DOCSLIB.ORG

Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Coralsᰔ† J

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Coralsᰔ† J APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2007, p. 5642–5647 Vol. 73, No. 17 0099-2240/07/$08.00ϩ0 doi:10.1128/AEM.00461-07 Copyright © 2007, American Society for Microbiology. All Rights Reserved. Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Coralsᰔ† J. Michael Beman,1‡ Kathryn J. Roberts,1§ Linda Wegley,2 Forest Rohwer,2 and Christopher A. Francis1* Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305,1 and Department of Biology, San Diego State University, San Diego, California 921822 Received 28 February 2007/Accepted 18 June 2007 Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A(amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs. The exceptional biological diversity of coral reef ecosystems available. However, it has become increasingly clear that many is relatively well characterized for many eukaryotic species mesophilic Crenarchaeota may be capable of ammonia oxida- (see, e.g., reference 32). However, diverse assemblages of mi- tion (9), based on the cultivation of an ammonia-oxidizing croorganisms from the domains Bacteria and Archaea are also archaeon (AOA) (21) and accumulating (meta)genomic (12, found in association with corals (2, 8, 11, 15, 20, 22, 30, 33, 34, 13, 21, 45, 46), molecular (1, 6, 10, 24, 25, 29, 31, 50), and 43, 49), yet very little is known about the ecological function of geochemical (19, 23) evidence. More specifically, amoA genes the microorganisms that comprise these communities (34, 35). putatively encoding the ␣-subunit of the ammonia monooxy- Among other important roles, it has been hypothesized that genase enzyme appear to be present in many mesophilic Cre- coral-associated microorganisms are critical for nutrient cy- narchaeota (10, 12, 13, 21, 25, 50), and Lam et al. (24) recently cling (34), and in fact corals have been shown to harbor sym- demonstrated that this gene is actively expressed by some biotic nitrogen (N)-fixing cyanobacteria, which may represent Crenarchaeota in the ocean. an appreciable source of this essential nutrient (26). In addi- Ammonia oxidation is the first and rate-limiting step of tion, specific bacterial ribotypes appear to be associated with chemoautotrophic nitrification—the overall oxidation of am- Ϫ Ϫ particular coral species (33, 34), with many of these types being monia (NH3) to nitrite (NO2 ) to nitrate (NO3 )—and there most closely related to known nitrogen fixers and antibiotic is clear evidence for nitrification in association with individual producers (34). corals (47), within coral reefs (48), and within reef cavities While these studies have provided some insight into the (37). Given the association between Crenarchaeota and corals ecological function of coral-associated Bacteria, members of (20, 49), we investigated the distribution and diversity of ar- the domain Archaea are also known to be associated with chaeal amoA gene fragments in DNA extracts recovered from corals: both mesophilic Euryarchaeota and Crenarchaeota are coral colonies in Panama, Bermuda, Hawaii, and Puerto Rico. widely distributed across different reef locations and coral spe- Our results indicate that archaeal amoA genes are associated cies (20, 49), and Archaea appear to be abundant on some coral with a variety of coral species. 8 Ϫ2 colonies, numbering Ͼ10 cells cm (49). Until recently, few Sample collection, DNA preparation, and amplification and insights into the ecology and physiology of these coral-associ- sequencing of archaeal amoA genes. Samples were collected ated Archaea—and the mesophilic Archaea in general—were from coral colonies at Whale Bone Bay, Bermuda (August 1999), Bocas del Toro, Panama (April 1999, June 2000, Feb- ruary 2005), La Parguerra, Puerto Rico (January 2002), and * Corresponding author. Mailing address: Department of Geologi- Kane’ohe Bay, HI (June 2003) by use of previously described cal and Environmental Sciences, Building 320 – Room 118, Stanford methods (49). Briefly, a punch and hammer or bone clippers University, Stanford, CA 94305-2115. Phone: (650) 724-0301. Fax: (650) 725-2199. E-mail: [email protected]. were used to collect a single sample from each healthy coral † Supplemental material for this article may be found at http://aem colony; samples were then placed in Ziploc bags underwater, .asm.org/. washed with 0.2 ␮M filtered and autoclaved seawater at the ‡ Present address: Department of Biological Sciences, University of surface, placed on ice, returned to the lab, and stored