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Bedard DL, Van Slyke G, Nübel U, Bateson MM, Brumfield S, An YJ, Becraft ED, Wood JM, Thiel V, Ward DM. Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities. Microorganisms 2023; 11:2921. [PMID: 38138064 PMCID: PMC10746008 DOI: 10.3390/microorganisms11122921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.
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Affiliation(s)
- Donna L. Bedard
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Greta Van Slyke
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Ulrich Nübel
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Mary M. Bateson
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
| | - Sue Brumfield
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA;
| | - Yong Jun An
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Department of Biology, University of North Alabama, Florence, AL 35632, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Research Informatics Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vera Thiel
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
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Gisriel CJ, Bryant DA, Brudvig GW, Cardona T. Molecular diversity and evolution of far-red light-acclimated photosystem I. FRONTIERS IN PLANT SCIENCE 2023; 14:1289199. [PMID: 38053766 PMCID: PMC10694217 DOI: 10.3389/fpls.2023.1289199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.
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Affiliation(s)
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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Gisriel CJ, Elias E, Shen G, Soulier NT, Brudvig GW, Croce R, Bryant DA. Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01048-4. [PMID: 37773575 DOI: 10.1007/s11120-023-01048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Allophycocyanins are phycobiliproteins that absorb red light and transfer the energy to the reaction centers of oxygenic photosynthesis in cyanobacteria and red algae. Recently, it was shown that some allophycocyanins absorb far-red light and that one subset of these allophycocyanins, comprising subunits from the ApcD4 and ApcB3 subfamilies (FRL-AP), form helical nanotubes. The lowest energy absorbance maximum of the oligomeric ApcD4-ApcB3 complexes occurs at 709 nm, which is unlike allophycocyanin (AP; ApcA-ApcB) and allophycocyanin B (AP-B; ApcD-ApcB) trimers that absorb maximally at ~ 650 nm and ~ 670 nm, respectively. The molecular bases of the different spectra of AP variants are presently unclear. To address this, we structurally compared FRL-AP with AP and AP-B, performed spectroscopic analyses on FRL-AP, and leveraged computational approaches. We show that among AP variants, the α-subunit constrains pyrrole ring A of its phycocyanobilin chromophore to different extents, and the coplanarity of ring A with rings B and C sets a baseline for the absorbance maximum of the chromophore. Upon oligomerization, the α-chromophores of all AP variants exhibit a red shift of the absorbance maximum of ~ 25 to 30 nm and band narrowing. We exclude excitonic coupling in FRL-AP as the basis for this red shift and extend the results to discuss AP and AP-B. Instead, we attribute these spectral changes to a conformational alteration of pyrrole ring D, which becomes more coplanar with rings B and C upon oligomerization. This study expands the molecular understanding of light-harvesting attributes of phycobiliproteins and will aid in designing phycobiliproteins for biotechnological applications.
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Affiliation(s)
| | - Eduard Elias
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, 1081 HV, Amsterdam, Netherlands
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nathan T Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, 1081 HV, Amsterdam, Netherlands.
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
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Soulier N, Walters K, Laremore TN, Shen G, Golbeck JH, Bryant DA. Acclimation of the photosynthetic apparatus to low light in a thermophilic Synechococcus sp. strain. PHOTOSYNTHESIS RESEARCH 2022; 153:21-42. [PMID: 35441927 DOI: 10.1007/s11120-022-00918-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Depending upon their growth responses to high and low irradiance, respectively, thermophilic Synechococcus sp. isolates from microbial mats associated with the effluent channels of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, can be described as either high-light (HL) or low-light (LL) ecotypes. Strains isolated from the bottom of the photic zone grow more rapidly at low irradiance compared to strains isolated from the uppermost layer of the mat, which conversely grow better at high irradiance. The LL-ecotypes develop far-red absorbance and fluorescence emission features after growth in LL. These isolates have a unique gene cluster that encodes a putative cyanobacteriochrome denoted LcyA, a putative sensor histidine kinase; an allophycocyanin (FRL-AP; ApcD4-ApcB3) that absorbs far-red light; and a putative chlorophyll a-binding protein, denoted IsiX, which is homologous to IsiA. The emergence of FRL absorbance in LL-adapted cells of Synechococcus sp. strain A1463 was analyzed in cultures responding to differences in light intensity. The far-red absorbance phenotype arises from expression of a novel antenna complex containing the FRL-AP, ApcD4-ApcB3, which is produced when cells were grown at very low irradiance. Additionally, the two GAF domains of LcyA were shown to bind phycocyanobilin and a [4Fe-4S] cluster, respectively. These ligands potentially enable this photoreceptor to respond to a variety of environmental factors including irradiance, redox potential, and/or oxygen concentration. The products of the gene clusters specific to LL-ecotypes likely facilitate growth in low-light environments through a process called Low-Light Photoacclimation.
