Professor Rick Cavicchioli
Honorary Professor

Professor Rick Cavicchioli

Science
School of Biotech & Biomolecular Science

About Me

Biography

My research area is environmental microbiology. I study Antarctic microorganisms, discovering which types live in and around Antarctica, learning how they evolve and grow in the cold, and assessing how they are likely to respond to ecosystem changes, including climate change. I have a special interest in Archaea – the third domain of life. The research is important because environmental microbes enable all other life forms on Earth to exist, and the vast majority of life on the planet grows at low temperatures.

Education

  • University of California, Los Angeles, CA, USA. Postdoctoral Fellow. 1991 – 1994. Molecular Microbiology
  • University of New England, Armidale, NSW, Australia. Ph.D. 1992. Molecular Microbiology
  • James Cook University, Townsville, Qld, Australia. M.Sc. 1986. Microbiology
  • James Cook University, Townsville, Qld, Australia. B.Sc. (Hons). 1984. Microbiology
  • James Cook University, Townsville, Qld, Australia. B.Sc. 1983. Chemistry/Biochemistry

Research

Research Goals

  • Determine what types of microbes are present in Antarctica and how diverse and unique they are.
  • Determine what processes Antarctic microbes perform, and how this affects ecosystem function.
  • Determine what interactions occur within communities, and how this affects ecosystem function.
  • Determine how gene exchange occurs, influences speciation, and enables dominance to arise.
  • Determine what factors control microbial biogeography in Antarctica.
  • Determine how Antarctic nanohaloarchaea interact with haloarchaea using a model system to study symbiosis in DPANN archaea.
  • Assess in what ways human activities (including climate change) impact Antarctic microbes and ecosystem function.

Research in Detail

My group recognizes the global importance of key and yet understudied environmental microbial groups, including cold-adapted Archaea. We choose model organisms to study and forge a new understanding of the molecular basis of adaptation through integrated studies of microbial physiology and ecology, protein biochemistry, genomics, proteomics and transcriptomics. This laboratory experimental approach flows on to environmental studies where we use approaches such as metagenomics and metaproteomics to examine whole Antarctic ecosystems (lake and Southern Ocean communities). The field-based projects have led to unexpected and novel insights about Antarctic microorganisms. The ‘peculiarities’ discovered have raised awareness of just how little is understood and how much remains to be learned about Antarctic biology.

The research has relevance because Antarctica is arguably the world’s most important continent for influencing the Earth’s climate and global ocean ecosystem. The uniqueness and sensitivity of Antarctica particularly demands that we rapidly improve our understanding of its biology. More so, most (~85%) of life on Earth lives at cold temperatures, and yet little is known about how the resident microbial communities drive critical biogeochemical processes (e.g. carbon cycle) that help to maintain the planet in a habitable state. The new insight we and other international groups of scientists are obtaining is timely as it is remedying critical gaps in our knowledge about Antarctic biology and has the potential to influence policy development aimed at mitigating and adapting to environmental change.

Selected articles

Research Grants

Current Student Projects

  • Metagenomics of Antarctic microbial communities – Pratibha Panwar (PhD)
  • Genomic reconstruction of a novel lineage of Antarctic haloarchaea – Josh Hamm (PhD)
  • Taxonomy of microorganisms in uncharacterized Antarctic lakes – Sabrina Haque (MSc)
  • Characterization of the evolution of Antarctic haloarchaea – Evan Landers (PhD)

Supervision Opportunities/Areas

Future students with an interest in undertaking Honours, MPhil, MSc or PhD studies within the stated Research Goals should contact me to discuss. Senior members of the group involved in supervision include Dr Timothy J. Williams, Dr Michelle A. Allen and Dr Liang Shen (Visiting Scholar). Specific projects available include:

  • grow and isolate new strains and previously uncultivated lineages of Antarctic life
  • study how and why microbes interact (e.g. host-virus, host-parasite, host-host)
  • identify microbial taxa present and the functions they perform in Antarctic lakes
  • study temporal changes (e.g. seasonal) and biogeographic distinctions in microbial populations
  • study genomic variation to determine what causes variation, what genes vary and why they vary