at Ϫ80°C Southern California, Los Angeles, CA 90089. Diploria strigosa Montastraea franksi § Present address: Ocean Sciences Department, University of Cali- until DNA extraction. , , fornia Santa Cruz, Santa Cruz, CA 95064. and Porites astreoides were sampled in both Bermuda and Pan- ᰔ Published ahead of print on 22 June 2007. ama, Colpophyllia natans and Porites furcata were sampled only 5642 VOL. 73, 2007 ARCHAEAL amoA GENES ASSOCIATED WITH CORALS 5643 in Panama, Acropora cervicornis and Acropora prolifera samples TABLE 1. Richness of archaeal amoA libraries from coralsa were collected in Puerto Rico, and samples were collected No. of No. of OTUs: from Porites compressa in Hawaii (see Table S1 in the supple- Coral HЈ clones Estimated Estimated mental material). For DNA extraction, each frozen coral sam- library Observed value sequenced by Chao1 by ACE ple was airbrushed (Ͻ2.7 bar) with 10ϫ TE (100 mM Tris [pH 8.0]-10 mM EDTA) to remove the tissue and associated mi- CN8C 23 9 31 27 1.9 crobes. Two milliliters of the coral tissue-TE slurry was pel- DS2 32 12 15 16 2.3 ϫ DS4 31 9 10 12 1.9 leted for 30 min at 10,000 g at 4°C. Total DNA was extracted MA7 33 7 17 31 1.1 from the pellet by use of the Ultra Clean soil DNA kit (Mo- PF1 32 3 3 3 0.93 Bio). PA6 29 7 7 7 1.8 Archaeal amoA gene fragments were amplified using the PA22 30 2 2 2 0.69 PCR primers Arch-amoAF (5Ј-STAATGGTCTGGCTTAGA a All OTUs were defined as having Յ5% difference in nucleic acid sequence CG-3Ј) and Arch-amoAR (5Ј-GCGGCCATCCATCTGTATG alignment, and all indices were calculated using DOTUR. T-3Ј) and conditions as previously described (10). Triplicate PCRs were pooled, gel purified, and cloned using the TOPO-TA cloning kit (Invitrogen). White transformants were observed coverage of our libraries. Significant P values were transferred to 96-well plates containing LB broth (with 50 evaluated after correcting for multiple pairwise comparisons by ␮ ϭ Ϫ g/ml kanamycin), grown overnight at 37°C, and PCR use of the Dunn-Sida´k method (42), where Pcorrected 1 Ϫ 1/k screened for the presence of inserts by use of T7 and M13R (1 Puncorrected) , where k is the total number of compari- vector primers. Sequencing of T7/M13 PCR products was per- sons (for seven archaeal amoA libraries, each compared with formed using vector primers on ABI 3730xl capillary sequenc- the corresponding six other libraries, k ϭ 7 ϫ 6 ϭ 42). ers (PE Applied Biosystems). Coral DNA extracts were also Distribution and richness of archaeal amoA genes associ- PCR screened for the presence of betaproteobacterial amoA ated with corals. DNA was extracted from coral colonies in genes by use of primers (AmoA-1F* and AmoA-2R) and con- Bocas del Toro, Panama, Whale Bone Bay, Bermuda, ditions described previously (36, 44). Kane’ohe Bay, HI, and La Parguerra, Puerto Rico and Richness, phylogenetic, and statistical analyses. Nucleotide screened for the archaeal amoA gene. These DNA samples sequences were assembled and edited using Sequencher v.4.2 were drawn from nine different species of coral: Acropora cer- (GeneCodes, Ann Arbor, MI), and nucleotide and amino acid vicornis, Acropora prolifera, Colpophyllia natans, Diploria stri- alignments were generated using MacClade (http://macclade gosa, Montastraea annularis, Montastraea franksi, Porites as- .org). Operational taxonomic units (OTUs) were defined as treoides, Porites compressa, and Porites furcata. From 40 sequence groups in which sequences differed by Յ5%, and all samples that were screened, the archaeal amoA gene was am- analyses of richness—including rarefaction analysis (14) and plified from a total of 12 samples (see Table S1 in the supple- both ACE (5) and Chao1 (3) nonparametric richness estima- mental material). In contrast, in no case could the betapro- tions—were performed using DOTUR (38). teobacterial amoA gene be PCR amplified. Neighbor-joining phylogenetic trees (based on Jukes-Can- Of the 12 samples from which the archaeal amoA gene was tor-corrected distances) and parsimony trees were constructed amplified, 10 were previously screened for archaeal 16S rRNA based on alignments of DNA sequences by use of ARB (http: genes, and all contained 16S rRNA genes from Crenarchaeota //www.arb-home.de) (27). Nucleic acid sequences (rather than (49). In addition, Wegley et al. (49) quantified Crenarchaeota predicted amino acid sequences) were analyzed in order to and Euryarchaeota for 3 of the 40 coral colonies included in this highlight the genetic (rather than protein-level) heterogeneity study via fluorescent in situ hybridization, and Archaea num- among communities.