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Affiliation(s)
- Nathan Soulier
- Department of Biochemistry and Molecular Biology, S-002 Frear Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Karim Walters
- Department of Biochemistry and Molecular Biology, S-002 Frear Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tatiana N Laremore
- Proteomics and Mass Spectrometry Core Facility, Huck Institute for the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, S-002 Frear Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, S-002 Frear Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, S-002 Frear Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA.
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Differential Phototactic Behavior of Closely Related Cyanobacterial Isolates from Yellowstone Hot Spring Biofilms. Appl Environ Microbiol 2022; 88:e0019622. [PMID: 35499327 DOI: 10.1128/aem.00196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phototrophic biofilms in most environments experience major changes in light levels throughout a diel cycle. Phototaxis can be a useful strategy for optimizing light exposure under these conditions, but little is known about its role in cyanobacteria from thermal springs. We examined two closely related Synechococcus isolates (Synechococcus OS-A dominates at 60 to 65°C and OS-B' at 50 to 55°C) from outflows of Octopus Spring in Yellowstone National Park. Both isolates exhibited phototaxis and photokinesis in white light, but with differences in speed and motility bias. OS-B' exhibited phototaxis toward UVA, blue, green, and red wavelengths, while OS-A primarily exhibited phototaxis toward red and green. OS-A also exhibited negative phototaxis under certain conditions. The repertoires of photoreceptors and signal transduction elements in both isolates were quite different from those characterized in other unicellular cyanobacteria. These differences in the photoresponses between OS-A and OS-B' in conjunction with in situ observations indicate that phototactic strategies may be quite versatile and finely tuned to the light and local environment. IMPORTANCE Optimizing light absorption is of paramount importance to photosynthetic organisms. Some photosynthetic microbes have evolved a sophisticated process called phototaxis to move toward or away from a light source. In many hot springs in Yellowstone National Park, cyanobacteria thrive in thick, laminated biofilms or microbial mats, where small movements can result in large changes in light exposure. We quantified the light-dependent motility behaviors in isolates representing two of the most abundant and closely related cyanobacterial species from these springs. We found that they exhibited unexpected differences in their speed, directionality, and responses to different intensities or qualities of light. An examination of their genomes revealed several variations from well-studied phototaxis-related genes. Studying these recently isolated cyanobacteria reveals that diverse phototactic strategies can exist even among close relatives in the same environment. It also provides insights into the importance of phototaxis for growth and survival in microbial biofilm communities.
