular S0 globule production and degradation in Chlorobaculumtepidum via dynamic cell-globule interactions. MICROBIOLOGY (READING, ENGLAND) 2016; 162:1125-1134. [PMID: 27121868 PMCID: PMC5772824 DOI: 10.1099/mic.0.000294] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022]
Abstract
The Chlorobiales are anoxygenic phototrophs that produce solid, extracellular elemental sulfur globules as an intermediate step in the oxidation of sulfide to sulfate. These organisms must export sulfur while preventing cell encrustation during S0 globule formation; during globule degradation they must find and mobilize the sulfur for intracellular oxidation to sulfate. To understand how the Chlorobiales address these challenges, we characterized the spatial relationships and physical dynamics of Chlorobaculum tepidum cells and S0 globules by light and electron microscopy. Cba. tepidum commonly formed globules at a distance from cells. Soluble polysulfides detected during globule production may allow for remote nucleation of globules. Polysulfides were also detected during globule degradation, probably produced as an intermediate of sulfur oxidation by attached cells. Polysulfides could feed unattached cells, which made up over 80% of the population and had comparable growth rates to attached cells. Given that S0 is formed remotely from cells, there is a question as to how cells are able to move toward S0 in order to attach. Time-lapse microscopy shows that Cba. tepidum is in fact capable of twitching motility, a finding supported by the presence of genes encoding type IV pili. Our results show how Cba. tepidum is able to avoid mineral encrustation and benefit from globule degradation even when not attached. In the environment, Cba. tepidum may also benefit from soluble sulfur species produced by other sulfur-oxidizing or sulfur-reducing bacteria as these organisms interact with its biogenic S0 globules.
Collapse
Affiliation(s)
- C. L. Marnocha
- Department of Geological Sciences, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - A. T. Levy
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - D. H. Powell
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - T. E. Hanson
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - C. S. Chan
- Department of Geological Sciences, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
3
|
Findlay AJ. Microbial impact on polysulfide dynamics in the environment. FEMS Microbiol Lett 2016; 363:fnw103. [DOI: 10.1093/femsle/fnw103] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 11/12/2022] Open
|
4
|
Hamilton TL, Jones DS, Schaperdoth I, Macalady JL. Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. Front Microbiol 2015; 5:756. [PMID: 25620962 PMCID: PMC4288042 DOI: 10.3389/fmicb.2014.00756] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022] Open
Abstract
The Frasassi and Acquasanta Terme cave systems in Italy host isolated lithoautotrophic ecosystems characterized by sulfur-oxidizing biofilms with up to 50% S(0) by mass. The net contributions of microbial taxa in the biofilms to production and consumption of S(0) are poorly understood and have implications for understanding the formation of geological sulfur deposits as well as the ecological niches of sulfur-oxidizing autotrophs. Filamentous Epsilonproteobacteria are among the principal biofilm architects in Frasassi and Acquasanta Terme streams, colonizing high-sulfide, low-oxygen niches relative to other major biofilm-forming populations. Metagenomic sequencing of eight biofilm samples indicated the presence of diverse and abundant Epsilonproteobacteria. Populations of Sulfurovum-like organisms were the most abundant Epsilonproteobacteria regardless of differences in biofilm morphology, temperature, or water chemistry. After assembling and binning the metagenomic data, we retrieved four nearly-complete genomes of Sulfurovum-like organisms as well as a Sulfuricurvum spp. Analyses of the binned and assembled metagenomic data indicate that the Epsilonproteobacteria are autotrophic and therefore provide organic carbon to the isolated subsurface ecosystem. Multiple homologs of sulfide-quinone oxidoreductase (Sqr), together with incomplete or absent Sox pathways, suggest that cave Sulfurovum-like Epsilonproteobacteria oxidize sulfide incompletely to S(0) using either O2 or nitrate as a terminal electron acceptor, consistent with previous evidence that they are most successful in niches with high dissolved sulfide to oxygen ratios. In contrast, we recovered homologs of the complete complement of Sox proteins affiliated Gammaproteobacteria and with less abundant Sulfuricurvum spp. and Arcobacter spp., suggesting that these populations are capable of the complete oxidation of sulfide to sulfate. These and other genomic data presented here offer new clues into the physiology and genetic potential of the largely uncultivated and ecologically successful cave Sulfurovum-like populations, and suggest that they play an integral role in subsurface S(0) formation.
