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Liu S, Yu S, Lu X, Yang H, Li Y, Xu X, Lu H, Fang Y. Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea. Front Microbiol 2022; 13:1032851. [PMID: 36386663 PMCID: PMC9640435 DOI: 10.3389/fmicb.2022.1032851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.
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Affiliation(s)
- Siwei Liu
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Shan Yu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
- *Correspondence: Shan Yu,
| | - Xindi Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Hailin Yang
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yuanyuan Li
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Xuemin Xu
- School of Earth and Space Sciences, Peking University, Beijing, China
- National Research Center for Geoanalysis, Beijing, China
| | - Hailong Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yunxin Fang
- Guangzhou Marine Geological Survey, Guangzhou, China
- Yunxin Fang,
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2
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Fuentes B, Choque A, Gómez F, Alarcón J, Castro-Nallar E, Arenas F, Contreras D, Mörchen R, Amelung W, Knief C, Moradi G, Klumpp E, Saavedra CP, Prietzel J, Klysubun W, Remonsellez F, Bol R. Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert. Front Microbiol 2022; 12:794743. [PMID: 35197940 PMCID: PMC8859261 DOI: 10.3389/fmicb.2021.794743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
The extreme environmental conditions and lack of water on the soil surface in hyperarid deserts hamper microbial life, allowing only highly specialized microbial communities to the establish colonies and survive. Until now, the microbial communities that inhabit or have inhabited soils of hyperarid environments at greater depths have been poorly studied. We analyzed for the first time the variation in microbial communities down to a depth of 3.4 m in one of the driest places of the world, the hyperarid Yungay region in the Atacama Desert, and we related it to changes in soil physico-chemical characteristics. We found that the moisture content changed from 2 to 11% with depth and enabled the differentiation of three depth intervals: (i) surface zone A (0–60 cm), (ii) intermediate zone B (60–220 cm), and (iii) deep zone C (220–340 cm). Each zone showed further specific physicochemical and mineralogical features. Likewise, some bacterial phyla were unique in each zone, i.e., members of the taxa Deinococcota, Halobacterota, and Latescibacterota in zone A; Crenarchaeota, Fusobacteriota, and Deltaproteobacterium Sva0485 in zone B; and Fervidibacteria and Campilobacterota in zone C, which indicates taxon-specific preferences in deep soil habitats. Differences in the microbiota between the zones were rather abrupt, which is concomitant with abrupt changes in the physical-chemical parameters. Overall, moisture content, total carbon (TC), pH, and electric conductivity (EC) were most predictive of microbial richness and diversity, while total sulfur (TS) and total phosphorous (TP) contents were additionally predictive of community composition. We also found statistically significant associations between taxa and soil properties, most of which involved moisture and TC contents. Our findings show that under-explored habitats for microbial survival and existence may prevail at greater soil depths near water or within water-bearing layers, a valuable substantiation also for the ongoing search for biosignatures on other planets, such as Mars.
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Affiliation(s)
- Bárbara Fuentes
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Alessandra Choque
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Francisco Gómez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Franko Arenas
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Contreras
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Ramona Mörchen
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Ghazal Moradi
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Erwin Klumpp
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jörg Prietzel
- Wissenschaftszentum Weihenstephan, Technical University München, Freising, Germany
| | - Wantana Klysubun
- Synchrotron Light Research Institute, Nakhon Ratchasima, Thailand
| | - Francisco Remonsellez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
- *Correspondence: Francisco Remonsellez,
| | - Roland Bol
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- Roland Bol,
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3
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Torres-Beltrán M, Vargas-Gastélum L, Magdaleno-Moncayo D, Riquelme M, Herguera-García JC, Prieto-Davó A, Lago-Lestón A. The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PeerJ 2021; 9:e12474. [PMID: 34993013 PMCID: PMC8679910 DOI: 10.7717/peerj.12474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022] Open
Abstract
Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
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Affiliation(s)
- Mónica Torres-Beltrán
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Lluvia Vargas-Gastélum
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Dante Magdaleno-Moncayo
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Meritxell Riquelme
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Juan Carlos Herguera-García
- Departamento de Ecología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Alejandra Prieto-Davó
- Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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4
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Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Environ Microbiol 2021; 23:4646-4660. [PMID: 34190392 DOI: 10.1111/1462-2920.15656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+ /H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+ -stimulated pyrophosphatase and capsule proteins.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manlin Xu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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5
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Kaushik R, Pandit MK, Meyerson LA, Chaudhari DS, Sharma M, Dhotre D, Shouche YS. Contrasting Composition, Diversity and Predictive Metabolic Potential of the Rhizobacterial Microbiomes Associated with Native and Invasive Prosopis Congeners. Curr Microbiol 2021; 78:2051-2060. [PMID: 33837467 DOI: 10.1007/s00284-021-02473-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/19/2021] [Indexed: 11/24/2022]
Abstract
Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria using high-throughput sequencing of the 16S rRNA gene. Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram revealed significant variation in the communities of these co-occurring Prosopis species. Additionally, Canonical Correspondence Analysis (CCA) based on microbial communities in addition to the soil physiochemical parameters viz. soil pH, electrical conductivity, moisture content and sampling depth showed ~ 80% of the variation in bacterial communities of the rhizosphere and control soil. We observed that Proteobacteria was the predominant phylum of P. juliflora rhizosphere and the control soil, while P. cineraria rhizosphere was dominated by Cyanobacteria. Notably, the invasive P. juliflora rhizosphere showed an enhanced abundance of bacterial phyla like Actinobacteria, Chloroflexi, Firmicutes and Acidobacteria compared to the native P. cineraria as well as the control soil. Predictive metagenomics revealed that the bacterial communities of the P. juliflora rhizosphere had a higher abundance of pathways involved in antimicrobial biosynthesis and degradation, suggesting probable exposure to enemy attack and an active response mechanism to counter it as compared to native P. cineraria. Interestingly, the higher antimicrobial biosynthesis predicted in the invasive rhizosphere microbiome is further corroborated by the fact that the bacterial isolates purified from the rhizosphere of P. juliflora belonged to genera like Streptomyces, Isoptericola and Brevibacterium from the phylum Actinobacteria, which are widely reported for their antibiotic production ability. In conclusion, our results demonstrate that the co-occurring native and invasive Prosopis species have significantly different rhizosphere bacterial communities in terms of composition, diversity and their predictive metabolic potentials. In addition, the rhizosphere microbiome of invasive Prosopis proffers it a fitness advantage and influences invasion success of the species.
