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Haghshenas L, Banihashemi S, Malekzadegan Y, Catanzaro R, Moghadam Ahmadi A, Marotta F. Microbiome as an endocrine organ and its relationship with eye diseases: Effective factors and new targeted approaches. World J Gastrointest Pathophysiol 2024; 15:96446. [PMID: 39355345 PMCID: PMC11440246 DOI: 10.4291/wjgp.v15.i5.96446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024] Open
Abstract
Microbiome is an endocrine organ that refers to both the complicated biological system of microbial species that colonize our bodies and their genomes and surroundings. Recent studies confirm the connection between the microbiome and eye diseases, which are involved in the pathogenesis of eye diseases, including age-related macular disorders, diabetic retinopathy, glaucoma, retinitis pigmentosa, dry eye, and uveitis. The aim of this review is to investigate the microbiome in relation to eye health. First, a brief introduction of the characteristics of the gut microorganisms terms of composition and work, the role of dysbiosis, the gut microbiome and the eye microbiome in the progression of eye illnesses are highlighted, then the relationship among the microbiome and the function of the immune system and eye diseases, the role of inflammation and aging and the immune system, It has been reviewed and finally, the control and treatment goals of microbiome and eye diseases, the role of food factors and supplements, biotherapy and antibiotics in relation to microbiome and eye health have been reviewed.
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Affiliation(s)
- Leila Haghshenas
- Department of Clinical Bioinformatics, Harvard Medical School, Boston, MA 02115, United States
| | - Sara Banihashemi
- Department of Bioscience, School of Science and Technology, Nottingham Trend University, Nottingham NG1 4FQ, United Kingdom
| | - Yalda Malekzadegan
- Department of Microbiology, Saveh University of Medical Sciences, Saveh 3919676651, Iran
| | - Roberto Catanzaro
- Department of Clinical and Experimental Medicine, University of Catania, Catania 95123, Catania, Italy
| | - Amir Moghadam Ahmadi
- Department of Neuroimmunology, Thomas Jefferson University Hospital, Philadelphia, PA 19107, United States
| | - Francesco Marotta
- Department of Human Nutrition and Food Sciences, Texas Women University, Milano 20154, Italy
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2
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Colman DR, Keller LM, Arteaga-Pozo E, Andrade-Barahona E, St Clair B, Shoemaker A, Cox A, Boyd ES. Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nat Commun 2024; 15:7506. [PMID: 39209850 PMCID: PMC11362583 DOI: 10.1038/s41467-024-51841-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| | - Lisa M Keller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Emilia Arteaga-Pozo
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Eva Andrade-Barahona
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Brian St Clair
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Anna Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Alysia Cox
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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3
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Felipe Benites L, Stephens TG, Van Etten J, James T, Christian WC, Barry K, Grigoriev IV, McDermott TR, Bhattacharya D. Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Commun Biol 2024; 7:312. [PMID: 38594478 PMCID: PMC11003980 DOI: 10.1038/s42003-024-05931-1] [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] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 04/11/2024] Open
Abstract
Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Julia Van Etten
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timeeka James
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William C Christian
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Timothy R McDermott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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4
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Marks TJ, Rowland IR. The Diversity of Bacteriophages in Hot Springs. Methods Mol Biol 2024; 2738:73-88. [PMID: 37966592 DOI: 10.1007/978-1-0716-3549-0_4] [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] [Indexed: 11/16/2023]
Abstract
Bacteriophages are ubiquitous in all environments that support microbial life. This includes hot springs, which can range in temperatures between 40 and 98 °C and pH levels between 1 and 9. Bacteriophages that survive in the higher temperatures of hot springs are known as thermophages. Thermophages have developed distinct adaptations allowing for thermostability in these extreme environments, including increased G + C DNA percentages, reliance upon the pentose phosphate metabolic pathway to avoid oxidative stress, and a codon preference for those with a GNA sequence leading to increased hydrophobic interactions and disulfide bonds. In this review, we discuss the diversity of characterized thermophages in hot spring environments that span five viral families: Myoviridae, Siphoviridae, Tectiviridae, Sphaerolipoviridae, and Inoviridae. Potential industrial and medicinal applications of thermophages will also be addressed.
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Affiliation(s)
- Timothy J Marks
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA.
| | - Isabella R Rowland
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA
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Zhou Y, Wang Y, Prangishvili D, Krupovic M. Exploring the Archaeal Virosphere by Metagenomics. Methods Mol Biol 2024; 2732:1-22. [PMID: 38060114 DOI: 10.1007/978-1-0716-3515-5_1] [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: 12/08/2023]
Abstract
During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.
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Affiliation(s)
- Yifan Zhou
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - David Prangishvili
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France.
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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Houghton KM, Carere CR, Stott MB, McDonald IR. Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields. Front Microbiol 2023; 14:1253773. [PMID: 37720161 PMCID: PMC10502179 DOI: 10.3389/fmicb.2023.1253773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.
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Affiliation(s)
- Karen M. Houghton
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Matthew B. Stott
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
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He Q, Wang S, Feng K, Michaletz ST, Hou W, Zhang W, Li F, Zhang Y, Wang D, Peng X, Yang X, Deng Y. High speciation rate of niche specialists in hot springs. THE ISME JOURNAL 2023:10.1038/s41396-023-01447-4. [PMID: 37286739 DOI: 10.1038/s41396-023-01447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Wenhui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
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Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir Island, Kurils, Russia. The taxonomic composition of the studied microbial communities was assessed by the 16S rRNA gene metabarcoding for bacteria and archaea, and by the 18S rRNA gene metabarcoding for protists. Richness and diversity of bacteria in the geothermal microbial communities decreased with the increase of temperature, while for archaea, the tendency was the opposite. Ciliophora was the most represented taxon of protists. The biofilms of various kinds that we found in a very local area of the geothermal system were different from each other by taxonomic composition, and the level of their taxonomic diversity was significantly influenced by water temperature.