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Wang T, Li J, Jing H, Qin S. Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function. MARINE ENVIRONMENTAL RESEARCH 2022; 177:105622. [PMID: 35429822 DOI: 10.1016/j.marenvres.2022.105622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jialin Li
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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Saghaï A, Zivanovic Y, Moreira D, Tavera R, López-García P. A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth. Genome Biol Evol 2021; 12:1207-1216. [PMID: 32544224 PMCID: PMC7486959 DOI: 10.1093/gbe/evaa122] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 01/05/2023] Open
Abstract
Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1-15 m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Soulier N, Bryant DA. The structural basis of far-red light absorbance by allophycocyanins. PHOTOSYNTHESIS RESEARCH 2021; 147:11-26. [PMID: 33058014 DOI: 10.1007/s11120-020-00787-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Phycobilisomes (PBS), the major light-harvesting antenna in cyanobacteria, are supramolecular complexes of colorless linkers and heterodimeric, pigment-binding phycobiliproteins. Phycocyanin and phycoerythrin commonly comprise peripheral rods, and a multi-cylindrical core is principally assembled from allophycocyanin (AP). Each AP subunit binds one phycocyanobilin (PCB) chromophore, a linear tetrapyrrole that predominantly absorbs in the orange-red region of the visible spectrum (600-700 nm). AP facilitates excitation energy transfer from PBS peripheral rods or from directly absorbed red light to accessory chlorophylls in the photosystems. Paralogous forms of AP that bind PCB and are capable of absorbing far-red light (FRL; 700-800 nm) have recently been identified in organisms performing two types of photoacclimation: FRL photoacclimation (FaRLiP) and low-light photoacclimation (LoLiP). The FRL-absorbing AP (FRL-AP) from the thermophilic LoLiP strain Synechococcus sp. A1463 was chosen as a platform for site-specific mutagenesis to probe the structural differences between APs that absorb in the visible region and FRL-APs and to identify residues essential for the FRL absorbance phenotype. Conversely, red light-absorbing allophycocyanin-B (AP-B; ~ 670 nm) from the same organism was used as a platform for creating a FRL-AP. We demonstrate that the protein environment immediately surrounding pyrrole ring A of PCB on the alpha subunit is mostly responsible for the FRL absorbance of FRL-APs. We also show that interactions between PCBs bound to alpha and beta subunits of adjacent protomers in trimeric AP complexes are responsible for a large bathochromic shift of about ~ 20 nm and notable sharpening of the long-wavelength absorbance band.
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Affiliation(s)
- Nathan Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- S-002 Frear Laboratory, Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
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Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water. Appl Environ Microbiol 2020; 86:AEM.00194-20. [PMID: 32978131 DOI: 10.1128/aem.00194-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
The compositions of Octopus Spring and Mushroom Spring (Yellowstone National Park, Wyoming, USA) microbial mats have been thoroughly studied, but the compositions of the effluent waters that flow above the mats have not. In this study, cells in the mats and overflowing waters of both springs were investigated at multiple sites where Synechococcus spp. are the dominant cyanobacteria (ca. 72°C to ca. 50°C), and on several dates. In addition to microscopic analyses of stained and autofluorescent cells, 16S rRNA gene sequencing was used to characterize the major taxa present and a protein-encoding gene (psaA) was sequenced and analyzed by ecotype simulation to predict species of Synechococcus The mats of both springs were similar in terms of the downstream distribution of predominant taxa detected previously. However, waters above these mats were predominated by taxa that reside in upstream mats or communities above the upper-temperature limit of the mat. A disturbance/recolonization study was performed at a site normally predominated by Synechococcus species adapted to low temperatures. After removing indigenous Synechococcus cells, Synechococcus species adapted to higher temperatures, which were predominant in the water overflowing this site, colonized the newly forming mat. Differences in recolonization under reduced and UV-screened irradiance suggested that, in addition to physical transport, environmental conditions likely select for species that are better adapted to these different conditions and can influence mat recovery. A transport model was developed and used to predict that, in Mushroom Spring, erosion predominates in the narrower and deeper upstream effluents and deposition predominates over erosion in wider and shallower downstream effluents.IMPORTANCE In flowing aquatic systems, cell erosion and deposition are important to the dispersal of cells from one location to another. Very little is known about microbial dispersal and the physical processes that underlie it. This study demonstrates its importance to colonization of downstream surfaces and especially to the recolonization and functioning of disturbed sites. Ecological systems in flowing environments are often, roughly speaking, pseudosteady, in that nutrients enter the system and by-products leave at relatively steady rates. Over time, material inputs and outputs must balance. Measurements of input fluxes (e.g., growth rates and proxies, such as photosynthesis rates) are frequent. However, erosion and deposition of cells are seldom measured and ecological significance is sometimes neglected. The importance of these parameters is immediately evident in any attempt to construct a model of long-time community behavior, as spatial ecological structure is significantly impacted and can be dominated by migration of organisms, even in small numbers.
