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Nguyen HK, Minato T, Teramoto T, Ogo S, Kakuta Y, Yoon KS. Disassembly and reassembly of the non-conventional thermophilic C-phycocyanin. J Biosci Bioeng 2024; 137:179-186. [PMID: 38238241 DOI: 10.1016/j.jbiosc.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 03/03/2024]
Abstract
C-phycocyanin (CPC), which contains open-chain tetrapyrroles, is a major light-harvesting red-fluorescent protein with an important role in aquatic photosynthesis. Recently, we reported a non-conventional CPC from Thermoleptolyngbya sp. O-77 (CPCO77) that contains two different structures, i.e., a hexameric structure and a non-conventional octameric structure. However, the assembly and disassembly mechanisms of the non-conventional octameric form of CPC remain unclear. To understand this assembly mechanism, we performed an in vitro experiment to study the disassembly and reassembly behaviors of CPC using isolated CPC subunits. The dissociation of the CPCO77 subunit was performed using a Phenyl-Sepharose column in 20 mM potassium phosphate buffer (pH 6.0) containing 7.0 M urea. For the first time, crystals of isolated CPC subunits were obtained and analyzed after separation. After the removal of urea from the purified α and β subunits, we performed an in vitro reassembly experiment for CPC and analyzed the reconstructed CPC using spectrophotometric and X-ray crystal structure analyses. The crystal structure of the reassembled CPC was nearly identical to that of the original CPCO77. The findings of this study indicate that the octameric CPCO77 is a naturally occurring form in the thermophilic cyanobacterium Thermoleptolyngbya sp. O-77.
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Affiliation(s)
- Hung Khac Nguyen
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
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2
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Cp*Ir complex with mesobiliverdin ligand isolated from Thermoleptolyngbya sp. O-77. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Minato T, Teramoto T, Adachi N, Hung NK, Yamada K, Kawasaki M, Akutsu M, Moriya T, Senda T, Ogo S, Kakuta Y, Yoon KS. Non-conventional octameric structure of C-phycocyanin. Commun Biol 2021; 4:1238. [PMID: 34716405 PMCID: PMC8556327 DOI: 10.1038/s42003-021-02767-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O–77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes. Takuo Minato and colleagues determine the crystal and cryo-EM structures of the native C-phycocyanin (CPC) from the thermophilic cyanobacterium, Thermoleptolyngbya sp. O77, which was found to adopt both a conventional hexameric structure and a novel octameric assembly. These findings provide new insights into the assembly of CPCs and their mechanism of energy transfer.
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Affiliation(s)
- Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Nguyen Khac Hung
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kaho Yamada
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Masato Akutsu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,Center for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan. .,Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan. .,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan. .,Center for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
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Draft Genome Sequences of Two Cyanobacteria Leptolyngbya spp. Isolated from Microbial Mats in Miravalles Thermal Spring, Costa Rica. Microbiol Resour Announc 2021; 10:e0055321. [PMID: 34647804 PMCID: PMC8515892 DOI: 10.1128/mra.00553-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequences of Leptolyngbya sp. strain 7M and Leptolyngbya sp. strain 15MV, isolated from Miravalles Thermal Spring, Costa Rica. The thermophilic cyanobacteria exhibit unique diversity features that provide insight into the adaptation and evolution of phototrophic microorganisms in geothermal habitats.
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Tang J, Li L, Li M, Du L, Shah MMR, Waleron MM, Waleron M, Waleron KF, Daroch M. Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China. Front Microbiol 2021; 12:696102. [PMID: 34566907 PMCID: PMC8461337 DOI: 10.3389/fmicb.2021.696102] [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] [Received: 04/16/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
Thermoleptolyngbya is a newly proposed genus of thermophilic cyanobacteria that are often abundant in thermal environments. However, a vast majority of Thermoleptolyngbya strains were not systematically identified, and genomic features of this genus are also sparse. Here, polyphasic approaches were employed to identify a thermophilic strain, PKUAC-SCTA183 (A183 hereafter), isolated from hot spring Erdaoqiao, Ganzi prefecture, China. Whole-genome sequencing of the strain revealed its allocation to Thermoleptolyngbya sp. and genetic adaptations to the hot spring environment. While the results of 16S rRNA were deemed inconclusive, the more comprehensive polyphasic approach encompassing phenetic, chemotaxic, and genomic approaches strongly suggest that a new taxon, Thermoleptolyngbya sichuanensis sp. nov., should be delineated around the A183 strain. The genome-scale phylogeny and average nucleotide/amino-acid identity confirmed the genetic divergence of the A183 strain from other strains of Thermoleptolyngbya along with traditional methods such as 16S-23S ITS and its secondary structure analyses. Comparative genomic and phylogenomic analyses revealed inconsistent genome structures between Thermoleptolyngbya A183 and O-77 strains. Further gene ontology analysis showed that the unique genes of the two strains were distributed in a wide range of functional categories. In addition, analysis of genes related to thermotolerance, signal transduction, and carbon/nitrogen/sulfur assimilation revealed the ability of this strain to adapt to inhospitable niches in hot springs, and these findings were preliminarily confirmed using experimental, cultivation-based approaches.
