1
|
Escudero C, Vera M, Oggerin M, Amils R. Active microbial biofilms in deep poor porous continental subsurface rocks. Sci Rep 2018; 8:1538. [PMID: 29367593 PMCID: PMC5784017 DOI: 10.1038/s41598-018-19903-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/08/2018] [Indexed: 11/24/2022] Open
Abstract
Deep continental subsurface is defined as oligotrophic environments where microorganisms present a very low metabolic rate. To date, due to the energetic cost of production and maintenance of biofilms, their existence has not been considered in poor porous subsurface rocks. We applied fluorescence in situ hybridization techniques and confocal laser scanning microscopy in samples from a continental deep drilling project to analyze the prokaryotic diversity and distribution and the possible existence of biofilms. Our results show the existence of natural microbial biofilms at all checked depths of the Iberian Pyrite Belt (IPB) subsurface and the co-occurrence of bacteria and archaea in this environment. This observation suggests that multi-species biofilms may be a common and widespread lifestyle in subsurface environments.
Collapse
Affiliation(s)
- Cristina Escudero
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Mario Vera
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Departamento de Ingeniería Hidráulica y Ambiental, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Av Vicuña Mackenna, 4860, Santiago, Chile
| | - Monike Oggerin
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
| |
Collapse
|
2
|
Perras AK, Wanner G, Klingl A, Mora M, Auerbach AK, Heinz V, Probst AJ, Huber H, Rachel R, Meck S, Moissl-Eichinger C. Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm. Front Microbiol 2014; 5:397. [PMID: 25140167 PMCID: PMC4122167 DOI: 10.3389/fmicb.2014.00397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/14/2014] [Indexed: 11/13/2022] Open
Abstract
Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.
Collapse
Affiliation(s)
- Alexandra K Perras
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany
| | - Andreas Klingl
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany ; Zellbiologie, Philipps-Universität Marburg Marburg, Germany ; LOEWE Research Centre for Synthetic Microbiology (Synmikro) Marbug, Germany
| | - Maximilian Mora
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Anna K Auerbach
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Veronika Heinz
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Alexander J Probst
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Harald Huber
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Reinhard Rachel
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Sandra Meck
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | | |
Collapse
|
3
|
Probst AJ, Birarda G, Holman HYN, DeSantis TZ, Wanner G, Andersen GL, Perras AK, Meck S, Völkel J, Bechtel HA, Wirth R, Moissl-Eichinger C. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species. PLoS One 2014; 9:e99801. [PMID: 24971452 PMCID: PMC4074051 DOI: 10.1371/journal.pone.0099801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/17/2014] [Indexed: 02/01/2023] Open
Abstract
Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.
Collapse
Affiliation(s)
- Alexander J. Probst
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
- Department for Bioinformatics, Second Genome Inc., South San Francisco, California, United States of America
| | - Giovanni Birarda
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hoi-Ying N. Holman
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Todd Z. DeSantis
- Department for Bioinformatics, Second Genome Inc., South San Francisco, California, United States of America
| | - Gerhard Wanner
- Department of Biology I, Biozentrum, LMU Munich, Planegg-Martinsried, Germany
| | - Gary L. Andersen
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Alexandra K. Perras
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Sandra Meck
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Jörg Völkel
- Department of Geomorphology and Soil Science, Technische Universität München, Center of Life and Food Sciences Weihenstephan, Freising, Germany
| | - Hans A. Bechtel
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Reinhard Wirth
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | | |
Collapse
|
4
|
Park SJ, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Chung WH, Kwon K, Lee JH, Madsen EL, Rhee SK. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments. PLoS One 2014; 9:e96449. [PMID: 24798206 PMCID: PMC4010524 DOI: 10.1371/journal.pone.0096449] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 04/09/2014] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. “Nitrosopumilus koreensis” AR1 and “Nitrosopumilus sediminis” AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.