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Wörmer L, Gajendra N, Schubotz F, Matys ED, Evans TW, Summons RE, Hinrichs KU. A micrometer-scale snapshot on phototroph spatial distributions: mass spectrometry imaging of microbial mats in Octopus Spring, Yellowstone National Park. GEOBIOLOGY 2020; 18:742-759. [PMID: 32936514 DOI: 10.1111/gbi.12411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial mats from alkaline hot springs in the Yellowstone National Park are ideal natural laboratories to study photosynthetic life under extreme conditions, as well as the nuanced interactions of oxygenic and anoxygenic phototrophs. They represent distinctive examples of chlorophototroph (i.e., chlorophyll or bacteriochlorophyll-based phototroph) diversity, and several novel phototrophs have been first described in these systems, all confined in space, coexisting and competing for niches defined by parameters such as light, oxygen, or temperature. In a novel approach, we employed mass spectrometry imaging of chloropigments, quinones, and intact polar lipids (IPLs) to describe the spatial distribution of different groups of chlorophototrophs along the ~ 1 cm thick microbial mat at 75 µm resolution and in the top ~ 1.5 mm green part of the mat at 25 µm resolution. We observed a fine-tuned sequence of oxygenic and anoxygenic chlorophototrophs with distinctive biomarker signatures populating the microbial mat. The transition of oxic to anoxic conditions is characterized by an accumulation of biomarkers indicative of anoxygenic phototrophy. It is also identified as a clear boundary for different species and ecotypes, which adjust their biomarker inventory, particularly the interplay of quinones and chloropigments, to prevailing conditions. Colocalization of the different biomarker groups led to the identification of characteristic IPL signatures and indicates that glycosidic diether glycerolipids are diagnostic for anoxygenic phototrophs in this mat system. The zoom-in into the upper green part further reveals how oxygenic and anoxygenic phototrophs share this microenvironment and informs on subtle, microscale adjustments in lipid composition of Synechococcus spp.
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Affiliation(s)
- Lars Wörmer
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Niroshan Gajendra
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florence Schubotz
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
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11
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Soulier N, Laremore TN, Bryant DA. Characterization of cyanobacterial allophycocyanins absorbing far-red light. PHOTOSYNTHESIS RESEARCH 2020; 145:189-207. [PMID: 32710194 DOI: 10.1007/s11120-020-00775-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Phycobiliproteins (PBPs) are pigment proteins that comprise phycobilisomes (PBS), major light-harvesting antenna complexes of cyanobacteria and red algae. PBS core substructures are made up of allophycocyanins (APs), a subfamily of PBPs. Five paralogous AP subunits are encoded by the Far-Red Light Photoacclimation (FaRLiP) gene cluster, which is transcriptionally activated in cells grown in far-red light (FRL; λ = 700 to 800 nm). FaRLiP gene expression enables some terrestrial cyanobacteria to remodel their PBS and photosystems and perform oxygenic photosynthesis in far-red light (FRL). Paralogous AP genes encoding a putative, FRL-absorbing AP (FRL-AP) are also found in an operon associated with improved low-light growth (LL; < 50 μmol photons m-2 s-1) in some thermophilic Synechococcus spp., a phenomenon termed low-light photoacclimation (LoLiP). In this study, apc genes from FaRLiP and LoLiP gene clusters were heterologously expressed individually and in combinations in Escherichia coli. The resulting novel FRL-APs were characterized and identified as major contributors to the FRL absorbance observed in whole cells after FaRLiP and potentially LoLiP. Post-translational modifications of native FRL-APs from FaRLiP cyanobacterium, Leptolyngbya sp. strain JSC-1, were analyzed by mass spectrometry. The PBP complexes made in two FaRLiP organisms were compared, revealing strain-specific diversity in the FaRLiP responses of cyanobacteria. Through analyses of native and recombinant proteins, we improved our understanding of how different cyanobacterial strains utilize specialized APs to acclimate to FRL and LL. We discuss some insights into structural changes that may allow these APs to absorb longer light wavelengths than their visible-light-absorbing paralogs.
