1
|
Su X, Zhang L, Meng H, Wang H, Zhao J, Sun X, Song X, Zhang X, Mao L. Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO 2 fixation pathways in coastal saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120743. [PMID: 38626484 DOI: 10.1016/j.jenvman.2024.120743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.
Collapse
Affiliation(s)
- Xunya Su
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Le Zhang
- China Agricultural University, Agronomy College, Beijing, 100193, China.
| | - Hao Meng
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Han Wang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Jiaxue Zhao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xuezhen Sun
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xianliang Song
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xiaopei Zhang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Lili Mao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| |
Collapse
|
2
|
Power JF, Carere CR, Welford HE, Hudson DT, Lee KC, Moreau JW, Ettema TJG, Reysenbach AL, Lee CK, Colman DR, Boyd ES, Morgan XC, McDonald IR, Craig Cary S, Stott MB. A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nat Commun 2024; 15:179. [PMID: 38167814 PMCID: PMC10762115 DOI: 10.1038/s41467-023-43960-2] [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: 04/18/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
Collapse
Affiliation(s)
- Jean F Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Carlo R Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Holly E Welford
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Daniel T Hudson
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
| | - Kevin C Lee
- Te Kura Pūtaiao | School of Science, Te Wānanga Aronui o Tāmaki Makau Rau | Auckland University of Technology, Auckland, 1010, Aotearoa New Zealand
| | - John W Moreau
- School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | | | - Charles K Lee
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Xochitl C Morgan
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian R McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - S Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand.
| |
Collapse
|
3
|
Wang X, Yin Y, Yu Z, Shen G, Cheng H, Tao S. Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160832. [PMID: 36521602 DOI: 10.1016/j.scitotenv.2022.160832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.
Collapse
Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
4
|
Skariah S, Abdul-Majid S, Hay AG, Acharya A, Kano N, Al-Ishaq RK, de Figueiredo P, Han A, Guzman A, Dargham SR, Sameer S, Kim GE, Khan S, Pillai P, Sultan AA. Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils. Microbiol Spectr 2023; 11:e0346222. [PMID: 36847511 PMCID: PMC10100838 DOI: 10.1128/spectrum.03462-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were Actinobacteria (32.3%), Proteobacteria (24.8%), Firmicutes (20.7%), Bacteroidetes (6.3%), and Chloroflexi (3.6%), though individual soils varied widely in the relative abundances of these and other phyla. Alpha diversity measured using feature richness (operational taxonomic units [OTUs]), Shannon's entropy, and Faith's phylogenetic diversity (PD) varied significantly between habitats (P = 0.016, P = 0.016, and P = 0.015, respectively). Sand, clay, and silt were significantly correlated with microbial diversity. Highly significant negative correlations were also seen at the class level between both classes Actinobacteria and Thermoleophilia (phylum Actinobacteria) and total sodium (R = -0.82 and P = 0.001 and R = -0.86, P = 0.000, respectively) and slowly available sodium (R = -0.81 and P = 0.001 and R = -0.8 and P = 0.002, respectively). Additionally, class Actinobacteria also showed significant negative correlation with sodium/calcium ratio (R = -0.81 and P = 0.001). More work is needed to understand if there is a causal relationship between these soil chemical parameters and the relative abundances of these bacteria. IMPORTANCE Soil microbes perform a multitude of essential biological functions, including organic matter decomposition, nutrient cycling, and soil structure preservation. Qatar is one of the most hostile and fragile arid environments on earth and is expected to face a disproportionate impact of climate change in the coming years. Thus, it is critical to establish a baseline understanding of microbial community composition and to assess how soil edaphic factors correlate with microbial community composition in this region. Although some previous studies have quantified culturable microbes in specific Qatari habitats, this approach has serious limitations, as in environmental samples, approximately only 0.5% of cells are culturable. Hence, this method vastly underestimates natural diversity within these habitats. Our study is the first to systematically characterize the chemistry and total microbiota associated with different habitats present in the State of Qatar.
Collapse
Affiliation(s)
- Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sara Abdul-Majid
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Anushree Acharya
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Noora Kano
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Raghad Khalid Al-Ishaq
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, Texas, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Adrian Guzman
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Soha Roger Dargham
- Biostatistics, Epidemiology, & Biomathematics Research Core, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Saad Sameer
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Gi Eun Kim
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sabiha Khan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Priyamvada Pillai
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| |
Collapse
|
5
|
Yin Z, Ye L, Jing C. Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16473-16482. [PMID: 36227700 DOI: 10.1021/acs.est.2c05764] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.
Collapse
Affiliation(s)
- Zhipeng Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ye
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| |
Collapse
|
6
|
Noell SE, Baptista MS, Smith E, McDonald IR, Lee CK, Stott MB, Amend JP, Cary SC. Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica. Front Microbiol 2022; 13:836943. [PMID: 35591982 PMCID: PMC9111169 DOI: 10.3389/fmicb.2022.836943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.