Collapse
Affiliation(s)
- Soo-Je Park
- Department of Biology, Jeju National University, Jeju, South Korea
| | - Rohit Ghai
- Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain
| | - Ana-Belén Martín-Cuadrado
- Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodríguez-Valera
- Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain
| | - Won-Hyong Chung
- Korean Bioinformation Center, KRIBB, Yuseong-gu, Daejeon, South Korea
| | - KaeKyoung Kwon
- Korea Institute of Ocean Science and Technology, Ansan, South Korea
| | - Jung-Hyun Lee
- Korea Institute of Ocean Science and Technology, Ansan, South Korea
| | - Eugene L. Madsen
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
- * E-mail:
| |
Collapse
|
5
|
Hawkins AN, Johnson KW, Bräuer SL. Southern Appalachian peatlands support high archaeal diversity. MICROBIAL ECOLOGY 2014; 67:587-602. [PMID: 24419541 DOI: 10.1007/s00248-013-0352-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.
Collapse
Affiliation(s)
- A N Hawkins
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
| | | | | |
Collapse
|
6
|
Bresinsky A. Ants, Plants and Fungi: A View on Some Patterns of Interaction and Diversity. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-642-38797-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
|
7
|
Abstract
Biofilms are currently viewed as the most common form in which microorganisms exist in nature. Bacterial biofilms play important roles in disease and industrial applications, and they have been studied in great detail. Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. Therefore, we aim to highlight the available information and indicate open questions in this field.
Collapse
Affiliation(s)
- Alvaro Orell
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;
| | | | | |
Collapse
|
8
|
Stratified Communities of Active Archaea in Shallow Sediments of the Pearl River Estuary, Southern China. Curr Microbiol 2013; 67:41-50. [DOI: 10.1007/s00284-013-0320-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
|
9
|
Abstract
Biofilms or multicellular structures become accepted as the dominant microbial lifestyle in Nature, but in the past they were only studied extensively in bacteria. Investigations on archaeal monospecies cultures have shown that many archaeal species are able to adhere on biotic and abiotic surfaces and form complex biofilm structures. Biofilm-forming archaea were identified in a broad range of extreme and moderate environments. Natural biofilms observed are mostly mixed communities composed of archaeal and bacterial species of various abundances. The physiological functions of the archaea identified in such mixed communities suggest a significant impact on the biochemical cycles maintaining the flow and recycling of the nutrients on earth. Therefore it is of high interest to investigate the characteristics and mechanisms underlying the archaeal biofilm formation. In the present review, I summarize and discuss the present investigations of biofilm-forming archaeal species, i.e. their diverse biofilm architectures in monospecies or mixed communities, the identified EPSs (extracellular polymeric substances), archaeal structures mediating surface adhesion or cell–cell connections, and the response to physical and chemical stressors implying that archaeal biofilm formation is an adaptive reaction to changing environmental conditions. A first insight into the molecular differentiation of cells within archaeal biofilms is given.
Collapse
|
10
|
Reigstad LJ, Jorgensen SL, Lauritzen SE, Schleper C, Urich T. Sulfur-oxidizing chemolithotrophic proteobacteria dominate the microbiota in high arctic thermal springs on Svalbard. ASTROBIOLOGY 2011; 11:665-678. [PMID: 21899440 DOI: 10.1089/ast.2010.0551] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The thermal springs Trollosen and Fisosen, located on the High Arctic archipelago Svalbard, discharge saline groundwaters rich in hydrogen sulfide and ammonium through a thick layer of permafrost. Large amounts of biomass that consist of filamentous microorganisms containing sulfur granules, as analyzed with energy dispersive X-ray analysis, were found in the outflow. Prokaryotic 16S rRNA gene libraries and quantitative polymerase chain reaction (qPCR) analyses reported bacteria of the γ- and ɛ-proteobacterial classes as the dominant organisms in the filaments and the planktonic fractions, closely related to known chemolithoautotrophic sulfur oxidizers (Thiotrix and Sulfurovum). Archaea comprised ∼1% of the microbial community, with the majority of sequences affiliated with the Thaumarchaeota. Archaeal and bacterial genes coding for a subunit of the enzyme ammonia monooxygenase (amoA) were detected, as well as 16S rRNA genes of Nitrospira, all of which is indicative of potential complete nitrification in both springs. 16S rRNA sequences related to methanogens and methanotrophs were detected as well. This study provides evidence that the microbial communities in Trollosen and Fisosen are sustained by chemolithotrophy, mainly through the oxidation of reduced sulfur compounds, and that ammonium and methane might be minor, additional sources of energy and carbon.