Collapse
Affiliation(s)
- Trinity L Hamilton
- Department of Geosciences, Penn State Astrobiology Research Center, The Pennsylvania State University University Park, PA, USA
| | - Daniel S Jones
- Department of Geosciences, Penn State Astrobiology Research Center, The Pennsylvania State University University Park, PA, USA ; Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
| | - Irene Schaperdoth
- Department of Geosciences, Penn State Astrobiology Research Center, The Pennsylvania State University University Park, PA, USA
| | - Jennifer L Macalady
- Department of Geosciences, Penn State Astrobiology Research Center, The Pennsylvania State University University Park, PA, USA
| |
Collapse
|
5
|
Holkenbrink C, Barbas SO, Mellerup A, Otaki H, Frigaard NU. Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system. Microbiology (Reading) 2011; 157:1229-1239. [DOI: 10.1099/mic.0.044669-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Green sulfur bacteria (GSB) oxidize sulfide and thiosulfate to sulfate, with extracellular globules of elemental sulfur as an intermediate. Here we investigated which genes are involved in the formation and consumption of these sulfur globules in the green sulfur bacterium Chlorobaculum tepidum. We show that sulfur globule oxidation is strictly dependent on the dissimilatory sulfite reductase (DSR) system. Deletion of dsrM/CT2244 or dsrT/CT2245, or the two dsrCABL clusters (CT0851–CT0854, CT2247–2250), abolished sulfur globule oxidation and prevented formation of sulfate from sulfide, whereas deletion of dsrU/CT2246 had no effect. The DSR system also seems to be involved in the formation of thiosulfate, because thiosulfate was released from wild-type cells during sulfide oxidation, but not from the dsr mutants. The dsr mutants incapable of complete substrate oxidation oxidized sulfide and thiosulfate about twice as fast as the wild-type, while having only slightly lower growth rates (70–80 % of wild-type). The increased oxidation rates seem to compensate for the incomplete substrate oxidation to satisfy the requirement for reducing equivalents during growth. A mutant in which two sulfide : quinone oxidoreductases (sqrD/CT0117 and sqrF/CT1087) were deleted exhibited a decreased sulfide oxidation rate (∼50 % of wild-type), yet formation and consumption of sulfur globules were not affected. The observation that mutants lacking the DSR system maintain efficient growth suggests that the DSR system is dispensable in environments with sufficiently high sulfide concentrations. Thus, the DSR system in GSB may have been acquired by horizontal gene transfer as a response to a need for enhanced substrate utilization in sulfide-limiting habitats.
Collapse
Affiliation(s)
- Carina Holkenbrink
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Santiago Ocón Barbas
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Mellerup
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hiroyo Otaki
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Niels-Ulrik Frigaard
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|
6
|
Sakurai H, Ogawa T, Shiga M, Inoue K. Inorganic sulfur oxidizing system in green sulfur bacteria. PHOTOSYNTHESIS RESEARCH 2010; 104:163-176. [PMID: 20143161 DOI: 10.1007/s11120-010-9531-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 01/16/2010] [Indexed: 05/28/2023]
Abstract
Green sulfur bacteria use various reduced sulfur compounds such as sulfide, elemental sulfur, and thiosulfate as electron donors for photoautotrophic growth. This article briefly summarizes what is known about the inorganic sulfur oxidizing systems of these bacteria with emphasis on the biochemical aspects. Enzymes that oxidize sulfide in green sulfur bacteria are membrane-bound sulfide-quinone oxidoreductase, periplasmic (sometimes membrane-bound) flavocytochrome c sulfide dehydrogenase, and monomeric flavocytochrome c (SoxF). Some green sulfur bacteria oxidize thiosulfate by the multienzyme system called either the TOMES (thiosulfate oxidizing multi-enzyme system) or Sox (sulfur oxidizing system) composed of the three periplasmic proteins: SoxB, SoxYZ, and SoxAXK with a soluble small molecule cytochrome c as the electron acceptor. The oxidation of sulfide and thiosulfate by these enzymes in vitro is assumed to yield two electrons and result in the transfer of a sulfur atom to persulfides, which are subsequently transformed to elemental sulfur. The elemental sulfur is temporarily stored in the form of globules attached to the extracellular surface of the outer membranes. The oxidation pathway of elemental sulfur to sulfate is currently unclear, although the participation of several proteins including those of the dissimilatory sulfite reductase system etc. is suggested from comparative genomic analyses.
Collapse
Affiliation(s)
- Hidehiro Sakurai
- Research Institute for Photosynthetic Hydrogen Production, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | | | | | | |
Collapse
|
7
|
Grimm F, Dobler N, Dahl C. Regulation of dsr genes encoding proteins responsible for the oxidation of stored sulfur in Allochromatium vinosum. MICROBIOLOGY-SGM 2009; 156:764-773. [PMID: 20007651 DOI: 10.1099/mic.0.034645-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sulfur globules are formed as obligatory intermediates during the oxidation of reduced sulfur compounds in many environmentally important photo- and chemolithoautotrophic bacteria. It is well established that the so-called Dsr proteins are essential for the oxidation of zero-valent sulfur accumulated in the globules; however, hardly anything is known about the regulation of dsr gene expression. Here, we present a closer look at the regulation of the dsr genes in the phototrophic sulfur bacterium Allochromatium vinosum. The dsr genes are expressed in a reduced sulfur compound-dependent manner and neither sulfite, the product of the reverse-acting dissimilatory sulfite reductase DsrAB, nor the alternative electron donor malate inhibit the gene expression. Moreover, we show the oxidation of sulfur to sulfite to be the rate-limiting step in the oxidation of sulfur to sulfate as sulfate production starts concomitantly with the upregulation of the expression of the dsr genes. Real-time RT-PCR experiments suggest that the genes dsrC and dsrS are additionally expressed from secondary internal promoters, pointing to a special function of the encoded proteins. Earlier structural analyses indicated the presence of a helix-turn-helix (HTH)-like motif in DsrC. We therefore assessed the DNA-binding capability of the protein and provide evidence for a possible regulatory function of DsrC.
Collapse
Affiliation(s)
- Frauke Grimm
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
| | - Nadine Dobler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
| |
Collapse
|
8
|
|