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Zhang HS, Feng QD, Zhang DY, Zhu GL, Yang L. Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau. Front Microbiol 2023; 13:994179. [PMID: 37180363 PMCID: PMC10172933 DOI: 10.3389/fmicb.2022.994179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/13/2022] [Indexed: 03/19/2023] Open
Abstract
Introduction:In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.Methods:In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.Results:Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.Discussion:In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.
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11
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Van Etten J, Cho CH, Yoon HS, Bhattacharya D. Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth. Semin Cell Dev Biol 2023; 134:4-13. [PMID: 35339358 DOI: 10.1016/j.semcdb.2022.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 01/08/2023]
Abstract
Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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12
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Salgado O, Guajardo-Leiva S, Moya-Beltrán A, Barbosa C, Ridley C, Tamayo-Leiva J, Quatrini R, Mojica FJM, Díez B. Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities. Front Microbiol 2022; 13:1069452. [DOI: 10.3389/fmicb.2022.1069452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42–80°C, pH 6–9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.
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13
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Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function. Curr Microbiol 2022; 80:4. [PMID: 36434287 DOI: 10.1007/s00284-022-03118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.
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Shift in Microbial Community Structure with Temperature in Deulajhari Hot Spring Cluster, Odisha, India. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hot springs are the reservoirs of novel hyperthermophilic and often mesophilic bacteria that provide information about the prevailing community structure. Here we analyzed the metagenome profile based 16S rRNA amplicon sequencing of the three different springs from Deulajhari hot spring cluster, S1, S2 and S3, having a range of temperature (43°C to 65°C), pH (7.14 – 8.10) and variation in N, P, K, TOC, Salinity, COD and TDS. These thermal spring clusters are covered with the dense vegetation of Pandanus and continuously enriched by plant leaf debris, thus resulting in a high amount of total organic carbon (TOC). The number of phyla varied among the springs: 20 in S1 (43°C), 18 in S2 (55°C) and 24 in S3 (65°C) from the 16S rRNA data. Out of the reported phyla in each spring, the most abundant were Chloroflexi, Proteobacteria, Chlorobi and Acidobacteria, which correlated with the temperature gradient. Various metabolic pathways such as ABC transporters, Two-component system, Purine metabolism were most abundantly present in the S2 sample compared to the other two. The CCA analysis revealed the correlation between physiochemical parameters and their functional annotation. The present study establishes the relation between the physiological parameters and the structural distribution of microbiota along the temperature gradient.
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15
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Simona C, Venturi S, Tassi F, Simona R, Cabassi J, Capecchiacci F, Bicocchi G, Vaselli O, Morrison HG, Sogin ML, Fazi S. Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiol Ecol 2022; 98:6650346. [PMID: 35883234 DOI: 10.1093/femsec/fiac088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Although terrestrial hydrothermal systems are considered among the most fascinating environments, how their unique and extreme conditions can affect microorganisms selection and the role in biogeochemical cycles has not yet been well elucidated. A combined geochemical and microbiological exploration in waters and sediments from ten sampling points along a sharp temperature gradient (15-90 °C) within an extremely acidic hydrothermal system (Pisciarelli Spring, Campi Flegrei area, southern Italy) displayed how hydrothermal fluids influence the microbial dynamics. This area was characterized by high levels of reduced gaseous species (e.g. H2S, H2, CH4, CO), and very low pH values (<2.3). Thermodynamic calculations revealed a high microbial catabolic potential in oxidation/reduction reactions of N-, S-, and Fe-bearing species. Overall, an increase of the archaeal/bacterial abundance ratio was observed by decreasing temperature and pH values. In particular, Archaea and Bacteria were present in almost equal cell abundance (up to 1.1 × 109 and 9.3 × 108 cell/g, respectively) in the <70 °C sampling points (average pH = 2.09); on the contrary, highest temperature waters (85-90 °C; average pH = 2.26) were characterized by low abundance of archaeal cells. The high-throughput sequencing of 16S rRNA gene indicated strong differences in archaeal and bacterial communities' composition along temperature gradient. However, the microbiome in this extreme environment was mainly constituted by chemoautotrophic microorganisms that were likely involved in N-, S-, and Fe-bearing species transformations (e.g. Acidianus infernus, Ferroplasma acidarmanus, Acidithiobacillus, Sulfobacillus, Thaumarchaeota), in agreement with thermodynamic calculations.
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Affiliation(s)
- Crognale Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Stefania Venturi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Franco Tassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Rossetti Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Jacopo Cabassi
- IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Francesco Capecchiacci
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy).,Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sezione di Napoli, Osservatorio Vesuviano, Via Diocleziano 328, 80125 Napoli, Italy
| | - Gabriele Bicocchi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy)
| | - Orlando Vaselli
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
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16
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Nagar S, Talwar C, Motelica-Heino M, Richnow HH, Shakarad M, Lal R, Negi RK. Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. Front Microbiol 2022; 13:848010. [PMID: 35495730 PMCID: PMC9044081 DOI: 10.3389/fmicb.2022.848010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Chandni Talwar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Mikael Motelica-Heino
- UMR 7327, Centre National de la Recherche Scientifique, Institut des Sciences de la Terre D'Orleans (ISTO), Université d'Orleans-Brgm, Orleans, France
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Mallikarjun Shakarad
- Evolutionary Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Rup Lal
- NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute, New Delhi, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
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17
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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18
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McKay LJ, Nigro OD, Dlakić M, Luttrell KM, Rusch DB, Fields MW, Inskeep WP. Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems. THE ISME JOURNAL 2022; 16:842-855. [PMID: 34650231 PMCID: PMC8857204 DOI: 10.1038/s41396-021-01132-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022]
Abstract
Modern linkages among magmatic, geochemical, and geobiological processes provide clues about the importance of thermophiles in the origin of biogeochemical cycles. The aim of this study was to identify the primary chemoautotrophs and host-virus interactions involved in microbial colonization and biogeochemical cycling at sublacustrine, vapor-dominated vents that represent the hottest measured ecosystems in Yellowstone National Park (~140 °C). Filamentous microbial communities exposed to extreme thermal and geochemical gradients were sampled using a remotely operated vehicle and subjected to random metagenome sequencing and microscopic analyses. Sulfurihydrogenibium (phylum Aquificae) was the predominant lineage (up to 84% relative abundance) detected at vents that discharged high levels of dissolved H2, H2S, and CO2. Metabolic analyses indicated carbon fixation by Sulfurihydrogenibium spp. was powered by the oxidation of reduced sulfur and H2, which provides organic carbon for heterotrophic community members. Highly variable Sulfurihydrogenibium genomes suggested the importance of intra-population diversity under extreme environmental and viral pressures. Numerous lytic viruses (primarily unclassified taxa) were associated with diverse archaea and bacteria in the vent community. Five circular dsDNA uncultivated virus genomes (UViGs) of ~40 kbp length were linked to the Sulfurihydrogenibium metagenome-assembled genome (MAG) by CRISPR spacer matches. Four UViGs contained consistent genome architecture and formed a monophyletic cluster with the recently proposed Pyrovirus genus within the Caudovirales. Sulfurihydrogenibium spp. also contained CRISPR arrays linked to plasmid DNA with genes for a novel type IV filament system and a highly expressed β-barrel porin. A diverse suite of transcribed secretion systems was consistent with direct microscopic analyses, which revealed an extensive extracellular matrix likely critical to community structure and function. We hypothesize these attributes are fundamental to the establishment and survival of microbial communities in highly turbulent, extreme-gradient environments.