Load more

Recommended publications
  • Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria.
    [Show full text]
  • Yu-Chen Ling and John W. Moreau
    Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig.
    [Show full text]
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
    [Show full text]
  • Oceans of Archaea Abundant Oceanic Crenarchaeota Appear to Derive from Thermophilic Ancestors That Invaded Low-Temperature Marine Environments
    Oceans of Archaea Abundant oceanic Crenarchaeota appear to derive from thermophilic ancestors that invaded low-temperature marine environments Edward F. DeLong arth’s microbiota is remarkably per- karyotes), Archaea, and Bacteria. Although al- vasive, thriving at extremely high ternative taxonomic schemes have been recently temperature, low and high pH, high proposed, whole-genome and other analyses E salinity, and low water availability. tend to support Woese’s three-domain concept. One lineage of microbial life in par- Well-known and cultivated archaea generally ticular, the Archaea, is especially adept at ex- fall into several major phenotypic groupings: ploiting environmental extremes. Despite their these include extreme halophiles, methanogens, success in these challenging habitats, the Ar- and extreme thermophiles and thermoacido- chaea may now also be viewed as a philes. Early on, extremely halo- cosmopolitan lot. These microbes philic archaea (haloarchaea) were exist in a wide variety of terres- first noticed as bright-red colonies trial, freshwater, and marine habi- Archaea exist in growing on salted fish or hides. tats, sometimes in very high abun- a wide variety For many years, halophilic isolates dance. The oceanic Marine Group of terrestrial, from salterns, salt deposits, and I Crenarchaeota, for example, ri- freshwater, and landlocked seas provided excellent val total bacterial biomass in wa- marine habitats, model systems for studying adap- ters below 100 m. These wide- tations to high salinity. It was only spread Archaea appear to derive sometimes in much later, however, that it was from thermophilic ancestors that very high realized that these salt-loving invaded diverse low-temperature abundance “bacteria” are actually members environments.
    [Show full text]
  • Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
    Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota
    [Show full text]
  • The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy The ISME Journal (2012) 6, 259–272 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide Zhili He1, Yvette Piceno2, Ye Deng1, Meiying Xu1,3, Zhenmei Lu1,4, Todd DeSantis2, Gary Andersen2, Sarah E Hobbie5, Peter B Reich6 and Jizhong Zhou1,2 1Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA; 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China; 4College of Life Sciences, Zhejiang University, Hangzhou, China; 5Department of Ecology, Evolution, and Behavior, St Paul, MN, USA and 6Department of Forest Resources, University of Minnesota, St Paul, MN, USA One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2.