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Affiliation(s)
- Rishabh Kaushik
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India.,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India. .,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India.
| | - Laura A Meyerson
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Diptaraj S Chaudhari
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
| | - Meesha Sharma
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India.,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Dhiraj Dhotre
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
| | - Yogesh S Shouche
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
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6
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Bertran E, Waldeck A, Wing BA, Halevy I, Leavitt WD, Bradley AS, Johnston DT. Oxygen isotope effects during microbial sulfate reduction: applications to sediment cell abundances. ISME JOURNAL 2020; 14:1508-1519. [PMID: 32152390 PMCID: PMC7242377 DOI: 10.1038/s41396-020-0618-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/31/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary cell abundances. This model is calibrated using data from a series of continuous culture experiments with two strains of sulfate reducing bacteria (freshwater bacterium Desulfovibrio vulgaris strain Hildenborough, and marine bacterium Desulfovibrio alaskensis strain G-20) grown on lactate across a range of metabolic rates and ambient sulfate concentrations. We use a combination of experimental sulfate oxygen isotope data and nonlinear regression fitting tools to solve for unknown kinetic, step-specific oxygen isotope effects. This approach enables identification of key isotopic reactions within the metabolic pathway, and defines a new, calibrated framework for understanding oxygen isotope variability in sulfate. This approach is then combined with porewater sulfate/sulfide concentration data and diagenetic modeling to reproduce measured 18O/16O in porewater sulfate. From here, we infer cell-specific sulfate reduction rates and predict abundance of active cells of sulfate reducing bacteria, the result of which is consistent with direct biological measurements.
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Affiliation(s)
- E Bertran
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
| | - A Waldeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - B A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - I Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - W D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA.,Department of Chemistry, Dartmouth College, Hanover, NH, USA.,Department of Biological Science, Dartmouth College, Hanover, NH, USA
| | - A S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - D T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
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7
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Payler SJ, Biddle JF, Sherwood Lollar B, Fox-Powell MG, Edwards T, Ngwenya BT, Paling SM, Cockell CS. An Ionic Limit to Life in the Deep Subsurface. Front Microbiol 2019; 10:426. [PMID: 30915051 PMCID: PMC6422919 DOI: 10.3389/fmicb.2019.00426] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/19/2019] [Indexed: 11/18/2022] Open
Abstract
The physical and chemical factors that can limit or prevent microbial growth in the deep subsurface are not well defined. Brines from an evaporite sequence were sampled in the Boulby Mine, United Kingdom between 800 and 1300 m depth. Ionic, hydrogen and oxygen isotopic composition were used to identify two brine sources, an aquifer situated in strata overlying the mine, and another ambiguous source distinct from the regional groundwater. The ability of the brines to support microbial replication was tested with culturing experiments using a diversity of inocula. The examined brines were found to be permissive for growth, except one. Testing this brine's physicochemical properties showed it to have low water activity and to be chaotropic, which we attribute to the high concentration of magnesium and chloride ions. Metagenomic sequencing of the brines that supported growth showed their microbial communities to be similar to each other and comparable to those found in other hypersaline environments. These data show that solutions high in dissolved ions can shape the microbial diversity of the continental deep subsurface biosphere. Furthermore, under certain circumstances, complex brines can establish a hard limit to microbial replication in the deep biosphere, highlighting the potential for subsurface uninhabitable aqueous environments at depths far shallower than a geothermally-defined limit to life.
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Affiliation(s)
- Samuel J. Payler
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer F. Biddle
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | | | - Mark G. Fox-Powell
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | | | - Bryne T. Ngwenya
- School of Geosciences, Kings Buildings, University of Edinburgh, Edinburgh, United Kingdom
| | - Sean M. Paling
- Boulby Underground Science Facility, Science and Technology Facilities Council, Swindon, United Kingdom
| | - Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
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8
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Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India. Sci Rep 2018; 8:17459. [PMID: 30498254 PMCID: PMC6265293 DOI: 10.1038/s41598-018-35940-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/05/2018] [Indexed: 11/08/2022] Open
Abstract
Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.
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9
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Puente-Sánchez F, Arce-Rodríguez A, Oggerin M, García-Villadangos M, Moreno-Paz M, Blanco Y, Rodríguez N, Bird L, Lincoln SA, Tornos F, Prieto-Ballesteros O, Freeman KH, Pieper DH, Timmis KN, Amils R, Parro V. Viable cyanobacteria in the deep continental subsurface. Proc Natl Acad Sci U S A 2018; 115:10702-10707. [PMID: 30275328 PMCID: PMC6196553 DOI: 10.1073/pnas.1808176115] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present molecular, microscopic, and metagenomic evidence that cyanobacteria predominate in deep subsurface rock samples from the Iberian Pyrite Belt Mars analog (southwestern Spain). Metagenomics showed the potential for a hydrogen-based lithoautotrophic cyanobacterial metabolism. Collectively, our results suggest that they may play an important role as primary producers within the deep-Earth biosphere. Our description of this previously unknown ecological niche for cyanobacteria paves the way for models on their origin and evolution, as well as on their potential presence in current or primitive biospheres in other planetary bodies, and on the extant, primitive, and putative extraterrestrial biospheres.