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Affiliation(s)
- Luke J. McKay
- grid.41891.350000 0001 2156 6108Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Olivia D. Nigro
- grid.256872.c0000 0000 8741 0387Department of Natural Science, Hawaii Pacific University, Honolulu, HI 96813 USA
| | - Mensur Dlakić
- grid.41891.350000 0001 2156 6108Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Karen M. Luttrell
- grid.64337.350000 0001 0662 7451Department of Geology & Geophysics, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Douglas B. Rusch
- grid.411377.70000 0001 0790 959XCenter for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405 USA
| | - Matthew W. Fields
- grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - William P. Inskeep
- grid.41891.350000 0001 2156 6108Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT 59717 USA ,grid.41891.350000 0001 2156 6108Thermal Biology Institute, Montana State University, Bozeman, MT 59717 USA
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19
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Peña-Ocaña BA, Ovando-Ovando CI, Puente-Sánchez F, Tamames J, Servín-Garcidueñas LE, González-Toril E, Gutiérrez-Sarmiento W, Jasso-Chávez R, Ruíz-Valdiviezo VM. Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake. ENVIRONMENTAL RESEARCH 2022; 203:111862. [PMID: 34400165 DOI: 10.1016/j.envres.2021.111862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
El Chichón volcano is one of the most active volcanoes in Mexico. Previous studies have described its poly-extreme conditions and its bacterial composition, although the functional features of the complete microbiome have not been characterized yet. By using metabarcoding analysis, metagenomics, metabolomics and enzymology techniques, the microbiome of the crater lake was characterized in this study. New information is provided on the taxonomic and functional diversity of the representative Archaea phyla, Crenarchaeota and Euryarchaeota, as well as those that are representative of Bacteria, Thermotogales and Aquificae. With culture of microbial consortia and with the genetic information collected from the natural environment sampling, metabolic interactions were identified between prokaryotes, which can withstand multiple extreme conditions. The existence of a close relationship between the biogeochemical cycles of carbon and sulfur in an active volcano has been proposed, while the relationship in the energy metabolism of thermoacidophilic bacteria and archaea in this multi-extreme environment was biochemically revealed for the first time. These findings contribute towards understanding microbial metabolism under extreme conditions, and provide potential knowledge pertaining to "microbial dark matter", which can be applied to biotechnological processes and evolutionary studies.
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Affiliation(s)
- Betsy Anaid Peña-Ocaña
- Tecnologico Nacional de México / IT de Tuxtla Gutierrez, Tuxtla Gutiérrez, Chiapas, Mexico; Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico
| | | | - Fernando Puente-Sánchez
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Department of Aquatic Sciences and Assessment, Swedish University for Agricultural Sciences (SLU), Lennart Hjelms väg 9, 756 51, Uppsala, Sweden
| | - Javier Tamames
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | | | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Mexico City, Mexico.
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20
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Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils. mSystems 2021; 6:e0075221. [PMID: 34812648 PMCID: PMC8609970 DOI: 10.1128/msystems.00752-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
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21
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Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats. Microbiol Spectr 2021; 9:e0069421. [PMID: 34787442 PMCID: PMC8597652 DOI: 10.1128/spectrum.00694-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community. IMPORTANCE Hot springs harbor microbial communities dominated by a limited variety of microorganisms and, as such, have become a model for studying community ecology and understanding how biotic and abiotic interactions shape their structure. Viruses in hot springs are shown to be ubiquitous, numerous, and active components of these communities. However, lytic and lysogenic viral communities of thermophilic phototrophic microbial mats (PMMs) remain largely unexplored. In this work, we use the power of viral metagenomics to reveal changes in the viral community following a mitomycin C induction experiment in PMMs. The importance of our research is that it will improve our understanding of viral lifestyles in PMMs via exploring the differences in the composition of natural and induced viral communities at the genome and gene levels. This novel information will contribute to deciphering which biotic and abiotic factors may control the transitions between lytic and lysogenic cycles in these extreme environments.
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22
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Reichart NJ, Bowers RM, Woyke T, Hatzenpichler R. High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics. Front Microbiol 2021; 12:668238. [PMID: 33968004 PMCID: PMC8098120 DOI: 10.3389/fmicb.2021.668238] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.
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Affiliation(s)
- Nicholas J Reichart
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Robert M Bowers
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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23
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Mueller RC, Peach JT, Skorupa DJ, Copié V, Bothner B, Peyton BM. An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol Ecol 2021; 97:6021323. [PMID: 33501490 DOI: 10.1093/femsec/fiaa246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.