Collapse
Affiliation(s)
- Stephen E Noell
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Mafalda S Baptista
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - Emily Smith
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K Lee
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - S Craig Cary
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
DeCastro ME, Escuder-Rodríguez JJ, Becerra M, Rodríguez-Belmonte E, González-Siso MI. Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide. Front Microbiol 2021; 12:769065. [PMID: 34899652 PMCID: PMC8661477 DOI: 10.3389/fmicb.2021.769065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.
Collapse
Affiliation(s)
| | | | | | | | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| |
Collapse
|
9
|
Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring. Appl Environ Microbiol 2021; 87:e0159821. [PMID: 34586901 PMCID: PMC8579995 DOI: 10.1128/aem.01598-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.
Collapse
|
10
|
McMahon S, Matthews JJ, Brasier A, Still J. Late Ediacaran life on land: desiccated microbial mats and large biofilm streamers. Proc Biol Sci 2021; 288:20211875. [PMID: 34727717 PMCID: PMC8564610 DOI: 10.1098/rspb.2021.1875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/14/2021] [Indexed: 12/18/2022] Open
Abstract
The Ediacaran period witnessed transformational change across the Earth-life system, but life on land during this interval is poorly understood. Non-marine/transitional Ediacaran sediments preserve a variety of probable microbially induced sedimentary structures and fossil matgrounds, and the ecology, biogeochemistry and sedimentological impacts of the organisms responsible are now ripe for investigation. Here, we report well-preserved fossils from emergent siliciclastic depositional environments in the Ediacaran of Newfoundland, Canada. These include exquisite, mouldically preserved microbial mats with desiccation cracks and flip-overs, abundant Arumberia-type fossils and, most notably, assemblages of centimetre-to-metre-scale, subparallel, branching, overlapping, gently curving ribbon-like features preserved by aluminosilicate and phosphate minerals, with associated filamentous microfossils. We present morphological, petrographic and taphonomic evidence that the ribbons are best interpreted as fossilized current-induced biofilm streamers, the earliest record of an important mode of life (macroscopic streamer formation) for terrestrial microbial ecosystems today. Their presence shows that late Ediacaran terrestrial environments could produce substantial biomass, and supports recent interpretations of Arumberia as a current-influenced microbial mat fossil, which we here suggest existed on a 'streamer-arumberiamorph spectrum'. Finally, the absence of classic Ediacaran macrobiota from these rocks despite evidently favourable conditions for soft tissue preservation upholds the consensus that those organisms were exclusively marine.
Collapse
Affiliation(s)
- S. McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3FD, UK
- School of Geosciences, Grant Institute, University of Edinburgh, Edinburgh EH9 3FE, UK
| | - J. J. Matthews
- Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
| | - A. Brasier
- School of Geosciences, University of Aberdeen, King's College, Aberdeen AB24 3UE, UK
| | - J. Still
- School of Geosciences, University of Aberdeen, King's College, Aberdeen AB24 3UE, UK
| |
Collapse
|
11
|
Chen Y, Nishihara A, Iino T, Ohkuma M, Haruta S. Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542397 DOI: 10.1099/ijsem.0.005014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31-91.10 %), average amino acid identity (91.45-92.10 %) and <70 % digital DNA-DNA hybridization value (41.8-44.2 %) with the three related species of the genus Caldicellulosiruptor. Strain YA01T grew at 50-78 °C (optimum, 70 °C) and at pH 5.0-9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).
Collapse
Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-0856, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| |
Collapse
|
12
|
Colman DR, Lindsay MR, Harnish A, Bilbrey EM, Amenabar MJ, Selensky MJ, Fecteau KM, Debes RV, Stott MB, Shock EL, Boyd ES. Seasonal hydrologic and geologic forcing drive hot spring geochemistry and microbial biodiversity. Environ Microbiol 2021; 23:4034-4053. [PMID: 34111905 DOI: 10.1111/1462-2920.15617] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/10/2021] [Accepted: 05/29/2021] [Indexed: 01/31/2023]
Abstract
Hot springs integrate hydrologic and geologic processes that vary over short- and long-term time scales. However, the influence of temporal hydrologic and geologic change on hot spring biodiversity is unknown. Here, we coordinated near-weekly, cross-seasonal (~140 days) geochemical and microbial community analyses of three widely studied hot springs with local precipitation data in Yellowstone National Park. One spring ('HFS') exhibited statistically significant, coupled microbial and geochemical variation across seasons that was associated with recent precipitation patterns. Two other spring communities, 'CP' and 'DS', exhibited minimal to no variation across seasons. Variability in the seasonal response of springs is attributed to differences in the timing and extent of aquifer recharge with oxidized near-surface water from precipitation. This influx of oxidized water is associated with changes in community composition, and in particular, the abundances of aerobic sulfide-/sulfur-oxidizers that can acidify waters. During sampling, a new spring formed after a period of heavy precipitation and its successional dynamics were also influenced by surface water recharge. Collectively, these results indicate that changes in short-term hydrology associated with precipitation can impact hot spring geochemistry and microbial biodiversity. These results point to potential susceptibility of certain hot springs and their biodiversity to sustained, longer-term hydrologic changes.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Annette Harnish