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Affiliation(s)
- Fernando Puente-Sánchez
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain;
| | - Alejandro Arce-Rodríguez
- Institute of Microbiology, Technical University Braunschweig, D-38023 Braunschweig, Germany
- Microbial Interactions and Processes Group, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Monike Oggerin
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Miriam García-Villadangos
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Nuria Rodríguez
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Laurence Bird
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Sara A Lincoln
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Fernando Tornos
- Instituto de Geociencias, CSIC-Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Olga Prieto-Ballesteros
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Katherine H Freeman
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Dietmar H Pieper
- Microbial Interactions and Processes Group, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, D-38023 Braunschweig, Germany
| | - Ricardo Amils
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
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Li J, Cui J, Yang Q, Cui G, Wei B, Wu Z, Wang Y, Zhou H. Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney. Front Microbiol 2017; 8:1378. [PMID: 28785251 PMCID: PMC5519607 DOI: 10.3389/fmicb.2017.01378] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting.
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Affiliation(s)
- Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Jiamei Cui
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Qunhui Yang
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Guojie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Bingbing Wei
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Zijun Wu
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
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11
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Matturro B, Ubaldi C, Rossetti S. Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination. Front Microbiol 2016; 7:1502. [PMID: 27708637 PMCID: PMC5030254 DOI: 10.3389/fmicb.2016.01502] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/08/2016] [Indexed: 11/13/2022] Open
Abstract
The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD. A long-term microcosm study revealed that autochthonous bacteria were able to sustain the PCB dechlorination at a high extent and the successive addition of an external fermentable organic substrate (lactate) caused the further depletion of the high-chlorinated PCBs (up to 70%). Next Generation Sequencing was used to describe the core microbiome of the marine sediment and to follow the changes caused by the treatments. OTUs affiliated to sulfur-oxidizing ε-proteobacteria, Sulfurovum, and Sulfurimonas, were predominant in the original sediment and increased up to 60% of total OTUs after lactate addition. Other OTUs detected in the sediment were affiliated to sulfate reducing (δ-proteobacteria) and to organohalide respiring bacteria within Chloroflexi phylum mainly belonging to Dehalococcoidia class. Among others, Dehalococcoides mccartyi was enriched during the treatments even though the screening of the specific reductive dehalogenase genes revealed the occurrence of undescribed strains, which deserve further investigations. Overall, this study highlighted the potential of members of Dehalococcoidia class in reducing the contamination level of the marine sediment from Mar Piccolo with relevant implications on the selection of sustainable bioremediation strategies to clean-up the site.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute - National Research Council, Monterotondo Italy
| | - Carla Ubaldi
- ENEA, Technical Unit for Environmental Characterization, Prevention and Remediation, Centro Ricerche Casaccia, Rome Italy
| | - Simona Rossetti
- Water Research Institute - National Research Council, Monterotondo Italy
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12
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Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF. Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents. Front Microbiol 2016; 7:1240. [PMID: 27547206 PMCID: PMC4974244 DOI: 10.3389/fmicb.2016.01240] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4 (+) generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
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Affiliation(s)
| | - Lucy C. Stewart
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
| | - Hilary G. Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, SeattleWA, USA
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, SeattleWA, USA
| | - Julie A. Huber
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
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13
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Dong C, Sheng H, Wang W, Zhou H, Shao Z. Bacterial distribution pattern in the surface sediments distinctive among shelf, slope and basin across the western Arctic Ocean. Polar Biol 2016. [DOI: 10.1007/s00300-016-1970-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Miettinen H, Kietäväinen R, Sohlberg E, Numminen M, Ahonen L, Itävaara M. Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland. Front Microbiol 2015; 6:1203. [PMID: 26579109 PMCID: PMC4626562 DOI: 10.3389/fmicb.2015.01203] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/15/2015] [Indexed: 02/01/2023] Open
Abstract
Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 10(4) cells mL(-1)) in water. The water for nucleic acid analysis went through high decompression (60-130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear.
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Affiliation(s)
- Hanna Miettinen
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
| | | | - Elina Sohlberg
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
| | - Mikko Numminen
- Pyhäsalmi Mine Oy, First Quantum Minerals Ltd.Pyhäsalmi, Finland
| | | | - Merja Itävaara
- Valtion Teknillinen Tutkimuskeskus Technical Research Centre of Finland Ltd.Espoo, Finland
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15
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Fichtel K, Logemann J, Fichtel J, Rullkötter J, Cypionka H, Engelen B. Temperature and pressure adaptation of a sulfate reducer from the deep subsurface. Front Microbiol 2015; 6:1078. [PMID: 26500624 PMCID: PMC4594026 DOI: 10.3389/fmicb.2015.01078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.