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Affiliation(s)
- Rebecca C Mueller
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA
| | - Dana J Skorupa
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
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24
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Yasir M, Qureshi AK, Azhar EI. 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients. PeerJ 2021; 9:e10995. [PMID: 33859871 PMCID: PMC8020870 DOI: 10.7717/peerj.10995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/02/2021] [Indexed: 12/05/2022] Open
Abstract
Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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25
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Choure K, Parsai S, Kotoky R, Srivastava A, Tilwari A, Rai PK, Sharma A, Pandey P. Comparative Metagenomic Analysis of Two Alkaline Hot Springs of Madhya Pradesh, India and Deciphering the Extremophiles for Industrial Enzymes. Front Genet 2021; 12:643423. [PMID: 33763123 PMCID: PMC7982539 DOI: 10.3389/fgene.2021.643423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022] Open
Abstract
Hot springs are considered to be a unique environment with extremophiles, that are sources of industrially important enzymes, and other biotechnological products. The objective of this study was to undertake, analyze, and characterize the microbiome of two major hot springs located in the state of Madhya Pradesh explicitly, Chhoti Anhoni (Hotspring 1), and Badi Anhoni (Hotspring 2) to find out the inhabitant microbial population, and their functional characteristics. The taxonomic analysis of the microbiome of the hot springs revealed the phylum Proteobacteria was the most abundant taxa in both the hot-springs, however, its abundance in hot-spring 1 (~88%) was more than the hot-spring 2 (~52%). The phylum Bacteroides (~10–22%) was found to be the second most abundant group in the hot-springs followed by Spirocheates (~2–11%), Firmicutes (~6–8%), Chloroflexi (1–5%), etc. The functional analysis of the microbiome revealed different features related to several functions including metabolism of organics and degradation of xenobiotic compounds. The functional analysis showed that most of the attributes of the microbiome was related to metabolism, followed by cellular processes and environmental information processing functions. The functional annotation of the microbiomes at KEGG level 3 annotated the sequences into 279 active features that showed variation in abundance between the hot spring samples, where hot-spring 1 was functionally more diverse. Interestingly, the abundance of functional genes from methanogenic bacteria, was higher in the hot-spring 2, which may be related to the relatively higher pH and temperature than Hotspring 1. The study showed the presence of different unassigned bacterial taxa with high abundance which indicates the potential of novel genera or phylotypes. Culturable isolates (28) were bio-prospected for industrially important enzymes including amylase, protease, lipase, gelatinase, pectinase, cellulase, lecithinase, and xylanase. Seven isolates (25%) had shown positive results for all the enzyme activities whereas 23 isolates (82%) produced Protease, 27 isolates (96%) produced lipase, 27 isolates produced amylase, 26 isolates (92%) produced cellulase, 19 isolates (67%) produced pectinase, 19 isolates (67%) could produce lecithinase, and 13 isolates (46%) produced gelatinase. The seven isolates, positive for all the enzymes were analyzed further for quantitative analysis and identified through molecular characterization.
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Affiliation(s)
- Kamlesh Choure
- Department of Biotechnology, AKS University, Satna, India
| | | | - Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, India
| | | | - Anita Tilwari
- Centre of Excellence in Biotechnology, Madhya Pradesh Council of Science and Technology, Bhopal, India
| | | | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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26
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Osborne P, Hall LJ, Kronfeld-Schor N, Thybert D, Haerty W. A rather dry subject; investigating the study of arid-associated microbial communities. ENVIRONMENTAL MICROBIOME 2020; 15:20. [PMID: 33902728 PMCID: PMC8067391 DOI: 10.1186/s40793-020-00367-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/12/2020] [Indexed: 05/08/2023]
Abstract
Almost one third of Earth's land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.
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Affiliation(s)
- Peter Osborne
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK.
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | | | - David Thybert
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
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27
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Peltek SE, Bryanskaya AV, Uvarova YE, Rozanov AS, Ivanisenko TV, Ivanisenko VA, Lazareva EV, Saik OV, Efimov VM, Zhmodik SM, Taran OP, Slynko NM, Shekhovtsov SV, Parmon VN, Dobretsov NL, Kolchanov NA. Young «oil site» of the Uzon Caldera as a habitat for unique microbial life. BMC Microbiol 2020; 20:349. [PMID: 33228530 PMCID: PMC7685581 DOI: 10.1186/s12866-020-02012-1] [Citation(s) in RCA: 2] [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: 09/15/2020] [Accepted: 10/15/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks. RESULTS The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities. CONCLUSIONS There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.
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Affiliation(s)
- Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
| | - Yuliya E Uvarova
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Aleksey S Rozanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Timofey V Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Vladimir A Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Olga V Saik
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Vadim M Efimov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Sergey M Zhmodik
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Oxana P Taran
- Institute of Chemistry and Chemical Technology SB RAS, FRC Krasnoyarsk Science Center SB RAS, Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036
- Siberian Federal University, Svobodny ave. 79, Krasnoyarsk, Russia, 660041
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay M Slynko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Sergey V Shekhovtsov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Valentin N Parmon
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay L Dobretsov
- Trofimuk Institute of Petroleum Geology and Geophysics SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Nikolay A Kolchanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
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28
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Palmer M, Hedlund BP, Roux S, Tsourkas PK, Doss RK, Stamereilers C, Mehta A, Dodsworth JA, Lodes M, Monsma S, Glavina del Rio T, Schoenfeld TW, Eloe-Fadrosh EA, Mead DA. Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. Front Microbiol 2020; 11:583361. [PMID: 33281778 PMCID: PMC7689252 DOI: 10.3389/fmicb.2020.583361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/16/2020] [Indexed: 12/27/2022] Open
Abstract
Despite the high abundance of Aquificae in many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) of Thermocrinis Octopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional viral species. Despite low overall similarity among viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a PolA-type DNA polymerase polyprotein with likely accessory functions, a DNA Pol III sliding clamp, a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsid, large and small subunits of terminase, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivated Caudovirales. These viruses are predicted to infect Aquificae, as multiple CRISPR spacers matching the viral genomes were identified within the genomes and metagenomic contigs from these bacteria. Based on the predicted atypical bi-directional replication strategy, low sequence similarity to known viral genomes, and unique position in gene-sharing networks, we propose a new putative genus, "Pyrovirus," in the order Caudovirales.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Ryan K. Doss
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Casey Stamereilers
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Astha Mehta
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jeremy A. Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | | | | | | | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
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29
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The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities. Microorganisms 2020; 8:microorganisms8111677. [PMID: 33137872 PMCID: PMC7692377 DOI: 10.3390/microorganisms8111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/28/2022] Open
Abstract
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.