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Evan M Bilbrey
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Matthew J Selensky
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Randall V Debes
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Everett L Shock
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.,School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water. Appl Environ Microbiol 2020; 86:AEM.00194-20. [PMID: 32978131 DOI: 10.1128/aem.00194-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
The compositions of Octopus Spring and Mushroom Spring (Yellowstone National Park, Wyoming, USA) microbial mats have been thoroughly studied, but the compositions of the effluent waters that flow above the mats have not. In this study, cells in the mats and overflowing waters of both springs were investigated at multiple sites where Synechococcus spp. are the dominant cyanobacteria (ca. 72°C to ca. 50°C), and on several dates. In addition to microscopic analyses of stained and autofluorescent cells, 16S rRNA gene sequencing was used to characterize the major taxa present and a protein-encoding gene (psaA) was sequenced and analyzed by ecotype simulation to predict species of Synechococcus The mats of both springs were similar in terms of the downstream distribution of predominant taxa detected previously. However, waters above these mats were predominated by taxa that reside in upstream mats or communities above the upper-temperature limit of the mat. A disturbance/recolonization study was performed at a site normally predominated by Synechococcus species adapted to low temperatures. After removing indigenous Synechococcus cells, Synechococcus species adapted to higher temperatures, which were predominant in the water overflowing this site, colonized the newly forming mat. Differences in recolonization under reduced and UV-screened irradiance suggested that, in addition to physical transport, environmental conditions likely select for species that are better adapted to these different conditions and can influence mat recovery. A transport model was developed and used to predict that, in Mushroom Spring, erosion predominates in the narrower and deeper upstream effluents and deposition predominates over erosion in wider and shallower downstream effluents.IMPORTANCE In flowing aquatic systems, cell erosion and deposition are important to the dispersal of cells from one location to another. Very little is known about microbial dispersal and the physical processes that underlie it. This study demonstrates its importance to colonization of downstream surfaces and especially to the recolonization and functioning of disturbed sites. Ecological systems in flowing environments are often, roughly speaking, pseudosteady, in that nutrients enter the system and by-products leave at relatively steady rates. Over time, material inputs and outputs must balance. Measurements of input fluxes (e.g., growth rates and proxies, such as photosynthesis rates) are frequent. However, erosion and deposition of cells are seldom measured and ecological significance is sometimes neglected. The importance of these parameters is immediately evident in any attempt to construct a model of long-time community behavior, as spatial ecological structure is significantly impacted and can be dominated by migration of organisms, even in small numbers.
Collapse
|
16
|
Mazumder P, Sharma SK, Taki K, Kalamdhad AS, Kumar M. Microbes involved in arsenic mobilization and respiration: a review on isolation, identification, isolates and implications. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:3443-3469. [PMID: 32170513 DOI: 10.1007/s10653-020-00549-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Microorganisms play an important role in arsenic (As) cycling in the environment. Microbes mobilize As directly or indirectly, and natural/geochemical processes such as sulphate and iron reduction, oxidative sulphide mineral dissolution, arsenite (AsO33-) oxidation and arsenate (AsO43-) respiration further aid in As cycle in the environment. Arsenate serves as an electron donor for the microbes during anaerobic conditions in the sediment. The present work reviews the recent development in As contamination, various As-metabolizing microbes and their phylogenetic diversity, to understand the role of microbial communities in As respiration and mobilization. It also summarizes the contemporary understanding of the intricate biochemistry and molecular biology of natural As metabolisms. Some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation are also discussed. The study indicates that there is an exigent need to have a clear understanding of environmental aspects of As mobilization and subsequent oxidation-reduction by a suitable microbial consortium.
Collapse
Affiliation(s)
- Payal Mazumder
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Subhash Kumar Sharma
- Environmental Engineering, National Institute of Technology, Tiruchirappalli, Tamil Nadu, India
| | - Kaling Taki
- Discipline of Civil Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Ajay S Kalamdhad
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
| |
Collapse
|
17
|
Massello FL, Chan CS, Chan KG, Goh KM, Donati E, Urbieta MS. Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature. Microorganisms 2020; 8:microorganisms8060906. [PMID: 32560103 PMCID: PMC7356817 DOI: 10.3390/microorganisms8060906] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.
Collapse
Affiliation(s)
- Francisco L. Massello
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (C.S.C.); (K.M.G.)
| | - Edgardo Donati
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
| | - María Sofía Urbieta
- CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900 Buenos Aires, Argentina; (F.L.M.); (E.D.)