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Affiliation(s)
- Nathan Soulier
- S-002 Frear Laboratory, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tatiana N Laremore
- Proteomics and Mass Spectrometry Core Facility, Huck Institute for the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Donald A Bryant
- S-002 Frear Laboratory, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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12
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Podar PT, Yang Z, Björnsdóttir SH, Podar M. Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland. Front Microbiol 2020; 11:1625. [PMID: 32760379 PMCID: PMC7372906 DOI: 10.3389/fmicb.2020.01625] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/22/2020] [Indexed: 11/21/2022] Open
Abstract
Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.
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Affiliation(s)
- Peter T. Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Zamin Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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13
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Becraft ED, Wood JM, Cohan FM, Ward DM. Biogeography of American Northwest Hot Spring A/B '-Lineage Synechococcus Populations. Front Microbiol 2020; 11:77. [PMID: 32153516 PMCID: PMC7050468 DOI: 10.3389/fmicb.2020.00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/15/2020] [Indexed: 12/17/2022] Open
Abstract
Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B'-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by <50 km than among springs separated by >50 km, and springs separated by >800 km shared sequence variants only rarely. Phylogenetic analyses provided evidence for endemic lineages that could be related to geographic isolation and/or geochemical differences on regional scales. Ecotype Simulation 2 was used to predict putative ecotypes (ecologically distinct populations), and their membership, and canonical correspondence analysis was used to examine the geographical and geochemical bases for variation in their distribution. Across the range of Oregon and Yellowstone, geographical separation explained the largest percentage of the differences in distribution of ecotypes (9.5% correlated to longitude; 9.4% to latitude), with geochemical differences explaining the largest percentage of the remaining differences in distribution (7.4-9.3% correlated to magnesium, sulfate, and sulfide). Among samples within the Greater Yellowstone Ecosystem, geochemical differences significantly explained the distribution of ecotypes (6.5-9.3% correlated to magnesium, boron, sulfate, silicon dioxide, chloride, and pH). Nevertheless, differences in the abundance and membership of ecotypes in Yellowstone springs with similar chemistry suggested that allopatry may be involved even at local scales. Synechococcus populations have diverged both by physical isolation and physiochemical differences, and populations on surprisingly local scales have been evolving independently.
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Affiliation(s)
- Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
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14
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Finke N, Simister RL, O'Neil AH, Nomosatryo S, Henny C, MacLean LC, Canfield DE, Konhauser K, Lalonde SV, Fowle DA, Crowe SA. Mesophilic microorganisms build terrestrial mats analogous to Precambrian microbial jungles. Nat Commun 2019; 10:4323. [PMID: 31541087 PMCID: PMC6754388 DOI: 10.1038/s41467-019-11541-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 07/03/2019] [Indexed: 12/02/2022] Open
Abstract
Development of Archean paleosols and patterns of Precambrian rock weathering suggest colonization of continents by subaerial microbial mats long before evolution of land plants in the Phanerozoic Eon. Modern analogues for such mats, however, have not been reported, and possible biogeochemical roles of these mats in the past remain largely conceptual. We show that photosynthetic, subaerial microbial mats from Indonesia grow on mafic bedrocks at ambient temperatures and form distinct layers with features similar to Precambrian mats and paleosols. Such subaerial mats could have supported a substantial aerobic biosphere, including nitrification and methanotrophy, and promoted methane emissions and oxidative weathering under ostensibly anoxic Precambrian atmospheres. High C-turnover rates and cell abundances would have made these mats prime locations for early microbial diversification. Growth of landmass in the late Archean to early Proterozoic Eons could have reorganized biogeochemical cycles between land and sea impacting atmospheric chemistry and climate.