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30
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Li L, Li W, Zou Q, Ma Z(S. Network analysis of the hot spring microbiome sketches out possible niche differentiations among ecological guilds. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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32
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Pérez V, Cortés J, Marchant F, Dorador C, Molina V, Cornejo-D’Ottone M, Hernández K, Jeffrey W, Barahona S, Hengst MB. Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System. Microorganisms 2020; 8:E208. [PMID: 32028722 PMCID: PMC7074759 DOI: 10.3390/microorganisms8020208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 11/30/2022] Open
Abstract
Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42-72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.
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Affiliation(s)
- Vilma Pérez
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Australian Centre for Ancient DNA (ACAD), University of Adelaide, Adelaide, SA 5005, Australia
| | - Johanna Cortés
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
| | - Francisca Marchant
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
| | - Cristina Dorador
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
| | - Verónica Molina
- Observatorio de Ecología Microbiana, Departamento de Biología Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso 2340000, Chile;
| | - Marcela Cornejo-D’Ottone
- Escuela de Ciencias del Mar & Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile;
| | - Klaudia Hernández
- Centro de Investigación Marina Quintay CIMARQ, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago 8320000, Chile;
| | - Wade Jeffrey
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, FL 32514, USA;
| | - Sergio Barahona
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Laboratorio de Microbiología Aplicada y Extremófilos, Universidad Católica del Norte, Antofagasta 1240000, Chile
| | - Martha B. Hengst
- Laboratorio de Ecologia Molecular y Microbiologia Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1240000, Chile; (V.P.);
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Chile, Santiago 8320000, Chile; (F.M.); (C.D.)
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Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW. Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats. ASTROBIOLOGY 2019; 19:1442-1458. [PMID: 31038352 PMCID: PMC6918859 DOI: 10.1089/ast.2018.1965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.
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Affiliation(s)
- Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
- Division School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Christopher J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M. Yau
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dag Ahrén
- Microbial Ecology Group, Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Lund, Sweden
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
| | - Kyle W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology and Environmental Sciences, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Joseph Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Charles R. Werth
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Texas, USA
| | - Isaac K. Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathleen M. Keating
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Radhika S. Khetani
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Brian S. Imai
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Glenn A. Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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34
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Nishiyama E, Higashi K, Mori H, Suda K, Nakamura H, Omori S, Maruyama S, Hongoh Y, Kurokawa K. The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan. Front Bioeng Biotechnol 2018; 6:202. [PMID: 30619848 PMCID: PMC6306410 DOI: 10.3389/fbioe.2018.00202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022] Open
Abstract
Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.
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Affiliation(s)
- Eri Nishiyama
- Biotechnological Research Support Division, FASMAC Co. Ltd, Kanagawa, Japan.,Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Koichi Higashi
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Konomi Suda
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hitomi Nakamura
- Department of Solid Earth Geochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Soichi Omori
- Faculty of Liberal Arts, The Open University of Japan, Chiba, Japan
| | - Shigenori Maruyama
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
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35
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Tang J, Liang Y, Jiang D, Li L, Luo Y, Shah MMR, Daroch M. Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China. BMC Microbiol 2018; 18:134. [PMID: 30332987 PMCID: PMC6191902 DOI: 10.1186/s12866-018-1271-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Ganzi Prefecture in Western China is situated geographically at the transition regions between Tibetan Plateau and Sichuan Basin in a highly tectonically active boundary area between the India and Eurasia plates. The region hosts various hot springs that span a wide range of temperature from 30 to 98 °C and are located at high altitude (up to 4200 m above sea level) in the region of large geothermal anomalies and active Xianshuihe slip-fault that has been active since Holocene. The site represents a biodiversity reservoir for thermophiles, yet their diversity and relationship to geochemical parameters are largely unknown. In the present work, bacterial diversity and community structure in 14 hot springs of Ganzi were investigated using Illumina MiSeq sequencing. Results Bacterial community compositions were evidently distinct among the 14 hot springs, and the bacterial communities in hot springs were majorly abundant in phyla Aquificae, Cyanobacteria and Proteobacteria. Both clustering and PCoA analysis suggested the existence of four bacterial community patterns in these hot springs. Temperature contributed to shaping bacterial community structure of hot springs as revealed by correlation analysis. Abundant unassigned-genus sequences detected in this study strongly implied the presence of novel genera or genetic resources in these hot springs. Conclusion The diversity of hot springs of Ganzi prefecture in Western Sichuan, China is evidently shaped by temperature. Interestingly disproportionally abundant unassigned-genus sequences detected in this study show indicate potential of novel genera or phylotypes. We hypothesize that frequent earthquakes and rapidly changing environment might have contributed to evolution of these potentially new lineages. Overall, this study provided first insight into the bacterial diversity of hot springs located in Western Sichuan, China and its comparison with other similar communities worldwide. Electronic supplementary material The online version of this article (10.1186/s12866-018-1271-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Tang
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Yuanmei Liang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Dong Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Liheng Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yifan Luo
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Md Mahfuzur R Shah
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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36
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Hunt KA, Jennings RM, Inskeep WP, Carlson RP. Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PLoS Comput Biol 2018; 14:e1006431. [PMID: 30260956 PMCID: PMC6177205 DOI: 10.1371/journal.pcbi.1006431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 10/09/2018] [Accepted: 08/13/2018] [Indexed: 11/18/2022] Open
Abstract
Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.
