Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats

Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.

[1]  Dmitry Antipov,et al.  Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..

[2]  E. Hopmans,et al.  13,16-Dimethyl Octacosanedioic Acid (iso-Diabolic Acid), a Common Membrane-Spanning Lipid of Acidobacteria Subdivisions 1 and 3 , 2011, Applied and Environmental Microbiology.

[3]  R. Thauer,et al.  Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. , 2013, Biochimica et biophysica acta.

[4]  A. Goldstein,et al.  Purification and properties , 1975 .

[5]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[6]  Brian C. Thomas,et al.  Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface , 2014, Nature Communications.

[7]  Filipa L. Sousa,et al.  Origins of major archaeal clades correspond to gene acquisitions from bacteria , 2014, Nature.

[8]  W. Grant,et al.  The ecology and taxonomy of halobacteria , 1986 .

[9]  B. Jørgensen,et al.  A Thiosulfate Shunt in the Sulfur Cycle of Marine Sediments , 1990, Science.

[10]  A. Ducluzeau,et al.  Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes , 2008, BMC Evolutionary Biology.

[11]  B. Tindall,et al.  Etophysiology of the aerobic halophilic archaebacteria , 1986 .

[12]  V. Müller,et al.  The Ferredoxin:NAD+ Oxidoreductase (Rnf) from the Acetogen Acetobacterium woodii Requires Na+ and Is Reversibly Coupled to the Membrane Potential* , 2013, The Journal of Biological Chemistry.

[13]  R. Thauer,et al.  Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase , 2013, Applied and Environmental Microbiology.

[14]  J. S. Sinninghe Damsté,et al.  Halanaeroarchaeum sulfurireducens gen. nov., sp. nov., the first obligately anaerobic sulfur-respiring haloarchaeon, isolated from a hypersaline lake. , 2016, International journal of systematic and evolutionary microbiology.

[15]  M. Alexe,et al.  Spatial and temporal distribution of archaeal diversity in meromictic, hypersaline Ocnei Lake (Transylvanian Basin, Romania) , 2014, Extremophiles.

[16]  M. Collins,et al.  Occurrence of menaquinones and some novel methylated menaquinones in the alkaliphilic, extremely halophilic archaebacterium Natronobacterium gregoryi , 1987 .

[17]  H. Deveau,et al.  CRISPR/Cas system and its role in phage-bacteria interactions. , 2010, Annual review of microbiology.

[18]  E. Ammar,et al.  Novel prokaryotic diversity in sediments of Tunisian multipond solar saltern. , 2010, Research in microbiology.

[19]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[20]  W. Doolittle,et al.  Archaeal diversity along a soil salinity gradient prone to disturbance. , 2005, Environmental microbiology.

[21]  D. Canfield,et al.  Community Composition of a Hypersaline Endoevaporitic Microbial Mat , 2005, Applied and Environmental Microbiology.

[22]  K. Keesman,et al.  Effect of Methanethiol Concentration on Sulfur Production in Biological Desulfurization Systems under Haloalkaline Conditions. , 2015, Environmental science & technology.

[23]  Eugene V Koonin,et al.  Genome reduction as the dominant mode of evolution , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[24]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[25]  L. Whyte,et al.  Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring , 2014, Extremophiles.

[26]  T. Erb,et al.  A Methylaspartate Cycle in Haloarchaea , 2011, Science.

[27]  H. Teeling,et al.  Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader , 2014, Environmental microbiology.

[28]  M. Klotz,et al.  Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. , 2013, Biochimica et biophysica acta.

[29]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[30]  M. Amoozegar,et al.  Prokaryotic Diversity in Aran-Bidgol Salt Lake, the Largest Hypersaline Playa in Iran , 2011, Microbes and environments.

[31]  P. Pevzner,et al.  False discovery rates of protein identifications: a strike against the two-peptide rule. , 2009, Journal of proteome research.