Collapse
|
11
|
Stratification of Archaeal communities in shallow sediments of the Pearl River Estuary, Southern China. Antonie van Leeuwenhoek 2011; 99:739-51. [DOI: 10.1007/s10482-011-9548-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
|
12
|
Park BJ, Park SJ, Yoon DN, Schouten S, Sinninghe Damsté JS, Rhee SK. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Microbiol 2010; 76:7575-87. [PMID: 20870784 PMCID: PMC2976178 DOI: 10.1128/aem.01478-10] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/17/2010] [Indexed: 11/20/2022] Open
Abstract
The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and "Candidatus Nitrosopumilus maritimus" (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [(13)C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.
Collapse
MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/growth & development
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria/classification
- Bacteria/growth & development
- Bacteria/isolation & purification
- Bacteria/metabolism
- Cluster Analysis
- Coculture Techniques
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Geologic Sediments/microbiology
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sulfur/metabolism
Collapse
Affiliation(s)
- Byoung-Joon Park
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Soo-Je Park
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Dae-No Yoon
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Stefan Schouten
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| |
Collapse
|
13
|
Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. MICROBIAL ECOLOGY 2010; 60:784-95. [PMID: 20725722 PMCID: PMC2974187 DOI: 10.1007/s00248-010-9734-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 08/01/2010] [Indexed: 05/22/2023]
Abstract
Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.
Collapse
Affiliation(s)
- Iris Porat
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | | | - Jennifer J. Mosher
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Craig C. Brandt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Scott C. Brooks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Liyuan Liang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Meghan M. Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Anthony V. Palumbo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| |
Collapse
|
14
|
Vissers EW, Bodelier PLE, Muyzer G, Laanbroek HJ. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol Lett 2009; 298:193-8. [PMID: 19656198 DOI: 10.1111/j.1574-6968.2009.01718.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F-958R and Parch519f-Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.
Collapse
Affiliation(s)
- Elisabeth W Vissers
- Department of Microbial Wetland Ecology, Centre for Limnology, Netherlands Institute of Ecology (NIOO-KNAW), Nieuwersluis, The Netherlands.
| | | | | | | |
Collapse
|
15
|
Bacterial and archaeal phylogenetic diversity of a cold sulfur-rich spring on the shoreline of Lake Erie, Michigan. Appl Environ Microbiol 2009; 75:5025-36. [PMID: 19542341 DOI: 10.1128/aem.00112-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H(2), 5.4 nM; CH(4), 2.70 microM) with concentrations of S(2-) (0.03 mM), SO(4)(2-) (14.8 mM), Ca(2+) (15.7 mM), and HCO(3)(-) (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments.
Collapse
|
16
|
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 2009; 33:855-69. [PMID: 19453522 DOI: 10.1111/j.1574-6976.2009.00179.x] [Citation(s) in RCA: 335] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.
Collapse
Affiliation(s)
- Tuba H Erguder
- Laboratory of Microbial Ecology and Technology (LabMET), Gent University, Gent, Belgium
| | | | | | | | | |
Collapse
|
17
|
Llirós M, Casamayor EO, Borrego C. High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study. FEMS Microbiol Ecol 2008; 66:331-42. [PMID: 18754782 DOI: 10.1111/j.1574-6941.2008.00583.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We surveyed the archaeal assemblage in a stratified sulfurous lake (Lake Vilar, Banyoles, Spain) over 5 consecutive years to detect potential seasonal and interannual trends in the free-living planktonic Archaea composition. The combination of different primer pairs and nested PCR steps revealed an unexpectedly rich archaeal community. Overall, 140 samples were analyzed, yielding 169 different 16S rRNA gene sequences spread over 14 Crenarchaeota (109 sequences) and six Euryarchaeota phylogenetic clusters. Most of the Crenarchaeota (98% of the total crenarchaeotal sequences) affiliated within the Miscellaneous Crenarchaeota Group (MCG) and were related to both marine and freshwater phylotypes. Euryarchaeota mainly grouped within the Deep Hydrothermal Vent Euryarchaeota (DHVE) cluster (80% of the euryarchaeotal sequences) and the remaining 20% distributed into three less abundant taxa, most of them composed of soil and sediment clones. The largest fraction of phylotypes from the two archaeal kingdoms (79% of the Crenarchaeota and 54% of the Euryarchaeota) was retrieved from the anoxic hypolimnion, indicating that these cold and sulfide-rich waters constitute an unexplored source of archaeal richness. The taxon rank-frequency distribution showed two abundant taxa (MCG and DHVE) that persisted in the water column through seasons, plus several rare ones that were only detected occasionally. Differences in richness distribution and seasonality were observed, but no clear correlations were obtained when multivariate statistical analyses were carried out.