Advice for prospective students

Hons/MPhil/MSc/PhD/undergrad-project/volunteer studies provide opportunities for students to gain experience and achieve high level qualifications in research-based science. An inherent part of performing research is to probe the unknown – exploring and discovering to provide clarity to often complex, intricate and certainly novel areas of science. Within the overarching Research Goals, there are a broad range of research topics available for students to pursue their interests, express their individual aptitude, and grow and develop as scientists. Guided by prior achievements and access to novel data and resources, as well as state of the art facilities, students will perform strong hypothesis driven investigations, while keeping a sharp eye open for serendipitous discovery. Projects are tailored to individuals on the basis of being provided ‘sufficient rope to explore but not too much to hang yourself'. New students are typically linked to other established members of the group, providing support spanning from the conceptual framework of their studies through to the lab-bench, computer-console and field-work ‘coal faces’ of the research. Students interested in interacting in a multi-disciplinary environment with a multi-national cohort of students, staff and scientific collaborators, should get in touch with me to discuss a future in environmental microbiology and Antarctic research.

Teaching and Outreach

Courses I teach

  • MICR3621: Microbial Genetics Advanced (Course convenor)
  • BABS3021: Microbial Genetics (Course convenor)

Professional affiliations and service positions

Awards and Acheivements

  • 2005 Frank Fenner Research Award: in recognition of distinguished contributions in any area of Australian research in microbiology by a scientist in a formative stage of their career
  • 2011 Fellow of the Australian Society for Microbiology: recognition as an Australian microbiologist who has shown the highest level of achievement in the discipline
Location
Room: 4105, E26
  • Books | 2007
    2007, Archaea: Molecular and Cellular Biology, Cavicchioli R, (ed.), ASM Press, USA
  • Book Chapters | 2007
    2007, 'The Archaea: an Invitation to Evolution', in Cavicchioli R (ed.), ARCHAEA: MOLECULAR AND CELLULAR BIOLOGY, AMER SOC MICROBIOLOGY, pp. 1 - 13, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000278887900002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Book Chapters | 2006
    2006, '17 Proteins from Psychrophiles', in Methods in Microbiology, Elsevier, pp. 395 - 436, http://dx.doi.org/10.1016/s0580-9517(08)70020-5
    Book Chapters | 2005
    Cavicchioli R; Goodchild A; Raftery M, 2005, 'Proteomics of Archaea', in Microbial Proteomics: Functional Biology of Whole Organisms, pp. 57 - 72, http://dx.doi.org/10.1002/0471973165.ch5
  • Journal articles | 2023
    2023, 'Molecular hydrogen in seawater supports growth of diverse marine bacteria', Nature Microbiology, 8, pp. 581 - 595, http://dx.doi.org/10.1038/s41564-023-01322-0
    Journal articles | 2022
    2022, 'Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake', Environmental Microbiology, 24, pp. 2576 - 2603, http://dx.doi.org/10.1111/1462-2920.16026
    Journal articles | 2022
    2022, 'Population structure of an Antarctic aquatic cyanobacterium', Microbiome, 10, pp. 207, http://dx.doi.org/10.1186/s40168-022-01404-x
    Journal articles | 2022
    2022, 'Thousands of small, novel genes predicted in global phage genomes', Cell Reports, 39, http://dx.doi.org/10.1016/j.celrep.2022.110984
    Journal articles | 2021
    2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, 39, pp. 499 - 509, http://dx.doi.org/10.1038/s41587-020-0718-6
    Journal articles | 2021
    2021, 'Ecology and molecular targets of hypermutation in the global microbiome', Nature Communications, 12, pp. 3076, http://dx.doi.org/10.1038/s41467-021-23402-7
    Journal articles | 2021
    2021, 'Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake', Frontiers in Microbiology, 12, http://dx.doi.org/10.3389/fmicb.2021.674758
    Journal articles | 2021
    2021, 'Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution', Microbiome, 9, pp. 136, http://dx.doi.org/10.1186/s40168-021-01084-z