- Correspondence:
| |
Collapse
|
18
|
Colman DR, Lindsay MR, Amenabar MJ, Boyd ES. The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems. ASTROBIOLOGY 2019; 19:1505-1522. [PMID: 31592688 DOI: 10.1089/ast.2018.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | - Melody R Lindsay
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | | | - Eric S Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Payne D, Dunham EC, Mohr E, Miller I, Arnold A, Erickson R, Fones EM, Lindsay MR, Colman DR, Boyd ES. Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity. Environ Microbiol 2019; 21:4180-4195. [PMID: 31397054 DOI: 10.1111/1462-2920.14775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023]
Abstract
Little is known about how the geological history of an environment shapes its physical and chemical properties and how these, in turn, influence the assembly of communities. Evening primrose (EP), a moderately acidic hot spring (pH 5.6, 77.4°C) in Yellowstone National Park (YNP), has undergone dramatic physicochemical change linked to seismic activity. Here, we show that this legacy of geologic change led to the development of an unusual sulphur-rich, anoxic chemical environment that supports a unique archaeal-dominated and anaerobic microbial community. Metagenomic sequencing and informatics analyses reveal that >96% of this community is supported by dissimilatory reduction or disproportionation of inorganic sulphur compounds, including a novel, deeply diverging sulphate-reducing thaumarchaeote. When compared to other YNP metagenomes, the inferred functions of EP populations were like those from sulphur-rich acidic springs, suggesting that sulphur may overprint the predominant influence of pH on the composition of hydrothermal communities. Together, these observations indicate that the dynamic geological history of EP underpins its unique geochemistry and biodiversity, emphasizing the need to consider the legacy of geologic change when describing processes that shape the assembly of communities.
Collapse
Affiliation(s)
- Devon Payne
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Eric C Dunham
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Elizabeth Mohr
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, 59717
| | - Isaac Miller
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Adrienne Arnold
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Reece Erickson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Elizabeth M Fones
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, 59717
| |
Collapse
|
21
|
Nishihara A, Matsuura K, Tank M, McGlynn SE, Thiel V, Haruta S. Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs. Microbes Environ 2018; 33:394-401. [PMID: 30473565 PMCID: PMC6307999 DOI: 10.1264/jsme2.me18041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.
Collapse
Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
| |
Collapse
|
22
|
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.
Collapse
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)
| |
Collapse
|
23
|
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
| |
Collapse
|
24
|
Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832. [PMID: 30026532 PMCID: PMC6053391 DOI: 10.1038/s41467-018-05284-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
Collapse
Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yi-Rui Yin
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China. .,College of Fisheries, Henan Normal University, 453007, Xinxiang, China.
| |
Collapse
|
25
|
Nishihara A, Haruta S, McGlynn SE, Thiel V, Matsuura K. Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide. Microbes Environ 2018; 33:10-18. [PMID: 29367473 PMCID: PMC5877335 DOI: 10.1264/jsme2.me17134] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022] Open
Abstract
The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72-75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth.
Collapse
Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shawn E. McGlynn
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
- Earth-Life Science Institute, Tokyo Institute of TechnologyOokayama, Meguro-ku, Tokyo 152–8551Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource ScienceWako-shi 351–0198Japan
- Blue Marble Space Institute of ScienceSeattle, WA 98145–1561USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| |
Collapse
|
26
|
Jennings RDM, Moran JJ, Jay ZJ, Beam JP, Whitmore LM, Kozubal MA, Kreuzer HW, Inskeep WP. Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities. Front Microbiol 2017; 8:88. [PMID: 28217111 PMCID: PMC5289995 DOI: 10.3389/fmicb.2017.00088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/12/2017] [Indexed: 11/13/2022] Open
Abstract
Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous “streamer” communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeota and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum fractions of autotrophic C in microbial biomass were >50% in the majority of communities analyzed. The significance of CO2 as a C source in these communities provides a foundation for understanding community assembly and succession, and metabolic linkages among early-branching thermophilic autotrophs and heterotrophs.
Collapse
Affiliation(s)
- Ryan de Montmollin Jennings
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Thermal Biology Institute, Montana State UniversityBozeman, MT, USA
| | - James J Moran
- Pacific Northwest National Laboratories Richland, WA, USA
| | - Zackary J Jay
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Thermal Biology Institute, Montana State UniversityBozeman, MT, USA
| | - Jacob P Beam
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Thermal Biology Institute, Montana State UniversityBozeman, MT, USA
| | | | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | | | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Thermal Biology Institute, Montana State UniversityBozeman, MT, USA
| |
Collapse
|
27
|
Merkel AY, Pimenov NV, Rusanov II, Slobodkin AI, Slobodkina GB, Tarnovetckii IY, Frolov EN, Dubin AV, Perevalova AA, Bonch-Osmolovskaya EA. Microbial diversity and autotrophic activity in Kamchatka hot springs. Extremophiles 2016; 21:307-317. [DOI: 10.1007/s00792-016-0903-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/27/2016] [Indexed: 12/26/2022]
|
28
|
Geesey GG, Barkay T, King S. Microbes in mercury-enriched geothermal springs in western North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:321-331. [PMID: 27344121 DOI: 10.1016/j.scitotenv.2016.06.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.
Collapse
Affiliation(s)
- Gill G Geesey
- Department of Microbiology and Immunology, Thermal Biology Institute, Montana State University, Bozeman, MT 59717-3520, USA.