[32]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[33]  M. Brosnan,et al.  Division of labour: how does folate metabolism partition between one-carbon metabolism and amino acid oxidation? , 2015, The Biochemical journal.

[34]  R. Thauer,et al.  Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid , 2004, Archives of Microbiology.

[35]  H. Zischka,et al.  The membrane proteome of Halobacterium salinarum , 2005, Proteomics.

[36]  A. Oren Thermodynamic limits to microbial life at high salt concentrations. , 2011, Environmental microbiology.

[37]  Zhihong Guo,et al.  Identification of a Hotdog Fold Thioesterase Involved in the Biosynthesis of Menaquinone in Escherichia coli , 2013, Journal of bacteriology.

[38]  Radhey S. Gupta,et al.  A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae , 2016, Antonie van Leeuwenhoek.

[39]  Filipa L. Sousa,et al.  One step beyond a ribosome: The ancient anaerobic core , 2016, Biochimica et biophysica acta.

[40]  Shiladitya DasSarma,et al.  Genomic Analysis of Anaerobic Respiration in the Archaeon Halobacterium sp. Strain NRC-1: Dimethyl Sulfoxide and Trimethylamine N-Oxide as Terminal Electron Acceptors , 2005, Journal of bacteriology.

[41]  Kenneth H. Williams,et al.  Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment , 2013, Nature Communications.

[42]  H. G. Trüper,et al.  Sulphur metabolism in Thiorhodaceae I. Quantitative measurements on growing cells ofChromatium okenii , 2005, Antonie van Leeuwenhoek.

[43]  C. Schröder,et al.  Abundance, Distribution, and Activity of Fe(II)-Oxidizing and Fe(III)-Reducing Microorganisms in Hypersaline Sediments of Lake Kasin, Southern Russia , 2012, Applied and Environmental Microbiology.

[44]  Jörg Simon,et al.  Enzymology and bioenergetics of respiratory nitrite ammonification. , 2002, FEMS microbiology reviews.

[45]  A. Oren,et al.  Anaerobic growth of halophilic archaeobacteria by reduction of dimethysulfoxide and trimethylamine N-oxide , 1990 .

[46]  Complete genome sequence of ‘Halanaeroarchaeum sulfurireducens’ M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee , 2016, Standards in genomic sciences.

[47]  E. Aro,et al.  Cyanobacterial NDH-1 complexes: novel insights and remaining puzzles. , 2011, Biochimica et biophysica acta.

[48]  A. Oren,et al.  Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems. , 2012, FEMS microbiology letters.

[49]  A. Stams,et al.  Constraints on the Biological Source(s) of the Orphan Branched Tetraether Membrane Lipids , 2009 .

[50]  R. M. Martínez-Espinosa,et al.  Nitrogen metabolism in haloarchaea , 2008, Saline systems.

[51]  A. Janssen,et al.  Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea , 2012, Proceedings of the National Academy of Sciences.

[52]  G. Fuchs,et al.  Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme , 2010, Nature.

[53]  R. Thauer,et al.  Energy conservation in chemotrophic anaerobic bacteria , 1977, Bacteriological reviews.

[54]  B. Roe,et al.  Survey of Archaeal Diversity Reveals an Abundance of Halophilic Archaea in a Low-Salt, Sulfide- and Sulfur-Rich Spring , 2004, Applied and Environmental Microbiology.

[55]  J. Eisen,et al.  Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola , 2009, PLoS genetics.

[56]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[57]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[58]  S. Imura,et al.  Dimethyl sulfoxide-respiring bacteria in Suribati Ike, a hypersaline lake, in Antarctica and the marine environment , 2006 .

[59]  Steven Salzberg,et al.  Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..

[60]  Hailiang Dong,et al.  Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. , 2007, Environmental microbiology.

[61]  Gipsi Lima-Mendez,et al.  ACLAME: A CLAssification of Mobile genetic Elements, update 2010 , 2009, Nucleic Acids Res..