    [Show full text]
  • Wide Diversity of Crenarchaeota Temperature Organisms8•9
    SCIENTIFIC CORRESPONDENCE a high-temperature ancestry for the low­ Wide diversity of Crenarchaeota temperature organisms8•9. This correlation also suggests that the ability to grow at SrR - The traditional perception of the sediment and marsh samples (5-32 °C) col­ low temperatures has arisen within the diversity of the bacteria-like Archaea based lected from Lakes Griffy and Lemon near Crenarchaeota in at least three separate on cultivation studies has been that the Bloomington, Indiana, and used it as tem­ instances. kingdom Euryarchaeota is a physiologically plate in the polymerase chain reaction The occurrence of diverse low-temper­ variable group including halophiles, (PCR) to amplify small-subunit rRNA ature Crenarchaeota in marine and terres­ thermophiles and methanogens, whereas genes (rDNA), as previously described4• trial environments is unexpected, and the kingdom Crenarchaeota is more homo­ We used an Archaea-specific forward shows that members of this kingdom of genous, consisting exclusively of sulphur­ primer (4Pa, see figure legend) and a uni­ the phylogenetic domain Archaea are dependent, extreme thermophiles 1• This versal reverse primer with a polylinker tail phenotypically more varied than was pre­ has led to the notion that the Crenarchaeo­ (1492RPL) for initial amplification to en­ viously thought. Because neither these ta are not widespread, but are restricted to rich for archaeal rRNA genes, and then organisms nor their close, high-tempera­ specialized habitats. Using sequence-based used forward primers specific to marine ture relatives have been cultivated, we techniques that sidestep the cultivation crenarchaeal sequences2•5 (89F), or to all have no information about their meta­ of organisms, crenarchaeal small-subunit known Crenarchaeota (542F), in conjunc­ bolic properties.
    [Show full text]
  • Life in Extreme Environments
    insight review articles Life in extreme environments Lynn J. Rothschild & Rocco L. Mancinelli NASA Ames Research Center, Moffett Field, California 94035-1000, USA (e-mail: [email protected]; [email protected]) Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring ‘extremophiles’. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe. ormal is passé; extreme is chic. While thriving in biological extremes (for example, nutritional Aristotle cautioned “everything in extremes, and extremes of population density, parasites, moderation”, the Romans, known for their prey, and so on). excesses, coined the word ‘extremus’, the ‘Extremophile’ conjures up images of prokaryotes, yet the superlative of exter (‘being on the outside’). taxonomic range spans all three domains. Although all NBy the fifteenth century ‘extreme’ had arrived, via Middle hyperthermophiles are members of the Archaea and French, to English. At the dawning of the twenty-first Bacteria, eukaryotes are common among the psychrophiles, century we know that the Solar System, and even Earth, acidophiles, alkaliphiles, piezophiles, xerophiles and contain environmental extremes unimaginable to the halophiles (which respectively thrive at low temperatures, low ‘ancients’ of the nineteenth century.
    [Show full text]
  • Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other
    Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other Archaea;Crenarchaeota;South;Other;Other Archaea;Crenarchaeota;terrestrial;Other;Other Archaea;Euryarchaeota;Halobacteria;Halobacteriales;Miscellaneous Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae Archaea;Euryarchaeota;Methanomicrobia;Methanocellales;Methanocellaceae Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosarcinaceae Archaea;Euryarchaeota;Thermoplasmata;Thermoplasmatales;Marine Bacteria;Acidobacteria;Acidobacteria;11-24;uncultured Bacteria;Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae Bacteria;Acidobacteria;Acidobacteria;BPC102;uncultured Bacteria;Acidobacteria;Acidobacteria;Bryobacter;uncultured Bacteria;Acidobacteria;Acidobacteria;Candidatus;Other Bacteria;Acidobacteria;Acidobacteria;DA023;uncultured Bacteria;Acidobacteria;Acidobacteria;DA023;unidentified Bacteria;Acidobacteria;Acidobacteria;DS-100;uncultured Bacteria;Acidobacteria;Acidobacteria;PAUC26f;uncultured Bacteria;Acidobacteria;Acidobacteria;RB41;uncultured Bacteria;Acidobacteria;Holophagae;32-20;uncultured Bacteria;Acidobacteria;Holophagae;43F-1404R;uncultured Bacteria;Acidobacteria;Holophagae;Holophagales;Holophagaceae Bacteria;Acidobacteria;Holophagae;NS72;uncultured Bacteria;Acidobacteria;Holophagae;SJA-36;uncultured Bacteria;Acidobacteria;Holophagae;Sva0725;uncultured Bacteria;Acidobacteria;Holophagae;iii1-8;uncultured Bacteria;Acidobacteria;RB25;uncultured;Other Bacteria;Actinobacteria;Actinobacteria;Actinobacteridae;Actinomycetales
    [Show full text]
  • Thermophiles and Thermozymes
    Thermophiles and Thermozymes Edited by María-Isabel González-Siso Printed Edition of the Special Issue Published in Microorganisms www.mdpi.com/journal/microorganisms Thermophiles and Thermozymes Thermophiles and Thermozymes Special Issue Editor Mar´ıa-Isabel Gonz´alez-Siso MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editor Mar´ıa-Isabel Gonzalez-Siso´ Universidade da Coruna˜ Spain Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Microorganisms (ISSN 2076-2607) from 2018 to 2019 (available at: https://www.mdpi.com/journal/ microorganisms/special issues/thermophiles) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-816-9 (Pbk) ISBN 978-3-03897-817-6 (PDF) c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editor ...................................... vii Mar´ıa-Isabel Gonz´alez-Siso Editorial for the Special Issue: Thermophiles and Thermozymes Reprinted from: Microorganisms 2019, 7, 62, doi:10.3390/microorganisms7030062 ........