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901-8525, USA.
| | - Sue King
- 2908 3rd Avenue North, Great Falls, MT 59401, USA.
| |
Collapse
|
29
|
Buelow HN, Winter AS, Van Horn DJ, Barrett JE, Gooseff MN, Schwartz E, Takacs-Vesbach CD. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1040. [PMID: 27486436 PMCID: PMC4947590 DOI: 10.3389/fmicb.2016.01040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.
Collapse
Affiliation(s)
- Heather N Buelow
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Ara S Winter
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - David J Van Horn
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - John E Barrett
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Michael N Gooseff
- Department of Civil, Architectural, and Environmental Engineering, Institute of Arctic and Alpine Research, University of Colorado Boulder Boulder, CO, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University Flagstaff, AZ, USA
| | | |
Collapse
|
30
|
Tamazawa S, Yamamoto K, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H. In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring. Microbes Environ 2016; 31:194-8. [PMID: 27297893 PMCID: PMC4912159 DOI: 10.1264/jsme2.me16013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We investigated the in situ gene expression profile of sulfur-turf microbial mats dominated by an uncultured large sausage-shaped Aquificae bacterium, a key metabolic player in sulfur-turfs in sulfidic hot springs. A reverse transcription-PCR analysis revealed that the genes responsible for sulfide, sulfite, and thiosulfate oxidation and carbon fixation via the reductive TCA cycle were continuously expressed in sulfur-turf mats taken at different sampling points, seasons, and years. These results suggest that the uncultured large sausage-shaped bacterium has the ability to grow chemolithoautotrophically and plays key roles as a primary producer in the sulfidic hot spring ecosystem in situ.
Collapse
Affiliation(s)
- Satoshi Tamazawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | | | | | | | | | | |
Collapse
|
31
|
Jay ZJ, Beam JP, Kozubal MA, Jennings RD, Rusch DB, Inskeep WP. The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park. Environ Microbiol 2016; 18:4755-4769. [PMID: 27130276 DOI: 10.1111/1462-2920.13366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/25/2016] [Indexed: 12/01/2022]
Abstract
High-temperature environments (> 70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of different Thermoproteales genera across geochemically distinct geothermal habitats of Yellowstone National Park, and to identify key functional attributes of major genera that correlate with environmental parameters. Curated sequence assemblies belonging to five genera were characterized in replicate samples of 11 high-temperature communities ranging in pH from 3 to 9. Thermocladium, Vulcanisaeta and Caldivirga spp. were the primary Thermoproteales populations present in low pH (pH < 5) habitats, whereas Thermoproteus populations were found in mildly-acidic (pH 5-6) sulfur sediments, and Pyrobaculum populations were confined to higher pH (pH > 6) sulfur sediments and/or filamentous 'streamer' communities. Metabolic reconstruction and comparative genomics among assemblies show that these populations are primarily chemoorganotrophs that utilize different electron acceptors depending on geochemical conditions. The presence of potential CO2 fixation pathways in some Thermoproteales populations appears to be linked with NiFe hydrogenases, which combined with high levels of H2 in many sulfidic systems, may provide the energy required to fix inorganic C.
Collapse
Affiliation(s)
- Zackary J Jay
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA
| | - Jacob P Beam
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA
| | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA
| | - Ryan deM Jennings
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA
| |
Collapse
|
32
|
Colman DR, Jay ZJ, Inskeep WP, Jennings RD, Maas KR, Rusch DB, Takacs-Vesbach CD. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. Front Microbiol 2016; 7:304. [PMID: 27014227 PMCID: PMC4791363 DOI: 10.3389/fmicb.2016.00304] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 02/24/2016] [Indexed: 11/24/2022] Open
Abstract
Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Kendra R Maas
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University Bloomington, IN, USA
| | | |
Collapse
|
33
|
Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings RD, Tringe SG, Inskeep WP. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Front Microbiol 2016; 7:25. [PMID: 26913020 PMCID: PMC4753309 DOI: 10.3389/fmicb.2016.00025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.
Collapse
Affiliation(s)
- Jacob P Beam
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Hans C Bernstein
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA; Biodetection Science and Biological Science Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Zackary J Jay
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State UniversityBozeman, MT, USA; Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA
| | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Susannah G Tringe
- United States Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| |
Collapse
|
34
|
Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, M Jennings RD, Kozubal MA, Tringe SG, Wagner M, Inskeep WP. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. THE ISME JOURNAL 2016; 10:210-24. [PMID: 26140529 PMCID: PMC4681859 DOI: 10.1038/ismej.2015.83] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 12/22/2022]
Abstract
The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The phylogeny and metabolic potential of Aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. Here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of Aigarchaeota in an oxic, hot spring filamentous 'streamer' community. Fluorescence in situ hybridization showed that these newly discovered Aigarchaeota are filamentous, which is consistent with the presence and transcription of an actin-encoding gene. Aigarchaeota filaments are intricately associated with other community members, which include both bacteria (for example, filamentous Thermocrinis spp.) and archaea. Metabolic reconstruction of genomic and metatranscriptomic data suggests that this aigarchaeon is an aerobic, chemoorganoheterotroph with autotrophic potential. A heme copper oxidase complex was identified in the environmental genome assembly and highly transcribed in situ. Potential electron donors include acetate, fatty acids, amino acids, sugars and aromatic compounds, which may originate from extracellular polymeric substances produced by other microorganisms shown to exist in close proximity and/or autochthonous dissolved organic carbon (OC). Transcripts related to genes specific to each of these potential electron donors were identified, indicating that this aigarchaeon likely utilizes several OC substrates. Characterized members of this lineage cannot synthesize heme, and other cofactors and vitamins de novo, which suggests auxotrophy. We propose the name Candidatus 'Calditenuis aerorheumensis' for this aigarchaeon, which describes its filamentous morphology and its primary electron acceptor, oxygen.