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Affiliation(s)
- Katja Fichtel
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörn Logemann
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörg Fichtel
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jürgen Rullkötter
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
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16
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Blöthe M, Wegorzewski A, Müller C, Simon F, Kuhn T, Schippers A. Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7692-7700. [PMID: 26020127 DOI: 10.1021/es504930v] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Polymetallic nodules (manganese nodules) have been formed on deep sea sediments over millions of years and are currently explored for their economic potential, particularly for cobalt, nickel, copper, and manganese. Here we explored microbial communities inside nodules from the northeastern equatorial Pacific. The nodules have a large connected pore space with a huge inner surface of 120 m(2)/g as analyzed by computer tomography and BET measurements. X-ray photoelectron spectroscopy (XPS) and electron microprobe analysis revealed a complex chemical fine structure. This consisted of layers with highly variable Mn/Fe ratios (<1 to >500) and mainly of turbostratic phyllomanganates such as 7 and 10 Å vernadites alternating with layers of Fe-bearing vernadite (δ-MnO2) epitaxially intergrown with amorphous feroxyhyte (δ-FeOOH). Using molecular 16S rRNA gene techniques (clone libraries, pyrosequencing, and real-time PCR), we show that polymetallic nodules provide a suitable habitat for prokaryotes with an abundant and diverse prokaryotic community dominated by nodule-specific Mn(IV)-reducing and Mn(II)-oxidizing bacteria. These bacteria were not detected in the nodule-surrounding sediment. The high abundance and dominance of Mn-cycling bacteria in the manganese nodules argue for a biologically driven closed manganese cycle inside the nodules relevant for their formation and potential degradation.
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Affiliation(s)
- Marco Blöthe
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Anna Wegorzewski
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Cornelia Müller
- ‡Leibniz Institute for Applied Geophysics, Stilleweg 2, 30655 Hannover, Germany
| | - Frank Simon
- §Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Thomas Kuhn
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Axel Schippers
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
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17
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Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, Matsui M. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater. BMC Microbiol 2014; 14:318. [PMID: 25539583 PMCID: PMC4326521 DOI: 10.1186/s12866-014-0318-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host. Results A total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHBˉ4 (PHB-negative mutant). Conclusions A new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0318-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Choon Pin Foong
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Nyok-Sean Lau
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Shigeru Deguchi
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Takashi Toyofuku
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Todd D Taylor
- Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Minami Matsui
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan.
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18
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Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea). ISME JOURNAL 2014; 9:1306-18. [PMID: 25500510 PMCID: PMC4438319 DOI: 10.1038/ismej.2014.217] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/08/2022]
Abstract
Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea.
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19
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Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 2014; 18:853-63. [PMID: 25108363 DOI: 10.1007/s00792-014-0676-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
Abstract
Subseafloor sediment samples derived from a sediment core of 60 m length were used to enrich psychrophilic aerobic bacteria on cellulose, xylan, chitin, and starch. A variety of species belonging to Alpha- and Gammaproteobacteria and to Flavobacteria were isolated from sediment depths between 12 and 42 mbsf. Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes. More than 200 open reading frames coding for glycoside hydrolases were identified, and more than 60 of them relevant for enzymatic degradation of lignocellulose. Four genes encoding β-glucosidases with less than 52% identities to characterized enzymes were chosen for recombinant expression in Escherichia coli. In addition one endomannanase, two endoxylanases, and three β-xylosidases were produced recombinantly. All genes could be actively expressed. Functional analysis revealed discrepancies and additional variability for the recombinant enzymes as compared to the sequence-based predictions.
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Affiliation(s)
- Barbara Klippel
- Institute of Technical Microbiology, Hamburg University of Technology, Kasernenstr. 12, 21073, Hamburg, Germany
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20
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Richness and diversity of bacteria in the Nansha carbonate platform (Core MD05-2896), South China Sea. World J Microbiol Biotechnol 2013; 29:1895-905. [PMID: 23700125 DOI: 10.1007/s11274-013-1354-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
We explored the bacterial diversity and vertical distribution along a sediment core (MD05-2896) from the coral reefs of the Nansha carbonate platform in the South China Sea. Bacterial diversity is determined by 16S rRNA molecular survey from twelve subsamples A, obtained via cloning, sequencing and phylogenetic analyses. We estimated the species richness by parametric and nonparametric models, which identified 326 ± 40 (SE) bacteria species. The dominant bacterial groups included Planctomycetes, Deltaproteobacteria, and candidate division OP3, which constituting 23.7, 10.4, and 9.5 % of bacterial 16S rRNAclone libraries, respectively. The observed stratification of bacterial communities was correlated with C/N ratio. This study improves our understanding of the species-environment relationship in the sub-sea floor sediment.
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21
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Lever MA. Functional gene surveys from ocean drilling expeditions - a review and perspective. FEMS Microbiol Ecol 2013; 84:1-23. [PMID: 23228016 DOI: 10.1111/1574-6941.12051] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 10/18/2012] [Accepted: 11/29/2012] [Indexed: 12/18/2022] Open
Abstract
The vast majority of microbes inhabiting the subseafloor remain uncultivated and their energy sources unknown. Thus, a focus of ocean drilling expeditions over the past decade has been to characterize the distribution of microbes associated with specific metabolic reactions. An important question has been whether microbes involved in key microbial processes, such as sulfate reduction and methanogenesis, differ fundamentally from their counterparts in surface environments. To this end, functional genes of anaerobic methane cycling (mcrA), sulfate reduction (dsrAB), acetogenesis (fhs), and dehalorespiration (rdhA) have been examined. A compilation of existing functional gene data suggests that subseafloor microbes involved in anaerobic methane cycling, sulfate reduction, acetogenesis, and dehalorespiration are not fundamentally different from their counterparts in the surface world. Moreover, quantifications of mcrA and dsrAB suggest that, unless the majority of subseafloor microbes involved in methane cycling and sulfate reduction are too genetically divergent to be detected with conventional methods, these processes only support a small fraction (< 1%) of total microbial biomass in the deep biosphere. Ecological explanations for the observed trends, target processes and methods for future investigations, and strategies for tackling the unresolved issue of microbial contamination in samples obtained by ocean drilling are discussed.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of BioScience, Aarhus University, Aarhus, Denmark.