Collapse
Affiliation(s)
- Marc Llirós
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | | | | |
Collapse
|
18
|
Park SJ, Park BJ, Rhee SK. Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles 2008; 12:605-15. [PMID: 18465082 DOI: 10.1007/s00792-008-0165-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 04/07/2008] [Indexed: 11/27/2022]
Abstract
Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase alpha-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0-1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1x10(7) to 4.9x10(7) per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.
Collapse
Affiliation(s)
- Soo-Je Park
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju, 361-763, Korea
| | | | | |
Collapse
|
19
|
Santoro AE, Francis CA, de Sieyes NR, Boehm AB. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ Microbiol 2008; 10:1068-79. [PMID: 18266758 DOI: 10.1111/j.1462-2920.2007.01547.x] [Citation(s) in RCA: 202] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A (amoA). The abundance of beta-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of beta-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a beta-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA. Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments.
Collapse
Affiliation(s)
- Alyson E Santoro
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.
| | | | | | | |
Collapse
|
20
|
Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG, Sinninghe Damsté JS. Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environ Microbiol 2007; 9:1001-16. [PMID: 17359272 DOI: 10.1111/j.1462-2920.2006.01227.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.
Collapse
Affiliation(s)
- Marco J L Coolen
- Royal Netherlands Institute for Sea Research, Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, the Netherlands.
| | | | | | | | | | | | | |
Collapse
|
21
|
Jékely G. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms. Biol Direct 2007; 2:3. [PMID: 17239231 PMCID: PMC1794243 DOI: 10.1186/1745-6150-2-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 01/19/2007] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusion of prokaryotic lineages. However, as yet there is no consensus regarding the nature of the prokaryotic group(s) ancestral to eukaryotes. Regardless of this, a hardly debatable fundamental novel characteristic of the last eukaryotic common ancestor was the ability to exploit prokaryotic biomass by the ingestion of entire cells, i.e. phagocytosis. The recent advances in our understanding of the social life of prokaryotes may help to explain the origin of this form of total exploitation. PRESENTATION OF THE HYPOTHESIS Here I propose that eukaryotic cells originated in a social environment, a differentiated microbial mat or biofilm that was maintained by the cooperative action of its members. Cooperation was costly (e.g. the production of developmental signals or an extracellular matrix) but yielded benefits that increased the overall fitness of the social group. I propose that eukaryotes originated as selfish cheaters that enjoyed the benefits of social aggregation but did not contribute to it themselves. The cheaters later evolved into predators that lysed other cells and eventually became professional phagotrophs. During several cycles of social aggregation and dispersal the number of cheaters was contained by a chicken game situation, i.e. reproductive success of cheaters was high when they were in low abundance but was reduced when they were over-represented. Radical changes in cell structure, including the loss of the rigid prokaryotic cell wall and the development of endomembranes, allowed the protoeukaryotes to avoid cheater control and to exploit nutrients more efficiently. Cellular changes were buffered by both the social benefits and the protective physico-chemical milieu of the interior of biofilms. Symbiosis with the mitochondial ancestor evolved after phagotrophy as alphaproteobacterial prey developed post-ingestion defence mechanisms to circumvent digestion in the food vacuole. Mitochondrial symbiosis triggered the origin of the nucleus. Cilia evolved last and allowed eukaryotes to predate also on planktonic prey. I will discuss how this scenario may possibly fit into the contrasting phylogenetic frameworks that have been proposed. TESTING THE HYPOTHESIS Some aspects of the hypothesis can be tested experimentally by studying the level of exploitation cheaters can reach in social microbes. It would be interesting to test whether absorption of nutrients from lysed fellow colony members can happen and if cheaters can evolve into predators that actively digest neighbouring cells. IMPLICATIONS OF THE HYPOTHESIS The hypothesis highlights the importance of social exploitation in cell evolution and how a social environment can buffer drastic cellular transformations that would be lethal for planktonic forms.
Collapse
Affiliation(s)
- Gáspár Jékely
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|