Collapse
Affiliation(s)
- Jacob P Beam
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Markus C Schmid
- Divison of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | | | - Ryan de M Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Mark A Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
- Sustainable Bioproducts LLC, Bozeman, MT, USA
| | | | - Michael Wagner
- Divison of Microbial Ecology, University of Vienna, Vienna, Austria
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
35
|
Lin KH, Liao BY, Chang HW, Huang SW, Chang TY, Yang CY, Wang YB, Lin YTK, Wu YW, Tang SL, Yu HT. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015; 16:1029. [PMID: 26630941 PMCID: PMC4668684 DOI: 10.1186/s12864-015-2230-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2230-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kuei-Han Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ben-Yang Liao
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Hao-Wei Chang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Molecular Microbiology and Microbial Pathogenesis Program, Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shiao-Wei Huang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ting-Yan Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Bin Wang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Teh Kirk Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Degree Program of Genome and Systems Biology, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan, Republic of China.
| |
Collapse
|
36
|
Inskeep WP, Jay ZJ, Macur RE, Clingenpeel S, Tenney A, Lovalvo D, Beam JP, Kozubal MA, Shanks WC, Morgan LA, Kan J, Gorby Y, Yooseph S, Nealson K. Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function. Front Microbiol 2015; 6:1044. [PMID: 26579074 PMCID: PMC4620420 DOI: 10.3389/fmicb.2015.01044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 09/14/2015] [Indexed: 12/02/2022] Open
Abstract
Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using 16S rRNA gene and random metagenome sequencing, and to determine how geochemical attributes of vent waters influence the distribution of specific microorganisms and their metabolic potential. Thermal vent waters and associated microbial biomass were sampled during two field seasons (2007–2008) using a remotely operated vehicle (ROV). Sublacustrine thermal vent waters (circa 50–90°C) contained elevated concentrations of numerous constituents associated with geothermal activity including dissolved hydrogen, sulfide, methane and carbon dioxide. Microorganisms associated with sulfur-rich filamentous “streamer” communities of Inflated Plain and West Thumb (pH range 5–6) were dominated by bacteria from the Aquificales, but also contained thermophilic archaea from the Crenarchaeota and Euryarchaeota. Novel groups of methanogens and members of the Korarchaeota were observed in vents from West Thumb and Elliot's Crater (pH 5–6). Conversely, metagenome sequence from Mary Bay vent sediments did not yield large assemblies, and contained diverse thermophilic and nonthermophilic bacterial relatives. Analysis of functional genes associated with the major vent populations indicated a direct linkage to high concentrations of carbon dioxide, reduced sulfur (sulfide and/or elemental S), hydrogen and methane in the deep thermal ecosystems. Our observations show that sublacustrine thermal vents in Yellowstone Lake support novel thermophilic communities, which contain microorganisms with functional attributes not found to date in terrestrial geothermal systems of YNP.
Collapse
Affiliation(s)
- William P Inskeep
- Thermal Biology Institute, Montana State University Bozeman, MT, USA ; Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Zackary J Jay
- Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Richard E Macur
- Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | | | | | | | - Jacob P Beam
- Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Mark A Kozubal
- Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | | | | | - Jinjun Kan
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
| | - Yuri Gorby
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
| | | | - Kenneth Nealson
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
| |
Collapse
|
37
|
Carbon source preference in chemosynthetic hot spring communities. Appl Environ Microbiol 2015; 81:3834-47. [PMID: 25819970 DOI: 10.1128/aem.00511-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/23/2015] [Indexed: 11/20/2022] Open
Abstract
Rates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73 °C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (K(m)) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in high-temperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available.
Collapse
|
38
|
Hedlund BP, Reysenbach AL, Huang L, Ong JC, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H. Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China. Front Microbiol 2015; 6:157. [PMID: 25774153 PMCID: PMC4343020 DOI: 10.3389/fmicb.2015.00157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/11/2015] [Indexed: 11/28/2022] Open
Abstract
The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.