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22
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Jorgensen SL, Hannisdal B, Lanzén A, Baumberger T, Flesland K, Fonseca R, Øvreås L, Steen IH, Thorseth IH, Pedersen RB, Schleper C. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci U S A 2012; 109:E2846-55. [PMID: 23027979 PMCID: PMC3479504 DOI: 10.1073/pnas.1207574109] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.
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Affiliation(s)
| | - Bjarte Hannisdal
- Centre for Geobiology, Department of Earth Science, University of Bergen, 5007 Bergen, Norway
| | - Anders Lanzén
- Centre for Geobiology, Department of Biology, and
- Computational Biology Unit, Uni Computing, Uni Research, 5007 Bergen, Norway
| | - Tamara Baumberger
- Centre for Geobiology, Department of Earth Science, University of Bergen, 5007 Bergen, Norway
- Institute for Geochemistry and Petrology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland
| | - Kristin Flesland
- Centre for Geobiology, Department of Earth Science, University of Bergen, 5007 Bergen, Norway
| | - Rita Fonseca
- Department of Geosciences, University of Évora, 7000 Évora, Portugal
- Creminer Laboratory of Robotics and Systems in Engineering Science (LARSyS), Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal; and
| | - Lise Øvreås
- Centre for Geobiology, Department of Biology, and
| | - Ida H. Steen
- Centre for Geobiology, Department of Biology, and
| | - Ingunn H. Thorseth
- Centre for Geobiology, Department of Earth Science, University of Bergen, 5007 Bergen, Norway
| | - Rolf B. Pedersen
- Centre for Geobiology, Department of Earth Science, University of Bergen, 5007 Bergen, Norway
| | - Christa Schleper
- Centre for Geobiology, Department of Biology, and
- Department of Genetics in Ecology, University of Vienna, A-1090 Vienna, Austria
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23
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Su KH, Sun CY, Dandekar A, Liu B, Sun WZ, Cao MC, Li N, Zhong XY, Guo XQ, Ma QL, Yang LY, Chen GJ. Experimental investigation of hydrate accumulation distribution in gas seeping system using a large scale three-dimensional simulation device. Chem Eng Sci 2012. [DOI: 10.1016/j.ces.2012.07.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Novel opportunity for understanding origin and evolution of life: perspectives on the exploration of subglacial environment of Lake Vostok, Antarctica. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0525-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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25
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Nigro LM, Harris K, Orcutt BN, Hyde A, Clayton-Luce S, Becker K, Teske A. Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A). Front Microbiol 2012; 3:232. [PMID: 22754551 PMCID: PMC3386569 DOI: 10.3389/fmicb.2012.00232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 06/07/2012] [Indexed: 02/01/2023] Open
Abstract
The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.
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Affiliation(s)
- Lisa M Nigro
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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26
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Nithya C, Pandian SK. Evaluation of bacterial diversity in Palk Bay sediments using terminal-restriction fragment length polymorphisms (T-RFLP). Appl Biochem Biotechnol 2012; 167:1763-77. [PMID: 22528645 DOI: 10.1007/s12010-012-9578-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 01/19/2012] [Indexed: 11/24/2022]
Abstract
Although it is known that Palk Bay sediments harbor diverse and novel bacteria with important ecological and environmental functions, a comprehensive view of their molecular diversity is still lacking. In the present study, bacterial diversity in Palk Bay sediments was characterized using the molecular method terminal-restriction fragment length polymorphisms (T-RFLP). The bacterial assemblages detected by T-RFLP analysis revealed that the nearshore sediment harbored high number of bacterial count, whereas the 2.5-m sediment harbored diverse and distinct bacterial composition with fine heterogeneity. The major bacterial groups detected in all the three sediment samples were Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria (including alpha (α), gamma (γ), delta (δ), and epsilon (ε)-Proteobacteria), and uncultured bacteria. This is the first study that reveals the presence of Bacteroidetes, delta (δ)- and epsilon (ε)-Proteobacteria, and uncultured bacteria in Palk Bay sediments. The hitherto unexplored wide microbial diversity of Palk Bay coastal area was unraveled in the current study through culture-independent approach. These data suggest that the continued use of cultivation-independent techniques will undoubtedly lead to the discovery of additional bacterial diversity and provide a direct means to learn more about the ecophysiology and biotechnological potential of Palk Bay coastal area.
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Affiliation(s)
- Chari Nithya
- Department of Biotechnology, Alagappa University, Karaikudi 630 003, Tamil Nadu, India.
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27
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Kadnikov VV, Mardanov AV, Beletsky AV, Shubenkova OV, Pogodaeva TV, Zemskaya TI, Ravin NV, Skryabin KG. Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal. FEMS Microbiol Ecol 2011; 79:348-58. [PMID: 22092495 DOI: 10.1111/j.1574-6941.2011.01221.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 09/20/2011] [Accepted: 10/01/2011] [Indexed: 02/03/2023] Open
Abstract
Gas hydrates in marine sediments have been known for many years but recently hydrates were found in the sediments of Lake Baikal, the largest freshwater basin in the world. Marine gas hydrates are associated with complex microbial communities involved in methanogenesis, methane oxidation, sulfate reduction and other biotransformations. However, the contribution of microorganisms to the formation of gas hydrates remains poorly understood. We examined the microbial communities in the hydrate-bearing sediments and water column of Lake Baikal using pyrosequencing of 16S rRNA genes. Aerobic methanotrophic bacteria dominated the water sample collected at the lake floor in the hydrate-bearing site. The shallow sediments were dominated by Archaea. Methanogens of the orders Methanomicrobiales and Methanosarcinales were abundant, whereas representatives of archaeal lineages known to perform anaerobic oxidation of methane, as well as sulfate-reducing bacteria, were not found. Affiliation of archaea to methanogenic rather than methane-oxidizing lineages was supported by analysis of the sequences of the methyl coenzyme M reductase gene. The deeper sediments located at 85-90 cm depth close to the hydrate were dominated by Bacteria, mostly assigned to Chloroflexi, candidate division JS1 and Caldiserica. Overall, our results are consistent with the biological origin of methane hydrates in Lake Baikal.