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Affiliation(s)
- N Finke
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Nordic center for earth evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - R L Simister
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | | | - S Nomosatryo
- Research center for Limnology, Indonesian Institute of Sciences (LIPI), Jawa Barat, Indonesia
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - C Henny
- Research center for Limnology, Indonesian Institute of Sciences (LIPI), Jawa Barat, Indonesia
| | | | - D E Canfield
- Nordic center for earth evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - K Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - S V Lalonde
- European Institute for Marine Studies, Technopôle Brest-Iroise, Plouzané, France
| | - D A Fowle
- Department of Geology, University of Kansas, Lawrence, KS, USA
| | - S A Crowe
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
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15
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Ho MY, Bryant DA. Global Transcriptional Profiling of the Cyanobacterium Chlorogloeopsis fritschii PCC 9212 in Far-Red Light: Insights Into the Regulation of Chlorophyll d Synthesis. Front Microbiol 2019; 10:465. [PMID: 30918500 PMCID: PMC6424891 DOI: 10.3389/fmicb.2019.00465] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
Some terrestrial cyanobacteria can acclimate to and then utilize far-red light (FRL; λ = 700–800 nm) to perform oxygenic photosynthesis through a process called Far-Red Light Photoacclimation (FaRLiP). During FaRLiP, cells synthesize chlorophylls (Chl) d and Chl f and extensively remodel their photosynthetic apparatus by modifying core subunits of photosystem (PS)I, PSII, and the phycobilisome (PBS). Three regulatory proteins, RfpA, RfpB, and RfpC, are encoded in the FaRLiP gene cluster; they sense FRL and control the synthesis of Chl f and expression of the FaRLiP gene cluster. It was previously uncertain if Chl d synthesis and other physiological and metabolic changes to FRL are regulated by RfpABC. In this study we show that Chl d synthesis is regulated by RfpABC; however, most other transcriptional changes leading to the FRL physiological state are not regulated by RfpABC. Surprisingly, we show that erythromycin induces Chl d synthesis in vivo. Transcriptomic and pigment analyses indicate that thiol compounds and/or cysteine proteases could be involved in Chl d synthesis in FRL. We conclude that the protein(s) responsible for Chl d synthesis is/are probably encoded within the FaRLiP gene cluster. Transcriptional responses to FRL help cells to conserve and produce energy and reducing power to overcome implicit light limitation of photosynthesis during the initial acclimation process to FRL.
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Affiliation(s)
- Ming-Yang Ho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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16
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Ohkubo S, Miyashita H. A niche for cyanobacteria producing chlorophyll f within a microbial mat. THE ISME JOURNAL 2017; 11:2368-2378. [PMID: 28622287 PMCID: PMC5607378 DOI: 10.1038/ismej.2017.98] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/03/2017] [Accepted: 05/15/2017] [Indexed: 11/09/2022]
Abstract
Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.
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Affiliation(s)
- Satoshi Ohkubo
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global and Environmental Studies, Kyoto University, Kyoto, Japan
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17
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Thiel V, Hügler M, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses. Front Microbiol 2017. [PMID: 28634470 PMCID: PMC5459899 DOI: 10.3389/fmicb.2017.00943] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Michael Hügler
- Department Microbiology and Molecular Biology, DVGW-Technologiezentrum WasserKarlsruhe, Germany
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States.,Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, United States
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18
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Ho MY, Soulier NT, Canniffe DP, Shen G, Bryant DA. Light regulation of pigment and photosystem biosynthesis in cyanobacteria. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:24-33. [PMID: 28391049 DOI: 10.1016/j.pbi.2017.03.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/13/2017] [Indexed: 05/28/2023]
Abstract
Most cyanobacteria are obligate oxygenic photoautotrophs, and thus their growth and survival is highly dependent on effective utilization of incident light. Cyanobacteria have evolved a diverse set of phytochromes and cyanobacteriochromes (CBCRs) that allow cells to respond to light in the range from ∼300nm to ∼750nm. Together with associated response regulators, these photosensory proteins control many aspects of cyanobacterial physiology and metabolism. These include far-red light photoacclimation (FaRLiP), complementary chromatic acclimation (CCA), low-light photoacclimation (LoLiP), photosystem content and stoichiometry (long-term adaptation), short-term acclimation (state transitions), circadian rhythm, phototaxis, photomorphogenesis/development, and cellular aggregation. This minireview highlights some discoveries concerning phytochromes and CBCRs as well as two acclimation processes that improve light harvesting and energy conversion under specific irradiance conditions: FaRLiP and CCA.