Collapse
Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA ; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Anna-Louise Reysenbach
- Biology Department and Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Liuquin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - John C Ong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Zizhang Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - Jeremy A Dodsworth
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA ; Department of Biology, California State University San Bernardino San Bernardino, CA, USA
| | - Reham Ahmed
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Amanda J Williams
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brandon R Briggs
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Yitai Liu
- Biology Department and Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Beijing, China ; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| |
Collapse
|
39
|
Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China. Sci Rep 2014; 4:7479. [PMID: 25524763 PMCID: PMC5378992 DOI: 10.1038/srep07479] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts.
Collapse
|
40
|
Colman DR, Thomas R, Maas KR, Takacs-Vesbach CD. Detection and analysis of elusive members of a novel and diverse archaeal community within a thermal spring streamer consortium. Extremophiles 2014; 19:307-13. [PMID: 25477209 DOI: 10.1007/s00792-014-0715-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/16/2014] [Indexed: 11/27/2022]
Abstract
Recent metagenomic analyses of Yellowstone National Park (YNP) thermal spring communities suggested the presence of minor archaeal populations that simultaneous PCR-based assays using traditional 'universal' 16S rRNA gene primers failed to detect. Here we use metagenomics to identify PCR primers effective at detecting elusive members of the Archaea, assess their efficacy, and describe the diverse and novel archaeal community from a circum-neutral thermal spring from the Bechler region of YNP. We determined that a less commonly used PCR primer, Arch349F, captured more diversity in this spring than the widely used A21F primer. A search of the PCR primers against the RDP 16S rRNA gene database indicated that Arch349F also captured the largest percentage of Archaea, including 41 % more than A21F. Pyrosequencing using the Arch349F primer recovered all of the phylotypes present in the clone-based portion of the study and the metagenome of this spring in addition to several other populations of Archaea, some of which are phylogenetically novel. In contrast to the lack of amplification with traditional 16S rRNA gene primers, our comprehensive analyses suggested a diverse archaeal community in the Bechler spring, with implications for recently discovered groups such as the Geoarchaeota and other undescribed archaeal groups.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM, 87131-0001, USA,
| | | | | | | |
Collapse
|
41
|
Hug K, Maher WA, Stott MB, Krikowa F, Foster S, Moreau JW. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand. Front Microbiol 2014; 5:569. [PMID: 25414696 PMCID: PMC4220137 DOI: 10.3389/fmicb.2014.00569] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/09/2014] [Indexed: 11/13/2022] Open
Abstract
Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with increased sequences from Aquificaceae, supports a role for methyltransferase in thermophilic arsenic resistance. Our study highlights microbial contributions to coupled arsenic and sulfur cycling at Champagne Pool, with implications for understanding the evolution of microbial arsenic resistance in sulfidic geothermal systems.
Collapse
Affiliation(s)
- Katrin Hug
- Geomicrobiology Laboratory, School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| | - William A. Maher
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | | | - Frank Krikowa
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | - Simon Foster
- Ecochemistry Laboratory, Institute for Applied Ecology, University of CanberraCanberra, ACT, Australia
| | - John W. Moreau
- Geomicrobiology Laboratory, School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| |
Collapse
|
42
|
Härtig C, Lohmayer R, Kolb S, Horn MA, Inskeep WP, Planer-Friedrich B. Chemolithotrophic growth of the aerobic hyperthermophilic bacteriumThermocrinis ruberOC 14/7/2 on monothioarsenate and arsenite. FEMS Microbiol Ecol 2014; 90:747-60. [DOI: 10.1111/1574-6941.12431] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/10/2014] [Accepted: 09/18/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Cornelia Härtig
- Department of Environmental Geochemistry; Bayreuth Center for Ecology and Environmental Research (BayCEER); University of Bayreuth; Bayreuth Germany
| | - Regina Lohmayer
- Department of Environmental Geochemistry; Bayreuth Center for Ecology and Environmental Research (BayCEER); University of Bayreuth; Bayreuth Germany
| | - Steffen Kolb
- Department of Ecological Microbiology; Bayreuth Center for Ecology and Environmental Research (BayCEER); University of Bayreuth; Bayreuth Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology; Bayreuth Center for Ecology and Environmental Research (BayCEER); University of Bayreuth; Bayreuth Germany
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences and Thermal Biology Institute (TBI); Montana State University; Bozeman MT USA
| | - Britta Planer-Friedrich
- Department of Environmental Geochemistry; Bayreuth Center for Ecology and Environmental Research (BayCEER); University of Bayreuth; Bayreuth Germany
| |
Collapse
|
43
|
Ferrera I, Banta AB, Reysenbach AL. Spatial patterns of Aquificales in deep-sea vents along the Eastern Lau Spreading Center (SW Pacific). Syst Appl Microbiol 2014; 37:442-8. [DOI: 10.1016/j.syapm.2014.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 11/28/2022]
|
44
|
Alsop EB, Boyd ES, Raymond J. Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution. BMC Ecol 2014; 14:16. [PMID: 24886397 PMCID: PMC4047435 DOI: 10.1186/1472-6785-14-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/16/2014] [Indexed: 11/13/2022] Open
Abstract
Background The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. Results By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Conclusions Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.