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Affiliation(s)
- Kristopher A. Hunt
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Ryan M. Jennings
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - William P. Inskeep
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (RPC)
| | - Ross P. Carlson
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (RPC)
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37
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Discovering novel hydrolases from hot environments. Biotechnol Adv 2018; 36:2077-2100. [PMID: 30266344 DOI: 10.1016/j.biotechadv.2018.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.
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38
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Crognale S, Venturi S, Tassi F, Rossetti S, Rashed H, Cabassi J, Capecchiacci F, Nisi B, Vaselli O, Morrison HG, Sogin ML, Fazi S. Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy). FEMS Microbiol Ecol 2018; 94:5105751. [DOI: 10.1093/femsec/fiy190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Simona Crognale
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Stefania Venturi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Franco Tassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Simona Rossetti
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Heba Rashed
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Jacopo Cabassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Francesco Capecchiacci
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Barbara Nisi
- IGG – CNR Institute of Geosciences and Earth Resources, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Orlando Vaselli
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
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Amenabar MJ, Colman DR, Poudel S, Roden EE, Boyd ES. Electron acceptor availability alters carbon and energy metabolism in a thermoacidophile. Environ Microbiol 2018; 20:2523-2537. [PMID: 29749696 DOI: 10.1111/1462-2920.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022]
Abstract
The thermoacidophilic Acidianus strain DS80 displays versatility in its energy metabolism and can grow autotrophically and heterotrophically with elemental sulfur (S°), ferric iron (Fe3+ ) or oxygen (O2 ) as electron acceptors. Here, we show that autotrophic and heterotrophic growth with S° as the electron acceptor is obligately dependent on hydrogen (H2 ) as electron donor; organic substrates such as acetate can only serve as a carbon source. In contrast, organic substrates such as acetate can serve as electron donor and carbon source for Fe3+ or O2 grown cells. During growth on S° or Fe3+ with H2 as an electron donor, the amount of CO2 assimilated into biomass decreased when cultures were provided with acetate. The addition of CO2 to cultures decreased the amount of acetate mineralized and assimilated and increased cell production in H2 /Fe3+ grown cells but had no effect on H2 /S° grown cells. In acetate/Fe3+ grown cells, the presence of H2 decreased the amount of acetate mineralized as CO2 in cultures compared to those without H2 . These results indicate that electron acceptor availability constrains the variety of carbon sources used by this strain. Addition of H2 to cultures overcomes this limitation and alters heterotrophic metabolism.
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Affiliation(s)
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Eric E Roden
- Department of Geosciences, University of Wisconsin, Madison, WI, USA.,NASA Astrobiology Institute, Mountain View, CA, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.,NASA Astrobiology Institute, Mountain View, CA, USA
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40
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Amenabar MJ, Boyd ES. Mechanisms of Mineral Substrate Acquisition in a Thermoacidophile. Appl Environ Microbiol 2018; 84:e00334-18. [PMID: 29625980 PMCID: PMC5981063 DOI: 10.1128/aem.00334-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/02/2018] [Indexed: 01/01/2023] Open
Abstract
The thermoacidophile Acidianus is widely distributed in Yellowstone National Park hot springs that span large gradients in pH (1.60 to 4.84), temperature (42 to 90°C), and mineralogical composition. To characterize the potential role of flexibility in mineral-dependent energy metabolism in contributing to the widespread ecological distribution of this organism, we characterized the spectrum of minerals capable of supporting metabolism and the mechanisms that it uses to access these minerals. The energy metabolism of Acidianus strain DS80 was supported by elemental sulfur (S0), a variety of iron (hydr)oxides, and arsenic sulfide. Strain DS80 reduced, oxidized, and disproportionated S0 Cells growing via S0 reduction and disproportionation did not require direct access to the mineral to reduce it, whereas cells growing via S0 oxidation did require direct access, observations that are attributable to the role of H2S produced by S0 reduction/disproportionation in solubilizing and increasing the bioavailability of S0 Cells growing via iron (hydr)oxide reduction did not require access to the mineral, suggesting that the cells reduce Fe(III) that is being leached by the acidic growth medium. Cells growing via oxidation of arsenic sulfide with Fe(III) did not require access to the mineral to grow. The stoichiometry of reactants to products indicates that cells oxidize soluble As(III) released from oxidation of arsenic sulfide by aqueous Fe(III). Taken together, these observations underscore the importance of feedbacks between abiotic and biotic reactions in influencing the bioavailability of mineral substrates and defining ecological niches capable of supporting microbial metabolism.IMPORTANCE Mineral sources of electron donor and acceptor that support microbial metabolism are abundant in the natural environment. However, the spectrum of minerals capable of supporting a given microbial strain and the mechanisms that are used to access these minerals in support of microbial energy metabolism are often unknown, in particular among thermoacidophiles. Here, we show that the thermoacidophile Acidianus strain DS80 is adapted to use a variety of iron (hydro)oxide minerals, elemental sulfur, and arsenic sulfide to support growth. Cells rely on a complex interplay of abiologically and biologically catalyzed reactions that increase the solubility or bioavailability of minerals, thereby enabling their use in microbial metabolism.
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Affiliation(s)
- Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- NASA Astrobiology Institute, Mountain View, California, USA
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41
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Kraus EA, Beeler SR, Mors RA, Floyd JG, Stamps BW, Nunn HS, Stevenson BS, Johnson HA, Shapiro RS, Loyd SJ, Spear JR, Corsetti FA. Microscale Biosignatures and Abiotic Mineral Authigenesis in Little Hot Creek, California. Front Microbiol 2018; 9:997. [PMID: 29887837 PMCID: PMC5981138 DOI: 10.3389/fmicb.2018.00997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/27/2018] [Indexed: 11/13/2022] Open
Abstract
Hot spring environments can create physical and chemical gradients favorable for unique microbial life. They can also include authigenic mineral precipitates that may preserve signs of biological activity on Earth and possibly other planets. The abiogenic or biogenic origins of such precipitates can be difficult to discern, therefore a better understanding of mineral formation processes is critical for the accurate interpretation of biosignatures from hot springs. Little Hot Creek (LHC) is a hot spring complex located in the Long Valley Caldera, California, that contains mineral precipitates composed of a carbonate base (largely submerged) topped by amorphous silica (largely emergent). The precipitates occur in close association with microbial mats and biofilms. Geological, geochemical, and microbiological data are consistent with mineral formation via degassing and evaporation rather than direct microbial involvement. However, the microfabric of the silica portion is stromatolitic in nature (i.e., wavy and finely laminated), suggesting that abiogenic mineralization has the potential to preserve textural biosignatures. Although geochemical and petrographic evidence suggests the calcite base was precipitated via abiogenic processes, endolithic microbial communities modified the structure of the calcite crystals, producing a textural biosignature. Our results reveal that even when mineral precipitation is largely abiogenic, the potential to preserve biosignatures in hot spring settings is high. The features found in the LHC structures may provide insight into the biogenicity of ancient Earth and extraterrestrial rocks.
