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Freches A, Fradinho JC. The biotechnological potential of the Chloroflexota phylum. Appl Environ Microbiol 2024; 90:e0175623. [PMID: 38709098 PMCID: PMC11218635 DOI: 10.1128/aem.01756-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.
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Affiliation(s)
- André Freches
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana Costa Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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2
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Mefferd CC, Zhou E, Seymour CO, Bernardo NA, Srivastava S, Bengtson AJ, Jiao JY, Dong H, Li WJ, Hedlund BP. Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China. Extremophiles 2022; 26:23. [PMID: 35802188 PMCID: PMC9270275 DOI: 10.1007/s00792-022-01272-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2-) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.
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Affiliation(s)
| | - Enmin Zhou
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
- School of Earth Sciences, Yunnan University, Kunming, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Noel A Bernardo
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Shreya Srivastava
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Amanda J Bengtson
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
- SWCA Environmental Consultants, Las Vegas, NV, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
- State Key Laboratory of Biogeology and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, USA.
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3
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Narsing Rao MP, Luo ZH, Dong ZY, Li Q, Liu BB, Guo SX, Nie GX, Li WJ. Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles. ENVIRONMENTAL RESEARCH 2022; 209:112888. [PMID: 35143804 DOI: 10.1016/j.envres.2022.112888] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/02/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Department of Pathogenic Biology, Binzhou Medical University, Yantai, 264003, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Guo-Xin Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
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4
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Schwartz SL, Momper L, Rangel LT, Magnabosco C, Amend JP, Fournier GP. Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi. Microbiologyopen 2022; 11:e1258. [PMID: 35212484 PMCID: PMC8756737 DOI: 10.1002/mbo3.1258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/09/1999] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.
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Affiliation(s)
- Sarah L. Schwartz
- Microbiology Graduate ProgramMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Lily Momper
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Exponent Inc.PasadenaCaliforniaUSA
| | - Luiz Thiberio Rangel
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | - Jan P. Amend
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Gregory P. Fournier
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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5
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Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2229147. [PMID: 35087906 PMCID: PMC8789413 DOI: 10.1155/2022/2229147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
Background Undeveloped ecosystems belong to rich source of microbial population, of which resources remain unearthed. A kind of polymeric compound system with high polyvinyl alcohol (PVA) content has been reported and named Taisui. Marker gene amplification showed that Taisui harbored little-explored microbial communities. Aim To address this issue, our study attempted to recover draft genomes and functional potential from microbial communities in Taisui using the metagenomic approach. Material and Methods. Taisui communities provided 97 novel bacterial genomes from 13 bacterial phyla, including bacteria candidate phylum. Two novel genus-level lineages were recovered from Planctomycetes and Chloroflexi. Based on the draft genomes, we expanded the number of taxa with potential productions of PKS and NRPS in phyla including Candidatus Dadabacteria, Chloroflexi, and Planctomycetes. Results A rich diversity of PVA dehydrogenase genes from 4 phyla, involving Proteobacteria, Acidobacteria, Acitinobacteria, and Planctomycetes, were identified. The phylogenetic tree of PVA dehydrogenase showed the possibility of horizontal gene transfer between microbes. Conclusion Our study underscores the substantial microbial diversity and PVA degradation potential in the previously unexplored Taisui system.
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Ward LM, Fischer WW, McGlynn SE. Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen. Microbes Environ 2021; 35. [PMID: 32727976 PMCID: PMC7511795 DOI: 10.1264/jsme2.me20030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species—here proposed as Candidatus Anthektikosiphon siderophilum—that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.
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Affiliation(s)
- Lewis M Ward
- Department of Earth & Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Woodward W Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology
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7
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Liu J, Liu W, Zhang Y, Chen C, Wu W, Zhang TC. Microbial communities in rare earth mining soil after in-situ leaching mining. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142521. [PMID: 33035989 DOI: 10.1016/j.scitotenv.2020.142521] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China.