Collapse
Affiliation(s)
| | | | - Jason Raymond
- School of Earth and Space Exploration, Arizona State University, ISTB4, Room 795, 781 E, Terrace Rd, Tempe, AZ 85287, USA.
| |
Collapse
|
45
|
Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol 2014; 80:3034-43. [PMID: 24610850 DOI: 10.1128/aem.03414-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.
Collapse
|
46
|
Carbon dioxide fixation by Metallosphaera yellowstonensis and acidothermophilic iron-oxidizing microbial communities from Yellowstone National Park. Appl Environ Microbiol 2014; 80:2665-71. [PMID: 24532073 DOI: 10.1128/aem.03416-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fixation of inorganic carbon has been documented in all three domains of life and results in the biosynthesis of diverse organic compounds that support heterotrophic organisms. The primary aim of this study was to assess carbon dioxide fixation in high-temperature Fe(III)-oxide mat communities and in pure cultures of a dominant Fe(II)-oxidizing organism (Metallosphaera yellowstonensis strain MK1) originally isolated from these environments. Protein-encoding genes of the complete 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) carbon dioxide fixation pathway were identified in M. yellowstonensis strain MK1. Highly similar M. yellowstonensis genes for this pathway were identified in metagenomes of replicate Fe(III)-oxide mats, as were genes for the reductive tricarboxylic acid cycle from Hydrogenobaculum spp. (Aquificales). Stable-isotope ((13)CO2) labeling demonstrated CO2 fixation by M. yellowstonensis strain MK1 and in ex situ assays containing live Fe(III)-oxide microbial mats. The results showed that strain MK1 fixes CO2 with a fractionation factor of ∼2.5‰. Analysis of the (13)C composition of dissolved inorganic C (DIC), dissolved organic C (DOC), landscape C, and microbial mat C showed that mat C is from both DIC and non-DIC sources. An isotopic mixing model showed that biomass C contains a minimum of 42% C of DIC origin, depending on the fraction of landscape C that is present. The significance of DIC as a major carbon source for Fe(III)-oxide mat communities provides a foundation for examining microbial interactions that are dependent on the activity of autotrophic organisms (i.e., Hydrogenobaculum and Metallosphaera spp.) in simplified natural communities.
Collapse
|
47
|
Beam JP, Jay ZJ, Kozubal MA, Inskeep WP. Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME JOURNAL 2013; 8:938-51. [PMID: 24196321 DOI: 10.1038/ismej.2013.193] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/06/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022]
Abstract
Novel lineages of the phylum Thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. The primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °C), acidic (pH~3) iron oxide and sulfur sediment environments of Yellowstone National Park (YNP). Metabolic reconstruction was coupled with detailed geochemical measurements of each geothermal habitat and reverse-transcriptase PCR to confirm the in situ activity of these populations. Phylogenetic analyses of ribosomal and housekeeping proteins place these archaea near the root of the thaumarchaeal branch. Metabolic reconstruction suggests that these populations are chemoorganotrophic and couple growth with the reduction of oxygen or nitrate in iron oxide habitats, or sulfur in hypoxic sulfur sediments. The iron oxide population has the potential for growth via the oxidation of sulfide to sulfate using a novel reverse sulfate reduction pathway. Possible carbon sources include aromatic compounds (for example, 4-hydroxyphenylacetate), complex carbohydrates (for example, starch), oligopeptides and amino acids. Both populations contain a type III ribulose bisphosphate carboxylase/oxygenase used for carbon dioxide fixation or adenosine monophosphate salvage. No evidence for the oxidation of ammonia was obtained from de novo sequence assemblies. Our results show that thermoacidophilic Thaumarchaeota from oxic iron mats and hypoxic sulfur sediments exhibit different respiratory machinery depending on the presence of oxygen versus sulfide, represent deeply rooted lineages within the phylum Thaumarchaeota and are endemic to numerous sites in YNP.
Collapse
Affiliation(s)
- Jacob P Beam
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Mark A Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| |
Collapse
|
48
|
Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings RD, Boyd ES, Spear JR, Roberto FF. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Front Microbiol 2013; 4:95. [PMID: 23720654 PMCID: PMC3654217 DOI: 10.3389/fmicb.2013.00095] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 04/03/2013] [Indexed: 12/21/2022] Open
Abstract
Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.
Collapse
Affiliation(s)
- William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA ; Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Inskeep WP, Jay ZJ, Tringe SG, Herrgård MJ, Rusch DB. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Front Microbiol 2013; 4:67. [PMID: 23653623 PMCID: PMC3644721 DOI: 10.3389/fmicb.2013.00067] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 03/09/2013] [Indexed: 01/24/2023] Open
Abstract
The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential, and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1) phototrophic mats, (2) "filamentous streamer" communities, and (3) archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments.
Collapse
Affiliation(s)
- William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman MT, USA ; Thermal Biology Institute, Montana State University Bozeman MT, USA
| | | | | | | | | | | |
Collapse
|