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Affiliation(s)
- Ming-Yang Ho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nathan T Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel P Canniffe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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19
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Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership. mSystems 2017; 2:mSystems00181-16. [PMID: 28289730 PMCID: PMC5340862 DOI: 10.1128/msystems.00181-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/30/2017] [Indexed: 02/06/2023] Open
Abstract
This study elucidates how a cyanobacterial primary producer acclimates to heterotrophic partnership by modulating the expression levels of key metabolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles of metabolic coupling in phototrophic-heterotrophic partnerships. The mechanisms by which microbes interact in communities remain poorly understood. Here, we interrogated specific interactions between photoautotrophic and heterotrophic members of a model consortium to infer mechanisms that mediate metabolic coupling and acclimation to partnership. This binary consortium was composed of a cyanobacterium, Thermosynechococcus elongatus BP-1, which supported growth of an obligate aerobic heterotroph, Meiothermus ruber strain A, by providing organic carbon, O2, and reduced nitrogen. Species-resolved transcriptomic analyses were used in combination with growth and photosynthesis kinetics to infer interactions and the environmental context under which they occur. We found that the efficiency of biomass production and resistance to stress induced by high levels of dissolved O2 increased, beyond axenic performance, as a result of heterotrophic partnership. Coordinated transcriptional responses transcending both species were observed and used to infer specific interactions resulting from the synthesis and exchange of resources. The cyanobacterium responded to heterotrophic partnership by altering expression of core genes involved with photosynthesis, carbon uptake/fixation, vitamin synthesis, and scavenging of reactive oxygen species (ROS). IMPORTANCE This study elucidates how a cyanobacterial primary producer acclimates to heterotrophic partnership by modulating the expression levels of key metabolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles of metabolic coupling in phototrophic-heterotrophic partnerships.
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20
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Photorespiration and Rate Synchronization in a Phototroph-Heterotroph Microbial Consortium. Processes (Basel) 2017. [DOI: 10.3390/pr5010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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21
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Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing. Front Microbiol 2016; 7:919. [PMID: 27379049 PMCID: PMC4911352 DOI: 10.3389/fmicb.2016.00919] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/27/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Christian G Klatt
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Agricultural Research Service, United States Department of Agriculture, University of MinnesotaSaint Paul, MN, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA; Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
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22
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Shen G, Gan F, Bryant DA. The siderophilic cyanobacterium Leptolyngbya sp. strain JSC-1 acclimates to iron starvation by expressing multiple isiA-family genes. PHOTOSYNTHESIS RESEARCH 2016; 128:325-340. [PMID: 27071628 DOI: 10.1007/s11120-016-0257-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
In the evolution of different cyanobacteria performing oxygenic photosynthesis, the core complexes of the two photosystems were highly conserved. However, cyanobacteria exhibit significant diversification in their light-harvesting complexes and have flexible regulatory mechanisms to acclimate to changes in their growth environments. In the siderophilic, filamentous cyanobacterium, Leptolyngbya sp. strain JSC-1, five different isiA-family genes occur in two gene clusters. During acclimation to Fe limitation, relative transcript levels for more than 600 genes increased more than twofold. Relative transcript levels were ~250 to 300 times higher for the isiA1 gene cluster (isiA1-isiB-isiC), and ~440- to 540-fold for the isiA2-isiA3-isiA4-cpcG2-isiA5 gene cluster after 48 h of iron starvation. Chl-protein complexes were isolated and further purified from cells grown under Fe-replete and Fe-depleted conditions. A single class of particles, trimeric PSI, was identified by image analysis of electron micrographs of negatively stained PSI complexes from Fe-replete cells. However, three major classes of particles were observed for the Chl-protein supercomplexes from cells grown under iron starvation conditions. Based on LC-MS-MS analyses, the five IsiA-family proteins were found in the largest supercomplexes together with core components of the two photosystems; however, IsiA5 was not present in complexes in which only the core subunits of PSI were detected. IsiA5 belongs to the same clade as PcbC proteins in a phylogenetic classification, and it is proposed that IsiA5 is most likely involved in supercomplexes containing PSII dimers. IsiA4, which is a fusion of an IsiA domain and a C-terminal PsaL domain, was found together with IsiA1, IsiA2, and IsiA3 in complexes with monomeric PSI. The data indicate that horizontal gene transfer, gene duplication, and divergence have played important roles in the adaptive evolution of this cyanobacterium to iron starvation conditions.