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Affiliation(s)
- Jie Tang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Liheng Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Meijin Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Lianming Du
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Md Mahfuzur R Shah
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Michal M Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Malgorzata Waleron
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof F Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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6
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Minato T, Teramoto T, Kakuta Y, Ogo S, Yoon KS. Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites. FEBS Open Bio 2020; 10:1219-1229. [PMID: 32170832 PMCID: PMC7327923 DOI: 10.1002/2211-5463.12837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The DNA‐binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.
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Affiliation(s)
- Takuo Minato
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.,Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, Fukuoka, Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan.,Center for Small Molecule Energy, Kyushu University, Fukuoka, Japan
| | - Ki-Seok Yoon
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan.,Center for Small Molecule Energy, Kyushu University, Fukuoka, Japan
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7
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Miralles I, Lázaro R, Sánchez-Marañón M, Soriano M, Ortega R. Biocrust cover and successional stages influence soil bacterial composition and diversity in semiarid ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:134654. [PMID: 31905575 DOI: 10.1016/j.scitotenv.2019.134654] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Biocrusts are an important drylands landscape component, which enriches the upper millimeters of the soil with organic matter and initiates biogeochemical cycles. However, little is known about the influence of biocrusts on soil bacterial community structure and diversity. Different biocrust types representing a successional gradient were studied. This gradient, from the earliest to the latest successional stages, consisted of an incipient cyanobacterial biocrust < mature cyanobacterial biocrusts < biocrust dominated by the Squamarina lentigera and Diploschistes diacapsis lichens < Biocrust characterized by the Lepraria isidiata lichen. Moreover, in each biocrust type, four different percentages of biocrust cover were also selected. Soil diversity gradually increased with biocrust successional stage and percentage of biocrust cover. The biocrust cover had an important role in the total abundance of bacteria, generally increasing in soils colonized by the highest percentages of cover. Biocrust successional stage was the most important factor, significantly influencing 108 soil bacteria genera, whereas biocrust cover showed significant differences in only 10 genera. Principal Component Analysis showed contrasting microbial composition across the biocrust successional gradient. Some bacterial taxa were dominant in the soil colonized by different biocrust types. Thus, Leptolyngbya, Rubrobacter, Solirubrobacter, Geodermatophilus, etc., were more abundant in incipient cyanobacteria; Nostocales, Chroococcidiopsaceae, Coleofasciculaceae etc., under mature cyanobacterial biocrusts; Truepera, Sphingobacteriaceae, Actinophytocola, Kribella, etc., below the S. lentigera and D. diacapsis community, and Bryobacter, Ohtaekwangia, Opitutus, Pedosphaeraceae, etc., in soils colonized by L. isidiata. Several soil bacteria taxa showed significant correlations (p < 0.05) with chemical soil properties (pH, total nitrogen, total organic carbon, available phosphorous and electrical conductivity). We discuss the role of biocrusts influencing these chemical soil parameters, including the presence of certain metabolites secreted by biocrusts, and also their effects on soil moisture and several physical soil features, as well as their association with different microclimates, all of which could favor a more selective environment for certain bacteria.
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Affiliation(s)
- I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
| | - R Lázaro
- Experimental Station of Arid Zones (CSIC), Almería, Spain
| | - M Sánchez-Marañón
- Department of Soil Science and Chemical Agriculture, University of Granada, 18071 Granada, Spain
| | - M Soriano
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
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8
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Momper L, Hu E, Moore KR, Skoog EJ, Tyler M, Evans AJ, Bosak T. Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs. Free Radic Biol Med 2019; 140:224-232. [PMID: 31163257 DOI: 10.1016/j.freeradbiomed.2019.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 01/23/2023]
Abstract
The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.
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Affiliation(s)
- Lily Momper
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eileen Hu
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kelsey R Moore
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emilie J Skoog
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Madeline Tyler
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Alexander J Evans
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
| | - Tanja Bosak
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Uribe-Lorío L, Brenes-Guillén L, Hernández-Ascencio W, Mora-Amador R, González G, Ramírez-Umaña CJ, Díez B, Pedrós-Alió C. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. Microbiologyopen 2019; 8:e893. [PMID: 31271524 PMCID: PMC6813449 DOI: 10.1002/mbo3.893] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 11/27/2022] Open
Abstract
We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.