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Affiliation(s)
- Emily A Kraus
- Geo- Environmental- Microbiology Laboratory, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Scott R Beeler
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - R Agustin Mors
- Laboratorio de Paleobiología y Geomicrobiología Experimental, Centro de Investigaciones en Ciencias de la Tierra (CONICET-UNC), Córdoba, Argentina
| | - James G Floyd
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | | | - Blake W Stamps
- Geo- Environmental- Microbiology Laboratory, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Heather S Nunn
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Hope A Johnson
- Department of Biological Sciences, California State University, Fullerton, Fullerton, CA, United States
| | - Russell S Shapiro
- Geological and Environmental Sciences, California State University, Chico, Chico, CA, United States
| | - Sean J Loyd
- Department of Geological Sciences, California State University, Fullerton, Fullerton, CA, United States
| | - John R Spear
- Geo- Environmental- Microbiology Laboratory, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Frank A Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
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42
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Jay ZJ, Beam JP, Dlakić M, Rusch DB, Kozubal MA, Inskeep WP. Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nat Microbiol 2018; 3:732-740. [PMID: 29760463 DOI: 10.1038/s41564-018-0163-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 04/16/2018] [Indexed: 11/09/2022]
Abstract
The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcriptional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). Phylogenomic analyses of replicate assemblies corresponding to two groups of Marsarchaeota indicate that they branch between the Crenarchaeota and all other major archaeal lineages. Transcriptomic analyses of several Fe(III) oxide mat communities reveal that these organisms were actively transcribing two different terminal oxidase complexes in situ and genes comprising an F420-dependent butanal catabolism. The broad distribution of Marsarchaeota in geothermal, microaerobic Fe(III) oxide mats suggests that similar habitat types probably played an important role in the evolution of archaea.
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Affiliation(s)
- Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering and Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Jacob P Beam
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Mensur Dlakić
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Douglas B Rusch
- Center for Bioinformatics, Indiana University, Bloomington, IN, USA
| | - Mark A Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.,Sustainable Bioproducts, Bozeman, MT, USA
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
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43
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Archaeal Viruses from High-Temperature Environments. Genes (Basel) 2018; 9:genes9030128. [PMID: 29495485 PMCID: PMC5867849 DOI: 10.3390/genes9030128] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal viruses are some of the most enigmatic viruses known, due to the small number that have been characterized to date. The number of known archaeal viruses lags behind known bacteriophages by over an order of magnitude. Despite this, the high levels of genetic and morphological diversity that archaeal viruses display has attracted researchers for over 45 years. Extreme natural environments, such as acidic hot springs, are almost exclusively populated by Archaea and their viruses, making these attractive environments for the discovery and characterization of new viruses. The archaeal viruses from these environments have provided insights into archaeal biology, gene function, and viral evolution. This review focuses on advances from over four decades of archaeal virology, with a particular focus on archaeal viruses from high temperature environments, the existing challenges in understanding archaeal virus gene function, and approaches being taken to overcome these limitations.
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44
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Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors. Extremophiles 2018; 22:525-535. [DOI: 10.1007/s00792-018-1014-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/11/2018] [Indexed: 10/18/2022]
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45
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Chiriac CM, Baricz A, Szekeres E, Rudi K, Dragoș N, Coman C. Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania. MICROBIAL ECOLOGY 2018; 75:38-51. [PMID: 28702708 DOI: 10.1007/s00248-017-1031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
A limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of "fossilized waters," while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432 m below the surface, with collected water temperatures ranging between 47 and 104 °C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80 °C. The abundances of bacterial 16S rRNA genes varied from approximately 105-106 mL-1 in the Pannonian to about 102-104 mL-1 in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.
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Affiliation(s)
- Cecilia M Chiriac
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Knut Rudi
- Chemistry, Biotechnology and Food Science Department, Norwegian University of Life Sciences, Aas, Norway
| | - Nicolae Dragoș
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania.
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46
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Zablocki O, van Zyl LJ, Kirby B, Trindade M. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses 2017; 9:E348. [PMID: 29156552 PMCID: PMC5707555 DOI: 10.3390/v9110348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
The current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 °C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction. Microscopy analysis revealed a mixture of regular- and 'jumbo'-sized tailed morphotypes (Caudovirales), lemon-shaped virions (Fuselloviridae-like; salterprovirus-like) and pleiomorphic virus-like particles. Metavirome analysis corroborated the presence of His1-like viruses and has expanded the current clade of salterproviruses using a polymerase B gene phylogeny. The most represented viral contig was to a cyanophage genome fragment, which may underline basic ecosystem functioning provided by these viruses. Furthermore, a putative Gemmata-related phage was assembled with high coverage, a previously undocumented phage-host association. This study demonstrated that a moderately thermophilic spring environment contained a highly novel pool of viruses and should encourage future characterization of a wider temperature range of hot springs throughout the world.