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Affiliation(s)
- Gaozhong Shen
- Department of Biochemistry and Molecular Biology, 4406 Althouse Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Fei Gan
- Department of Biochemistry and Molecular Biology, 4406 Althouse Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, 4406 Althouse Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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23
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Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM. Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Front Microbiol 2016; 6:1540. [PMID: 26834710 PMCID: PMC4712262 DOI: 10.3389/fmicb.2015.01540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022] Open
Abstract
Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.
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Affiliation(s)
- Melanie C Melendrez
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
| | - John F Heidelberg
- Department of Biological Sciences, College of Letters, Arts and Sciences, University of Southern California Los Angeles, CA, USA
| | - Douglas B Rusch
- Informatics Group, J. Craig Venter Institute Rockville, MD, USA
| | | | - David M Ward
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
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Zhao C, Gan F, Shen G, Bryant DA. RfpA, RfpB, and RfpC are the Master Control Elements of Far-Red Light Photoacclimation (FaRLiP). Front Microbiol 2015; 6:1303. [PMID: 26635768 PMCID: PMC4658448 DOI: 10.3389/fmicb.2015.01303] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/06/2015] [Indexed: 11/24/2022] Open
Abstract
Terrestrial cyanobacteria often occur in niches that are strongly enriched in far-red light (FRL; λ > 700 nm). Some cyanobacteria exhibit a complex and extensive photoacclimation response, known as FRL photoacclimation (FaRLiP). During the FaRLiP response, specialized paralogous proteins replace 17 core subunits of the three major photosynthetic complexes: Photosystem (PS) I, PS II, and the phycobilisome. Additionally, the cells synthesize both chlorophyll (Chl) f and Chl d. Using biparental mating from Escherichia coli, we constructed null mutants of three genes, rfpA, rfpB, and rfpC, in the cyanobacteria Chlorogloeopsis fritschii PCC 9212 and Chroococcidiopsis thermalis PCC 7203. The resulting mutants were no longer able to modify their photosynthetic apparatus to absorb FRL, were no longer able to synthesize Chl f, inappropriately synthesized Chl d in white light, and were unable to transcribe genes of the FaRLiP gene cluster. We conclude that RfpA, RfpB, and RfpC constitute a FRL-activated signal transduction cascade that is the master control switch for the FaRLiP response. FRL is proposed to activate (or inactivate) the histidine kinase activity of RfpA, which leads to formation of the active state of RfpB, the key response regulator and transcription activator. RfpC may act as a phosphate shuttle between RfpA and RfpB. Our results show that reverse genetics via conjugation will be a powerful approach in detailed studies of the FaRLiP response.
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Affiliation(s)
- Chi Zhao
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Fei Gan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
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Gan F, Bryant DA. Adaptive and acclimative responses of cyanobacteria to far-red light. Environ Microbiol 2015; 17:3450-65. [DOI: 10.1111/1462-2920.12992] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/09/2015] [Accepted: 07/17/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Fei Gan
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
- Department of Chemistry and Biochemistry; Montana State University; Bozeman MT 59717 USA
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Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol 2015; 6:604. [PMID: 26157428 PMCID: PMC4477158 DOI: 10.3389/fmicb.2015.00604] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
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Affiliation(s)
- Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Shane Nowack
- Department of Mathematical Sciences, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Kurt LaButti
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Joel Martin
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | | | | | | | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
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Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front Microbiol 2015; 6:590. [PMID: 26157420 PMCID: PMC4475828 DOI: 10.3389/fmicb.2015.00590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/29/2015] [Indexed: 01/18/2023] Open
Abstract
Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.
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Affiliation(s)
- Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, MEUSA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
| | | | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSWAustralia
| | - Sheila I. Jensen
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, HellerupDenmark
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PAUSA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MTUSA
| | | | | | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
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