    Journal articles | 2021
    2021, 'Remarkably coherent population structure for a dominant Antarctic Chlorobium species', Microbiome, 9, http://dx.doi.org/10.1186/s40168-021-01173-z
    Journal articles | 2021
    2021, 'Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake', Frontiers in Microbiology, 12, pp. 741077, http://dx.doi.org/10.3389/fmicb.2021.741077
    Journal articles | 2020
    2020, 'Ecology and molecular targets of hypermutation in the global microbiome', , http://dx.doi.org/10.1101/2020.04.01.020958
    Journal articles | 2020
    2020, 'Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community', Microbiome, 8, pp. 116, http://dx.doi.org/10.1186/s40168-020-00889-8
    Journal articles | 2019
    Cavicchioli R, 2019, 'A vision for a ‘microbcentric’ future', Microbial Biotechnology, 12, pp. 26 - 29, http://dx.doi.org/10.1111/1751-7915.13262
    Journal articles | 2019
    2019, 'Scientists’ warning to humanity: microorganisms and climate change', Nature Reviews Microbiology, 17, pp. 569 - 586, http://dx.doi.org/10.1038/s41579-019-0222-5
    Journal articles | 2019
    2019, 'Sucrose metabolism in haloarchaea: Reassessment using genomics, proteomics, and metagenomics', Applied and Environmental Microbiology, 85, http://dx.doi.org/10.1128/AEM.02935-18
    Journal articles | 2019
    2019, 'The urgent need for microbiology literacy in society', Environmental Microbiology, 21, pp. 1513 - 1528, http://dx.doi.org/10.1111/1462-2920.14611
    Journal articles | 2019
    2019, 'Unexpected host dependency of Antarctic Nanohaloarchaeota', Proceedings of the National Academy of Sciences of the United States of America, 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116
    Journal articles | 2018
    Tschitschko B; Erdmann S; DeMaere MZ; Roux S; Panwar P; Allen MA; Williams TJ; Brazendale S; Hancock AM; Eloe-Fadrosh EA; Cavicchioli R, 2018, 'Genomic variation and biogeography of Antarctic haloarchaea', Microbiome, 6, http://dx.doi.org/10.1186/s40168-018-0495-3
    Journal articles | 2018
    2018, 'Extreme Excitement about Archaea', Cell, 172, pp. 1153 - 1154, http://dx.doi.org/10.1016/j.cell.2018.02.038
    Journal articles | 2017
    Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, 7, http://dx.doi.org/10.1038/srep44480
    Journal articles | 2017
    Erdmann S; Tschitschko B; Zhong L; Raftery MJ; Cavicchioli R, 2017, 'A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells', Nature Microbiology, 2, pp. 1446 - 1455, http://dx.doi.org/10.1038/s41564-017-0009-2
    Journal articles | 2017
    Jayawardena MB; Yee LH; Poljak A; Cavicchioli R; Kjelleberg SJ; Siddiqui KS, 2017, 'Enhancement of lipase stability and productivity through chemical modification and its application to latex-based polymer emulsions', Process Biochemistry, 57, pp. 131 - 140, http://dx.doi.org/10.1016/j.procbio.2017.03.014
    Journal articles | 2017
    Paez-Espino D; Chen IM A; Palaniappan K; Ratner A; Chu K; Szeto E; Pillay M; Huang J; Markowitz VM; Nielsen T; Huntemann M; Reddy TB K; Pavlopoulos GA; Sullivan MB; Campbell BJ; Chen F; McMahon K; Hallam SJ; Denef V; Cavicchioli R; Caffrey SM; Streit WR; Webster J; Handley KM; Salekdeh GH; Tsesmetzis N; Setubal JC; Pope PB; Liu WT; Rivers AR; Ivanova NN; Kyrpides NC, 2017, 'IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses', Nucleic Acids Research, 45, pp. D457 - D465, http://dx.doi.org/10.1093/nar/gkw1030
    Journal articles | 2017
    Williams TJ; Allen M; Tschitschko B; Cavicchioli R, 2017, 'Glycerol metabolism of haloarchaea', Environmental Microbiology, 19, pp. 864 - 877, http://dx.doi.org/10.1111/1462-2920.13580
    Journal articles | 2017
    Williams TJ; Liao Y; Ye J; Kuchel RP; Poljak A; Raftery MJ; Cavicchioli R, 2017, 'Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi', Environmental Microbiology, 19, pp. 2210 - 2227, http://dx.doi.org/10.1111/1462-2920.13705
    Journal articles | 2016
    Anderson IJ; DasSarma P; Lucas S; Copeland A; Lapidus A; Del Rio TG; Tice H; Dalin E; Bruce DC; Goodwin L; Pitluck S; Sims D; Brettin TS; Detter JC; Han CS; Larimer F; Hauser L; Land M; Ivanova N; Richardson P; Cavicchioli R; DasSarma S; Woese CR; Kyrpides NC, 2016, 'Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34', Standards in Genomic Sciences, 11, http://dx.doi.org/10.1186/s40793-016-0194-2