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, China
| | - Yingbin Zhang
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Tian C Zhang
- Department of Civil & Environmental Engineering, University of Nebraska-Lincoln, Omaha, USA
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8
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Ward LM, Idei A, Nakagawa M, Ueno Y, Fischer WW, McGlynn SE. Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs. Microbes Environ 2019; 34:278-292. [PMID: 31413226 PMCID: PMC6759342 DOI: 10.1264/jsme2.me19017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Division of Geological and Planetary Sciences, California Institute of Technology
| | - Airi Idei
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Tokyo Institute of Technology.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology
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9
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Gaisin VA, Burganskaya EI, Grouzdev DS, Ashikhmin AA, Kostrikina NA, Bryantseva IA, Koziaeva VV, Gorlenko VM. ‘Candidatus Viridilinea mediisalina’, a novel phototrophic Chloroflexi bacterium from a Siberian soda lake. FEMS Microbiol Lett 2019; 366:5364544. [DOI: 10.1093/femsle/fnz043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Vasil A Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Ekaterina I Burganskaya
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Denis S Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences”, Institutskaya ave. 2, Pushchino 142290, Russian Federation
| | - Nadezda A Kostrikina
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Irina A Bryantseva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Veronika V Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
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10
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Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00571-18. [PMID: 29930071 PMCID: PMC6013628 DOI: 10.1128/genomea.00571-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here, we present a draft genome sequence of Nak82, the second genome sequence available for the Chloroflexi class Ardenticatenia and the first from a sulfidic terrestrial hot spring. Nak82 is genetically and metabolically distinct from Ardenticatena maritima and likely represents a new genus- or family-level lineage lacking high-potential respiratory pathways. Here, we present a draft genome sequence of Nak82, the second genome sequence available for the Chloroflexi class Ardenticatenia and the first from a sulfidic terrestrial hot spring. Nak82 is genetically and metabolically distinct from Ardenticatena maritima and likely represents a new genus- or family-level lineage lacking high-potential respiratory pathways.
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11
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Ward LM, Hemp J, Shih PM, McGlynn SE, Fischer WW. Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer. Front Microbiol 2018. [PMID: 29515543 PMCID: PMC5826079 DOI: 10.3389/fmicb.2018.00260] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.
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Affiliation(s)
- Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - James Hemp
- Department of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Patrick M Shih
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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12
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Ward LM, Idei A, Terajima S, Kakegawa T, Fischer WW, McGlynn SE. Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations. GEOBIOLOGY 2017; 15:817-835. [PMID: 29035022 DOI: 10.1111/gbi.12266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Banded iron formations (BIFs) are rock deposits common in the Archean and Paleoproterozoic (and regionally Neoproterozoic) sedimentary successions. Multiple hypotheses for their deposition exist, principally invoking the precipitation of iron via the metabolic activities of oxygenic, photoferrotrophic, and/or aerobic iron-oxidizing bacteria. Some isolated environments support chemistry and mineralogy analogous to processes involved in BIF deposition, and their study can aid in untangling the factors that lead to iron precipitation. One such process analog system occurs at Okuoku-hachikurou (OHK) Onsen in Akita Prefecture, Japan. OHK is an iron- and CO2 -rich, circumneutral hot spring that produces a range of precipitated mineral textures containing fine laminae of aragonite and iron oxides that resemble BIF fabrics. Here, we have performed 16S rRNA gene amplicon sequencing of microbial communities across the range of microenvironments in OHK to describe the microbial diversity present and to gain insight into the cycling of iron, oxygen, and carbon in this ecosystem. These analyses suggest that productivity at OHK is based on aerobic iron-oxidizing Gallionellaceae. In contrast to other BIF analog sites, Cyanobacteria, anoxygenic phototrophs, and iron-reducing micro-organisms are present at only low abundances. These observations support a hypothesis where low growth yields and the high stoichiometry of iron oxidized per carbon fixed by aerobic iron-oxidizing chemoautotrophs like Gallionellaceae result in accumulation of iron oxide phases without stoichiometric buildup of organic matter. This system supports little dissimilatory iron reduction, further setting OHK apart from other process analog sites where iron oxidation is primarily driven by phototrophic organisms. This positions OHK as a study area where the controls on primary productivity in iron-rich environments can be further elucidated. When compared with geological data, the metabolisms and mineralogy at OHK are most similar to specific BIF occurrences deposited after the Great Oxygenation Event, and generally discordant with those that accumulated before it.
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Affiliation(s)
- L M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - A Idei
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
| | - S Terajima
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - T Kakegawa
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - S E McGlynn
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, WA, USA
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