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Affiliation(s)
- Olivier Zablocki
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Bronwyn Kirby
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
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47
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Campbell KM, Kouris A, England W, Anderson RE, McCleskey RB, Nordstrom DK, Whitaker RJ. Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs. Environ Microbiol 2017; 19:2334-2347. [PMID: 28276174 DOI: 10.1111/1462-2920.13728] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/25/2017] [Indexed: 12/01/2022]
Abstract
Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over 3 years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs. Although geography controls regional geochemical composition and population differentiation, temporal changes in population were not explained by corresponding variation in geochemistry. The data suggest that the influence of extinction, bottleneck events and/or selective sweeps within a spring and low migration between springs shape these populations. We suggest that hydrologic events such as storm events and surface snowmelt runoff destabilize smaller hot spring environments with smaller populations and result in high variation in the S. islandicus population over time. Therefore, physical abiotic features such as hot spring size and position in the landscape are important factors shaping the stability and diversity of the S. islandicus meta-population within Yellowstone National Park.
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Affiliation(s)
| | - Angela Kouris
- Department of Microbiology 601 S. Goodwin Ave, Urbana IL 61801 and Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, IL 61801
| | - Whitney England
- Department of Microbiology 601 S. Goodwin Ave, Urbana IL 61801 and Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, IL 61801
| | - Rika E Anderson
- Department of Microbiology 601 S. Goodwin Ave, Urbana IL 61801 and Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, IL 61801.,Biology Department, Carleton College, Northfield, MN, 55057
| | | | | | - Rachel J Whitaker
- Department of Microbiology 601 S. Goodwin Ave, Urbana IL 61801 and Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Drive, Urbana, IL 61801
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48
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Ghilamicael AM, Budambula NLM, Anami SE, Mehari T, Boga HI. Evaluation of prokaryotic diversity of five hot springs in Eritrea. BMC Microbiol 2017; 17:203. [PMID: 28938870 PMCID: PMC5610464 DOI: 10.1186/s12866-017-1113-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Background Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the springs range from 49.5 °C to 100 °C while pH levels varied from 6.97 to 7.54. Akwar and Maiwooi have high carbonate levels. The springs near the seashore, Garbanabra and Gelti, are more saline with higher levels of sodium and chlorides. Elegedi, situated in the Alid volcanic area, has the highest temperature, iron and sulfate concentrations. Results The five hot springs shared 901 of 4371 OTUs recovered while the three sample types (water, wet sediment and microbial mats) also shared 1429 OTUs. The Chao1 OTU estimate in water sample was significantly higher than the wet sediment and microbial mat samples. As indicated by NMDS, the community samples at genus level showed location specific clustering. Certain genera correlated with temperature, sodium, carbonate, iron, sulfate and ammonium levels in water. The abundant phyla included Proteobacteria (6.2–82.3%), Firmicutes (1.6–63.5%), Deinococcus-Thermus (0.0–19.2%), Planctomycetes (0.0–11.8%), Aquificae (0.0–9.9%), Chlorobi (0.0–22.3%) and Bacteroidetes (2.7–8.4%). Conclusion There were significant differences in microbial community structure within the five locations and sample types at OTU level. The occurence of Aquificae, Deinococcus-Thermus, some Cyanobacteria and Crenarchaeota were highly dependent on temperature. The Halobacterium, unclassified Thaumarchaeota, Actinobacteria and Cyanobacteria showed significant correlation with salinity occurring abundantly in Garbanabra and Gelti. Firmicutes and unclassified Rhodocylaceae were higher in the microbial mat samples, while Archaea were prominent in the wet sediment samples. Electronic supplementary material The online version of this article (10.1186/s12866-017-1113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanuel M Ghilamicael
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | | | - Sylvester E Anami
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Tadesse Mehari
- National Commission for Higher Education in Eritrea, Asmara, Eritrea
| | - Hamadi I Boga
- Taita Taveta University, P.O. Box 635-80300, Voi, Kenya.
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49
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Chaudhuri B, Chowdhury T, Chattopadhyay B. Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India. GENOMICS DATA 2017; 12:122-129. [PMID: 28507897 PMCID: PMC5423328 DOI: 10.1016/j.gdata.2017.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 11/30/2022]
Abstract
Various aspects of hot springs at Bakreshwar (Lat. 23°52'48″N; Long. 87°22'40″E) in West Bengal, India have been investigated since the middle of 20th century, but comprehending the complete diversity and the complexity of the microbial population therein has been in the continuing process. Some of these microorganisms are found to have immense industrial importance. Microbes generally exist in milieus of varying complexities and diversities. Attempting the usually employed cultivation-based techniques in experimentation with those microbes had confronted various limitations. To overcome these limitations a strategy based on high-throughput sequencing of 16S rRNA gene amplicon analysis was employed for studying the differential diversity and the detailed nature of microbial population of the two hot springs of Bakreshwar (54 °C & 65 °C). Paired-end libraries of amplified V-3 hyper-variable 16S rDNA fragments from sets of samples that varied in their contents, ranging from a single bacterium to highly complex communities were sequenced. The comparison revealed the differential aspects in the two hot spring waters; the samples at 54 °C showed the bacterial phylum Firmicutes (65.85%) and Synergistetes (27.24%) predominating and those from hot spring water at 65 °C showed the abundance of the phyla Firmicutes (96.10%) and Proteobacteria (3.36%). The presence of Archaea in the hot springs could not be ascertained.
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Affiliation(s)
| | | | - Brajadulal Chattopadhyay
- Department of Physics, Jadavpur University, Raja Subodh Chandra Mallick Road, Kolkata 700 032, West Bengal, India
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50
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Ward L, Taylor MW, Power JF, Scott BJ, McDonald IR, Stott MB. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring. THE ISME JOURNAL 2017; 11:1158-1167. [PMID: 28072418 PMCID: PMC5437927 DOI: 10.1038/ismej.2016.193] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/21/2016] [Accepted: 11/19/2016] [Indexed: 11/08/2022]
Abstract
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.
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Affiliation(s)
- Laura Ward
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Michael W Taylor
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Jean F Power
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
| | - Bradley J Scott
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
| | - Ian R McDonald
- University of Waikato, School of Science, Hamilton, New Zealand
| | - Matthew B Stott
- GNS Science, Wairakei Research Centre, Wairakei, Taup, New Zealand
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