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Affiliation(s)
- Vitaly V Kadnikov
- Centre Bioengineering of Russian Academy of Sciences, Moscow, Russia
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28
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Lymperopoulou DS, Kormas KA, Karagouni AD. Variability of prokaryotic community structure in a drinking water reservoir (Marathonas, Greece). Microbes Environ 2011; 27:1-8. [PMID: 21971081 PMCID: PMC4036031 DOI: 10.1264/jsme2.me11253] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H′ 0.81–3.28 and 1.36–1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning.
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Affiliation(s)
- Despoina S Lymperopoulou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, Microbiology Group, Athens, Greece.
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29
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Tin S, Bizzoco RW, Kelley ST. Role of the terrestrial subsurface in shaping geothermal spring microbial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:491-499. [PMID: 23761312 DOI: 10.1111/j.1758-2229.2011.00248.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this study, we explored the possibility that dispersal from terrestrial subsurface sources 'seeds' the development of geothermal spring microbial assemblages. We combined microscopy and culture-independent molecular approaches to survey the bacterial diversity of spring source waters in Yellowstone National Park, Lassen Volcanic National Park, and Russia's Kamchatka peninsula. Microscopic analysis uncovered clear evidence of microbial cells from spring sources in all three regions. Analysis of source water phylogenetic diversity identified members of all bacteria groups found previously in downstream sediments, as well as many other phylogenetic groups. Closely related or identical 16S sequences were determined from the source waters of geographically distant, chemically distinct springs, and we found no association between spring water chemistry and microbial diversity. In the source waters of two different Yellowstone springs, we also discovered a phylogenetic group of uncultured Firmicutes never before reported in geothermal habitats that were closely related to uncultured bacteria found in the hyper-arid Atacama Desert. Altogether, our results suggest geothermal features can be connected via the subsurface over long distances and that subsurface sources provide a potentially diverse source of microorganisms for downstream surface mat communities.
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Affiliation(s)
- Sara Tin
- Department of Biology, 5500 Campanile Drive, San Diego State University, San Diego, CA 92182-4614, USA
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30
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Nunoura T, Inagaki F, Delwiche ME, Colwell FS, Takai K. Subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (ODP Leg204) in the cascadia margin. Microbes Environ 2011; 23:317-25. [PMID: 21558725 DOI: 10.1264/jsme2.me08514] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prokaryotic communities in deep subseafloor sediment collected during Ocean Drilling Program (ODP) Leg 204 from the South Hydrate Ridge (SHR) on the Cascadia Margin were analyzed by 16S rRNA gene clone sequencing and a fluorescent quantitative PCR technique. The microbial communities came from sites with contrasting geological characteristics on the SHR: sites 1244 and 1245 (located on the flank of the ridge, hydrate-rich sediment) and site 1251 (located on the slope basin of SHR, hydrate-poor sediment). The overall copy numbers of the 16S rRNA gene, and the proportion of archaeal 16S rRNA gene in all 16S rRNA gene community in sediment were larger on the slope basin than on the flank of the SHR. Archaeal community structure around the sulfate-methane transition zone at site 1251 (4.5 mbsf) was intensively investigated using two different PCR primer sets. A relatively abundant distribution of the 16S rRNA gene sequences related to mesophilic methanogen of the genus Methanoculleus was identified at a depth of 43.2 mbsf, and suggested that the methanogens occur in relatively shallow zones of sediment. This study demonstrated that the subseafloor microbial communities shown by 16S rRNA gene clone analyses were not directly associated with subseafloor methane hydrate deposits.
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Affiliation(s)
- Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC) 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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31
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Hamdan LJ, Gillevet PM, Pohlman JW, Sikaroodi M, Greinert J, Coffin RB. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand. FEMS Microbiol Ecol 2011; 77:518-32. [DOI: 10.1111/j.1574-6941.2011.01133.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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32
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 324] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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33
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Monitoring of the microbial community composition in deep subsurface saline aquifers during CO2 storage in Ketzin, Germany. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.egypro.2011.02.388] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Blazejak A, Schippers A. High abundance of JS-1- andChloroflexi-relatedBacteriain deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol 2010; 72:198-207. [DOI: 10.1111/j.1574-6941.2010.00838.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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35
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Kato S, Takano Y, Kakegawa T, Oba H, Inoue K, Kobayashi C, Utsumi M, Marumo K, Kobayashi K, Ito Y, Ishibashi JI, Yamagishi A. Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough. Appl Environ Microbiol 2010; 76:2968-79. [PMID: 20228114 PMCID: PMC2863450 DOI: 10.1128/aem.00478-10] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/20/2022] Open
Abstract
The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments.