[62]  M. Ilbert,et al.  Rhodanese Functions as Sulfur Supplier for Key Enzymes in Sulfur Energy Metabolism , 2012, The Journal of Biological Chemistry.

[63]  J. Meyer,et al.  Classification and phylogeny of hydrogenases. , 2001, FEMS microbiology reviews.

[64]  J. Leigh,et al.  Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic Archaeon Methanococcus maripaludis , 2003, Journal of bacteriology.

[65]  Eric Smith,et al.  The Emergence and Early Evolution of Biological Carbon-Fixation , 2012, PLoS Comput. Biol..

[66]  P. Vignais,et al.  Occurrence, classification, and biological function of hydrogenases: an overview. , 2007, Chemical reviews.

[67]  A. Oren,et al.  Differences in lateral gene transfer in hypersaline versus thermal environments , 2011, BMC Evolutionary Biology.

[68]  M. Borghini,et al.  Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation , 2013, Scientific Reports.

[69]  N. Youssef,et al.  Phylogenetic Diversities and Community Structure of Members of the Extremely Halophilic Archaea (Order Halobacteriales) in Multiple Saline Sediment Habitats , 2011, Applied and Environmental Microbiology.

[70]  B. Berks,et al.  Thiosulfate Reduction in Salmonella enterica Is Driven by the Proton Motive Force , 2011, Journal of bacteriology.

[71]  A. Oren ANAEROBIC GROWTH OF HALOPHILIC ARCHAEOBACTERIA BY REDUCTION OF FUMARATE , 1991 .

[72]  Richard M. Leggett,et al.  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries , 2013, Bioinform..

[73]  P. Schönheit,et al.  Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus. , 1997, European journal of biochemistry.

[74]  P. Roman,et al.  Quantification of individual polysulfides in lab-scale and full-scale desulfurisation bioreactors , 2014 .

[75]  P. Schönheit,et al.  Acetyl Coenzyme A Synthetase (ADP Forming) from the Hyperthermophilic Archaeon Pyrococcus furiosus: Identification, Cloning, Separate Expression of the Encoding Genes,acdAI and acdBI, in Escherichia coli, and In Vitro Reconstitution of the Active Heterotetrameric Enzyme from Its Recombinant Subunits , 1999, Journal of bacteriology.

[76]  Shukun Tang,et al.  The Futalosine Pathway Played an Important Role in Menaquinone Biosynthesis during Early Prokaryote Evolution , 2014, Genome biology and evolution.

[77]  Erin A. Becker,et al.  Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response , 2014, PLoS genetics.

[78]  M. Ferrer,et al.  Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon , 2015, The ISME Journal.

[79]  C. Klein,et al.  The function of the periplasmic Sud protein in polysulfide respiration of Wolinella succinogenes. , 1998, European journal of biochemistry.

[80]  E. Marcotte,et al.  Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation , 2007, Nature Biotechnology.

[81]  Stefan Schouten,et al.  Separation of core and intact polar archaeal tetraether lipids using silica columns: insights into living and fossil biomass contributions. , 2009 .

[82]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[83]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[84]  R. Amils,et al.  Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment , 2013, Aquatic biosystems.

[85]  L. Maia,et al.  Molybdenum and tungsten-dependent formate dehydrogenases , 2014, JBIC Journal of Biological Inorganic Chemistry.

[86]  M. Keller,et al.  Anaerobic respiration with elemental sulfur and with disulfides , 1998 .

[87]  Robert Huber,et al.  Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus. , 2008, International journal of systematic and evolutionary microbiology.

[88]  Juan Du,et al.  Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase , 2011, Nature.

[89]  A. Oren,et al.  Haloferax sulfurifontis sp. nov., a halophilic archaeon isolated from a sulfide- and sulfur-rich spring. , 2004, International journal of systematic and evolutionary microbiology.