    Journal articles | 2016
    Cavicchioli R, 2016, 'On the concept of a psychrophile', ISME Journal, 10, pp. 793 - 795, http://dx.doi.org/10.1038/ismej.2015.160
    Journal articles | 2016
    Danovaro R; Dell'anno A; Corinaldesi C; Rastelli E; Cavicchioli R; Krupovic M; Noble RT; Nunoura T; Prangishvili D, 2016, 'Virus-mediated archaeal hecatomb in the deep seafloor', Science Advances, 2, http://dx.doi.org/10.1126/sciadv.1600492
    Journal articles | 2016
    Liao Y; Williams TJ; Walsh JC; Ji M; Poljak A; Curmi PM G; Duggin IG; Cavicchioli R, 2016, 'Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Investigating acetamidase gene function', Scientific Reports, 6, http://dx.doi.org/10.1038/srep34639
    Journal articles | 2016
    Liao Y; Williams TJ; Ye J; Charlesworth J; Burns BP; Poljak A; Raftery MJ; Cavicchioli R, 2016, 'Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi', Scientific Reports, 6, http://dx.doi.org/10.1038/srep37454
    Journal articles | 2016
    Richards SL; Cawley AT; Cavicchioli R; Suann CJ; Pickford R; Raftery MJ, 2016, 'Aptamer based peptide enrichment for quantitative analysis of gonadotropin-releasing hormone by LC-MS/MS', Talanta, 150, pp. 671 - 680, http://dx.doi.org/10.1016/j.talanta.2016.01.006
    Journal articles | 2016
    Taha ; Siddiqui KS; Campanaro S; Najnin T; Deshpande N; Williams TJ; Aldrich-Wright J; Wilkins M; Curmi PM G; Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental microbiology, 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229
    Journal articles | 2016
    Tschitschko B; Williams TJ; Allen MA; Zhong L; Raftery MJ; Cavicchioli R, 2016, 'Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics.', Appl Environ Microbiol, 82, pp. 3165 - 3173, http://dx.doi.org/10.1128/AEM.00473-16
    Journal articles | 2016
    2016, 'Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii', Scientific Reports, 6, http://dx.doi.org/10.1038/srep24278
    Journal articles | 2015
    Cavicchioli R; Erdmann S, 2015, 'The discovery of Antarctic RNA viruses: A new game changer', Molecular Ecology, 24, pp. 4809 - 4811, http://dx.doi.org/10.1111/mec.13387
    Journal articles | 2015
    Ertan H; Cassel C; Verma A; Poljak A; Charlton T; Aldrich-Wright J; Omar SM; Siddiqui KS; Cavicchioli R, 2015, 'A new broad specificity alkaline metalloprotease from a Pseudomonas sp. isolated from refrigerated milk: Role of calcium in improving enzyme productivity', Journal of Molecular Catalysis B: Enzymatic, 113, pp. 1 - 8, http://dx.doi.org/10.1016/j.molcatb.2014.12.010
    Journal articles | 2015
    Sun T; Socki RA; Bish DL; Harvey RP; Bao H; Niles PB; Cavicchioli R; Tonui E, 2015, 'Lost cold Antarctic deserts inferred from unusual sulfate formation and isotope signatures', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms8579
    Journal articles | 2015
    2015, 'Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation', The ISME Journal, 9, pp. 2094 - 2107, http://dx.doi.org/10.1038/ismej.2015.110
    Journal articles | 2015
    2015, 'Microbial ecology of Antarctic aquatic systems', Nature Reviews Microbiology, 13, pp. 691 - 706, http://dx.doi.org/10.1038/nrmicro3549
    Journal articles | 2014
    2014, 'Marine metaproteomics: Deciphering the microbial metabolic food web', Trends in Microbiology, 22, pp. 248 - 260, http://dx.doi.org/10.1016/j.tim.2014.03.004
    Journal articles | 2014
    2014, 'Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea', ISME JOURNAL, 8, pp. 1645 - 1658, http://dx.doi.org/10.1038/ismej.2014.65
    Journal articles | 2014
    2014, 'Versatile peroxidase degradation of humic substances: Use of isothermal titration calorimetry to assess kinetics, and applications to industrial wastes', Journal of Biotechnology, 178, pp. 1 - 11, http://dx.doi.org/10.1016/j.jbiotec.2014.03.002
    Journal articles | 2014
    2014, 'Viruses of haloarchaea', Life, 4, pp. 681 - 715, http://dx.doi.org/10.3390/life4040681
    Journal articles | 2013