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Affiliation(s)
- Shingo Kato
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Yoshinori Takano
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Takeshi Kakegawa
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Hironori Oba
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Kazuhiko Inoue
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Chiyori Kobayashi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Motoo Utsumi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Katsumi Marumo
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Kensei Kobayashi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Yuki Ito
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Jun-ichiro Ishibashi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan, Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, Graduate School of Science, Tohoku University, Aramaki-aza-aoba, Sendai, Miyagi 980-8578, Japan, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan, Institute for Geology and Geoinformation, National Institute of Advanced Industrial Science and Technology, 1-1-1 Central 7 Higashi, Tsukuba, Ibaraki 305-8567, Japan, Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan, Department of Earth and Planetary Science, Faculty of Science, Kyushu University, 6-101 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
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Pachiadaki MG, Lykousis V, Stefanou EG, Kormas KA. Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea). FEMS Microbiol Ecol 2010; 72:429-44. [PMID: 20370830 DOI: 10.1111/j.1574-6941.2010.00857.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We investigated 16S rRNA gene diversity at a high sediment depth resolution (every 5 cm, top 30 cm) in an active site of the Kazan mud volcano, East Mediterranean Sea. A total of 242 archaeal and 374 bacterial clones were analysed, which were attributed to 38 and 205 unique phylotypes, respectively (> or = 98% similarity). Most of the archaeal phylotypes were related to ANME-1, -2 and -3 members originating from habitats where anaerobic oxidation of methane (AOM) occurs, although they occurred in sediment layers with no apparent AOM (below the sulphate depletion depth). Proteobacteria were the most abundant and diverse bacterial group, with the Gammaproteobacteria dominating in most sediment layers and these were related to phylotypes involved in methane cycling. The Deltaproteobacteria included several of the sulphate-reducers related to AOM. The rest of the bacterial phylotypes belonged to 15 known phyla and three unaffiliated groups, with representatives from similar habitats. Diversity index H was in the range 0.56-1.73 and 1.47-3.82 for Archaea and Bacteria, respectively, revealing different depth patterns for the two groups. At 15 and 20 cm below the sea floor, the prokaryotic communities were highly similar, hosting AOM-specific Archaea and Bacteria. Our study revealed different dominant phyla in proximate sediment layers.
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Affiliation(s)
- Maria G Pachiadaki
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes-Heraklion, Greece
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37
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Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol Ecol 2009; 48:357-67. [PMID: 19712305 DOI: 10.1016/j.femsec.2004.02.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Culturable bacteria were detected in deep-sea sediment samples collected from the Nankai Trough site 1173 (Ocean Drilling Program, ODP, Leg 190) at 4.15 m below the seafloor with 4791 m of overlying water. In this deep ocean near surface sediment, mainly fermentative heterotrophs, autotrophic acetogens and sulfate-reducing bacteria were enriched by using two different non-selective enrichment culture media. Culturable bacterial population shifts within the deep marine sediment enrichments were monitored by using denaturating gradient gel electrophoresis (DGGE). DGGE analysis revealed a decrease in the number of 16S rRNA gene fragments from high to low carbon concentrations, and from low to high dilution of inoculum, suggesting that fast-growing bacteria were numerically dominant in enrichment culture samples. The dominant 16S rRNA fragments observed in DGGE gels were assigned to the Firmicutes, Proteobacteria (gamma and delta subgroups) and Spirochaeta phyla. Continual sub-culture and purification resulted in two isolates which were phylogenetically identified as members of the genera Acetobacterium and Marinilactibacillus. Our results, which combine enrichment culturing with DGGE analysis, indicated that enrichment cultures derived from inoculum dilution and media with various concentrations of carbon could facilitate the detection and isolation of a greater number of environmentally relevant bacterial species than when using traditional enrichment techniques alone.
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38
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Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol 2009; 50:213-30. [PMID: 19712362 DOI: 10.1016/j.femsec.2004.06.014] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities inhabiting recent (< or =1 million years old; Ma) seafloor basalts from the Arctic spreading ridges were analyzed using traditional enrichment culturing methods in combination with culture-independent molecular phylogenetic techniques. Fragments of 16S rDNA were amplified from the basalt samples by polymerase chain reaction, and fingerprints of the bacterial and archaeal communities were generated using denaturing gradient gel electrophoresis. This analysis indicates a substantial degree of complexity in the samples studied, showing 20-40 dominating bands per profile for the bacterial assemblages. For the archaeal assemblages, a much lower number of bands (6-12) were detected. The phylogenetic affiliations of the predominant electrophoretic bands were inferred by performing a comparative 16S rRNA gene sequence analysis. Sequences obtained from basalts affiliated with eight main phylogenetic groups of Bacteria, but were limited to only one group of the Archaea. The most frequently retrieved bacterial sequences affiliated with the gamma-proteobacteria, alpha-proteobacteria, Chloroflexi, Firmicutes, and Actinobacteria. The archaeal sequences were restricted to the marine Group 1: Crenarchaeota. Our results indicate that the basalt harbors a distinctive microbial community, as the majority of the sequences differed from those retrieved from the surrounding seawater as well as from sequences previously reported from seawater and deep-sea sediments. Most of the sequences did not match precisely any sequences in the database, indicating that the indigenous Arctic ridge basalt microbial community is yet uncharacterized. Results from enrichment cultures showed that autolithotrophic methanogens and iron reducing bacteria were present in the seafloor basalts. We suggest that microbial catalyzed cycling of iron may be important in low-temperature alteration of ocean crust basalt. The phylogenetic and physiological diversity of the seafloor basalt microorganisms differed from those previously reported from deep-sea hydrothermal systems.
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Roussel EG, Sauvadet AL, Chaduteau C, Fouquet Y, Charlou JL, Prieur D, Cambon Bonavita MA. Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin. Environ Microbiol 2009; 11:2446-62. [PMID: 19624712 DOI: 10.1111/j.1462-2920.2009.01976.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.
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Affiliation(s)
- Erwan G Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Université de Bretagne Occidentale, Ifremer, France.