    [Show full text]
  • And Iron-Reducing Thaumarchaeote from a Terrestrial Acidic Hot Spring
    The ISME Journal (2019) 13:2465–2474 https://doi.org/10.1038/s41396-019-0447-3 ARTICLE Isolation and characterization of a thermophilic sulfur- and iron- reducing thaumarchaeote from a terrestrial acidic hot spring 1,2 1 1 1,3 1,3 4 Shingo Kato ● Takashi Itoh ● Masahiro Yuki ● Mai Nagamori ● Masafumi Ohnishi ● Katsuyuki Uematsu ● 2 3 1 Katsuhiko Suzuki ● Tomonori Takashina ● Moriya Ohkuma Received: 10 September 2018 / Revised: 18 April 2019 / Accepted: 3 May 2019 / Published online: 6 June 2019 © International Society for Microbial Ecology 2019 Abstract A deep-branching clade of Thaumarchaeota, conventionally called Terrestrial hot spring creanarchaeotic group (THSCG), is a missing link between thaumarchaeotic ammonia oxidizers and the deeper-branching non-ammonia oxidizers, such as Crenarchaeota and Candidatus Korarchaeota. Here, we report isolation of the first cultivated representative from the THSCG, named as NAS-02. Physiological characterization demonstrated that the isolate was a thermoacidophilic, sulfur- and iron-reducing organoheterotroph, which was supported by gene contents encoded in its complete genome. There was no evidence for ammonia oxidation by the isolate. Members in THSCG are likely thermophiles, and may play roles in 1234567890();,: 1234567890();,: degrading cell debris as a scavenger and in biogeochemical cycling of sulfur and iron in the hot environments, as suggested by the physiological characteristics of the isolate and the geographical distribution of the 16S rRNA gene sequences of THSCG in terrestrial hot springs and marine hydrothermal fields. Phylogenetic analysis suggests that the THSCG lineage represented by NAS-02 has gained the ability of sulfur reduction via horizontal gene transfer. Based on the phylogeny and physiology, we propose the name Conexivisphaera calidus gen.
    [Show full text]
  • Co-Occurrence Patterns for Abundant Marine Archaeal and Bacterial Lineages in the Deep Chlorophyll Maximum of Coastal California
    The ISME Journal (2011) 5, 1077–1085 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California J Michael Beman, Joshua A Steele and Jed A Fuhrman Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, USA Microorganisms remineralize and respire half of marine primary production, yet the niches occupied by specific microbial groups, and how these different groups may interact, are poorly understood. In this study, we identify co-occurrence patterns for marine Archaea and specific bacterial groups in the chlorophyll maximum of the Southern California Bight. Quantitative PCR time series of marine group 1 (MG1) Crenarchaeota 16S rRNA genes varied substantially over time but were well- correlated (r2 ¼ 0.94, Po0.001) with ammonia monooxygenase subunit A (amoA) genes, and were more weakly related to 16S rRNA genes for all Archaea (r2 ¼ 0.39), indicating that other archaeal groups (for example, Euryarchaeota) were numerically important. These data sets were compared with variability in bacterial community composition based on automated ribosomal intergenic spacer analysis (ARISA). We found that archaeal amoA gene copies and a SAR11 (or Pelagibacter) group Ib operational taxonomic unit (OTU) displayed strong co-variation through time (r2 ¼ 0.55, Po0.05), and archaeal amoA and MG1 16S rRNA genes also co-occurred with two SAR86 and two Bacteroidetes OTUs. The relative abundance of these groups increased and decreased in synchrony over the course of the time series, and peaked during periods of seasonal transition.
    [Show full text]