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Affiliation(s)
- Lorena Uribe-Lorío
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Laura Brenes-Guillén
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Walter Hernández-Ascencio
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Raúl Mora-Amador
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | - Gino González
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Beatriz Díez
- Departamento de Microbiología y Genética, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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10
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Rozanov AS, Bryanskaya AV, Ivanisenko TV, Malup TK, Peltek SE. Biodiversity of the microbial mat of the Garga hot spring. BMC Evol Biol 2017; 17:254. [PMID: 29297382 PMCID: PMC5751763 DOI: 10.1186/s12862-017-1106-9] [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] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. RESULTS In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. CONCLUSIONS High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.
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Affiliation(s)
- Alexey Sergeevich Rozanov
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Alla Victorovna Bryanskaya
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey Vladimirovich Ivanisenko
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana Konstantinovna Malup
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey Evgenievich Peltek
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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11
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Yoon KS, Nguyen NT, Tran KT, Tsuji K, Ogo S. Nitrogen Fixation Genes and Nitrogenase Activity of the Non-Heterocystous Cyanobacterium Thermoleptolyngbya sp. O-77. Microbes Environ 2017; 32:324-329. [PMID: 29176306 PMCID: PMC5745016 DOI: 10.1264/jsme2.me17015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 μmol m−2 s−1 suppressed the effects of illumination.
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Affiliation(s)
- Ki-Seok Yoon
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University.,Center for Small Molecule Energy, Kyushu University
| | - Nga T Nguyen
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University
| | - Kien Trung Tran
- Center for Small Molecule Energy, Kyushu University.,Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University
| | - Kohsei Tsuji
- Center for Small Molecule Energy, Kyushu University.,Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University.,Center for Small Molecule Energy, Kyushu University.,Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University
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12
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Sciuto K, Moro I. Detection of the new cosmopolitan genus Thermoleptolyngbya (Cyanobacteria, Leptolyngbyaceae) using the 16S rRNA gene and 16S-23S ITS region. Mol Phylogenet Evol 2016; 105:15-35. [PMID: 27546720 DOI: 10.1016/j.ympev.2016.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/19/2016] [Accepted: 08/15/2016] [Indexed: 01/22/2023]
Abstract
Cyanobacteria are widespread prokaryotes that are able to live in extreme conditions such as thermal springs. Strains attributable to the genus Leptolyngbya are among the most common cyanobacteria sampled from thermal environments. Leptolyngbya is a character-poor taxon that was demonstrated to be polyphyletic based on molecular analyses. The recent joining of 16S rRNA gene phylogenies with 16S-23S ITS secondary structure analysis is a useful approach to detect new cryptic taxa and has led to the separation of new genera from Leptolyngbya and to the description of new species inside this genus and in other related groups. In this study, phylogenetic investigations based on both the 16S rRNA gene and the 16S-23S ITS region were performed alongside 16S rRNA and 16S-23S ITS secondary structure analyses on cyanobacteria of the family Leptolyngbyaceae. These analyses focused on filamentous strains sampled from thermal springs with a morphology ascribable to the genus Leptolyngbya. The phylogenetic reconstructions showed that the Leptolyngbya-like thermal strains grouped into a monophyletic lineage that was distinct from Leptolyngbya. The 16S-23S ITS secondary structure results supported the separation of this cluster. A new genus named Thermoleptolyngbya was erected to encompass these strains, and two species were described inside this new taxon: T. albertanoae and T. oregonensis.
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MESH Headings
- Base Sequence
- Cyanobacteria/classification
- Cyanobacteria/genetics
- Cyanobacteria/ultrastructure
- DNA, Ribosomal Spacer/genetics
- Ecosystem
- Geography
- Nucleic Acid Conformation
- Phylogeny
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
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Affiliation(s)
- Katia Sciuto
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Isabella Moro
- Department of Biology, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy
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13
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Weisz DA, Gross ML, Pakrasi HB. The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II. FRONTIERS IN PLANT SCIENCE 2016; 7:617. [PMID: 27242823 PMCID: PMC4862242 DOI: 10.3389/fpls.2016.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/22/2016] [Indexed: 05/23/2023]
Abstract
Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has been gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. We conclude with an outlook for the opportunity of future MS contributions to PSII research.
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Affiliation(s)
- Daniel A. Weisz
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Himadri B. Pakrasi
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
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