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40
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Kallmeyer J, Smith DC. An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts. FEMS Microbiol Ecol 2009; 69:125-31. [DOI: 10.1111/j.1574-6941.2009.00684.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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41
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Forschner SR, Sheffer R, Rowley DC, Smith DC. Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic Basin. Environ Microbiol 2009; 11:630-9. [DOI: 10.1111/j.1462-2920.2008.01834.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Ning J, Liebich J, Kästner M, Zhou J, Schäffer A, Burauel P. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl Microbiol Biotechnol 2009; 82:983-93. [PMID: 19247649 DOI: 10.1007/s00253-009-1912-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 02/04/2009] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
Abstract
Based on the comparative study of the DNA extracts from two soil samples obtained by three commercial DNA extraction kits, we evaluated the influence of the DNA quantity and purity indices (the absorbance ratios A260/280 and A260/230, as well as the absorbance value A320 indicating the amount of humic substances) on polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and a functional gene microarray used in the study of microbial communities. Numbers and intensities of the DGGE bands are more affected by the A260/280 and A320 values than by the ratio A260/230 and conditionally affected by the DNA yield. Moreover, we demonstrated that the DGGE band pattern was also affected by the preferential extraction due to chemical agents applied in the extraction. Unlike DGGE, microarray is more affected by the A260/230 and A320 values. Until now, the successful PCR performance is the mostly used criterion for soil DNA purity. However, since PCR was more influenced by the A260/280 ratio than by A260/230, it is not accurate enough any more for microbial community assessed by non-PCR-based methods such as microarray. This study provides some useful hints on how to choose effective DNA extraction method for the subsequent assessment of microbial community.
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Affiliation(s)
- Jing Ning
- Agrosphere Institute (ICG-4), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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43
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Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 2008; 66:181-96. [DOI: 10.1111/j.1574-6941.2008.00566.x] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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44
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Dang H, Li J, Chen M, Li T, Zeng Z, Yin X. Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9877-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Teske A, Biddle JF. Analysis of Deep Subsurface Microbial Communities by Functional Genes andGenomics. MODERN APPROACHES IN SOLID EARTH SCIENCES 2008. [DOI: 10.1007/978-1-4020-8306-8_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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46
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Spatial Distribution of the Subseafloor Life: Diversity and Biogeography. MODERN APPROACHES IN SOLID EARTH SCIENCES 2008. [DOI: 10.1007/978-1-4020-8306-8_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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47
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Abundance and diversity of microbial life in ocean crust. Nature 2008; 453:653-6. [PMID: 18509444 DOI: 10.1038/nature06899] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Accepted: 03/12/2008] [Indexed: 11/09/2022]
Abstract
Oceanic lithosphere exposed at the sea floor undergoes seawater-rock alteration reactions involving the oxidation and hydration of glassy basalt. Basalt alteration reactions are theoretically capable of supplying sufficient energy for chemolithoautotrophic growth. Such reactions have been shown to generate microbial biomass in the laboratory, but field-based support for the existence of microbes that are supported by basalt alteration is lacking. Here, using quantitative polymerase chain reaction, in situ hybridization and microscopy, we demonstrate that prokaryotic cell abundances on seafloor-exposed basalts are 3-4 orders of magnitude greater than in overlying deep sea water. Phylogenetic analyses of basaltic lavas from the East Pacific Rise (9 degrees N) and around Hawaii reveal that the basalt-hosted biosphere harbours high bacterial community richness and that community membership is shared between these sites. We hypothesize that alteration reactions fuel chemolithoautotrophic microorganisms, which constitute a trophic base of the basalt habitat, with important implications for deep-sea carbon cycling and chemical exchange between basalt and sea water.
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48
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Colwell FS, Boyd S, Delwiche ME, Reed DW, Phelps TJ, Newby DT. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin. Appl Environ Microbiol 2008; 74:3444-52. [PMID: 18344348 PMCID: PMC2423016 DOI: 10.1128/aem.02114-07] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 03/02/2008] [Indexed: 11/20/2022] Open
Abstract
Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor, Methanoculleus submarinus produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (mcrA) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.
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Affiliation(s)
- F S Colwell
- College of Oceanic and Atmospheric Sciences, Oregon State University, 104 COAS Admin. Bldg., Corvallis, OR 97331-5503, USA.
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49
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Aller JY, Kemp PF. Are Archaea inherently less diverse than Bacteria in the same environments? FEMS Microbiol Ecol 2008; 65:74-87. [PMID: 18479447 DOI: 10.1111/j.1574-6941.2008.00498.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Like Bacteria, Archaea occur in a wide variety of environments, only some of which can be considered 'extreme'. We compare archaeal diversity, as represented by 173 16S rRNA gene libraries described in published reports, to bacterial diversity in 79 libraries from the same source environments. An objective assessment indicated that 114 archaeal libraries and 45 bacterial libraries were large enough to yield stable estimates of total phylotype richness. Archaeal libraries were seldom as large or diverse as bacterial libraries from the same environments. However, a relatively larger proportion of libraries were large enough to effectively capture rare as well as dominant phylotypes in archaeal communities. In contrast to bacterial libraries, the number of phylotypes did not correlate with library size; thus, 'larger' may not necessarily be 'better' for determining diversity in archaeal libraries. Differences in diversity suggest possible differences in ecological roles of Archaea and Bacteria; however, information is lacking on relative abundances and metabolic activities within the sampled communities, as well as the possible existence of microhabitats. The significance of phylogenetic diversity as opposed to functional diversity remains unclear, and should be a high priority for continuing research.
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Affiliation(s)
- Josephine Y Aller
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
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50
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Süss J, Herrmann K, Seidel M, Cypionka H, Engelen B, Sass H. Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels. MICROBIAL ECOLOGY 2008; 55:371-83. [PMID: 17874305 DOI: 10.1007/s00248-007-9282-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 05/22/2007] [Indexed: 05/17/2023]
Abstract
Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.
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Affiliation(s)
- Jacqueline Süss
- Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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