    Demaere MZ; Williams TJ; Allen MA; Brown MV; Gibson JA E; Rich J; Lauro FM; Dyall-Smith M; Davenport KW; Woyke T; Kyrpides NC; Tringe SG; Cavicchioli R, 2013, 'High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake', Proceedings of the National Academy of Sciences of the United States of America, 110, pp. 16939 - 16944, http://dx.doi.org/10.1073/pnas.1307090110
    Journal articles | 2013
    Lagkouvardos I; Weinmaier T; Lauro FM; Cavicchioli R; Rattei T; Horn M, 2013, 'Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae', ISME Journal, 8, pp. 115 - 125, http://dx.doi.org/10.1038/ismej.2013.142
    Journal articles | 2013
    2013, 'Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects', Nature communications, 4, pp. 2457, http://dx.doi.org/10.1038/ncomms3457
    Journal articles | 2013
    2013, 'Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics', Environmental Microbiology, 15, pp. 1318 - 1333, http://dx.doi.org/10.1111/1462-2920.12035
    Journal articles | 2013
    2013, 'Key microbial drivers in Antarctic aquatic environments', FEMS Microbiology Reviews, 37, pp. 303 - 335, http://dx.doi.org/10.1111/1574-6976.12007
    Journal articles | 2013
    2013, 'Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake', ISME Journal, 7, pp. 1944 - 1961, http://dx.doi.org/10.1038/ismej.2013.69
    Journal articles | 2013
    2013, 'Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean', Proceedings of the National Academy of Sciences of the United States of America, 110, pp. 11463 - 11468, http://dx.doi.org/10.1073/pnas.1304246110
    Journal articles | 2013
    2013, 'Psychrophiles', Annual Review of Earth and Planetary Sciences, 41, pp. 87 - 115, http://dx.doi.org/10.1146/annurev-earth-040610-133514
    Journal articles | 2013
    2013, 'Shotgun redox proteomics: Identification and Quantitation of Carbonylated Proteins in the UVB-Resistant Marine Bacterium, Photobacterium angustum S14', PLoS ONE, 8, pp. 1 - 15, http://dx.doi.org/10.1371/journal.pone.0068112
    Journal articles | 2013
    2013, 'The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics', Environmental Microbiology, 15, pp. 1302 - 1317, http://dx.doi.org/10.1111/1462-2920.12017
    Journal articles | 2012
    2012, 'A metagenomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters', ISME Journal, 6, pp. 1901 - 1915, http://dx.doi.org/10.1038/ismej.2012.31
    Journal articles | 2012
    2012, 'A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters', ISME Journal, 6, pp. 1883 - 1900, http://dx.doi.org/10.1038/ismej.2012.28
    Journal articles | 2012
    2012, 'Global biogeography of SAR11 marine bacteria', Molecular Systems Biology, 8, pp. 595, http://dx.doi.org/10.1038/msb.2012.28
    Journal articles | 2012
    2012, 'Kinetic and thermodynamic characterization of the functional properties of a hybrid versatile peroxidase using isothermal titration calorimetry: insight into manganese peroxidase activation and lignin peroxidase inhibition', Biochimie, 94, pp. 1221 - 1231, http://dx.doi.org/10.1016/j.biochi.2012.02.012
    Journal articles | 2011
    Yau S; Cavicchioli R, 2011, 'Microbial communities in Antarctic lakes: entirely new perspectives from metagenomics and metaproteomics.', Microbiology Australia, 32, pp. 157 - 159, http://dx.doi.org/10.1071/MA11157
    Journal articles | 2011
    2011, 'An integrative study of a meromictic lake ecosystem in Antarctica', ISME Journal, 5, pp. 879 - 895, http://dx.doi.org/10.1038/ismej.2010.185
    Journal articles | 2011
    2011, 'Archaea – timeline of the third domain', Nature Reviews Microbiology, 9, pp. 51 - 61, http://dx.doi.org/10.1038/nrmicro2482
    Journal articles | 2011
    2011, 'Biotechnological uses of enzymes from psychrophiles', Microbial Biotechnology, 4, pp. 449 - 460, http://dx.doi.org/10.1111/j.1751-7915.2011.00258.x
    Journal articles | 2011
    2011, 'Chaperonins from an Antarctic archaeon are predominantly monomeric: open state crystal structure.', Environmental Microbiology, 13, pp. 2232 - 2249, http://dx.doi.org/10.1111/j.1462-2920.2011.02477.x
    Journal articles | 2011
    2011, 'Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics', Environmental Microbiology, 13, pp. 2186 - 2203, http://dx.doi.org/10.1111/j.1462-2920.2011.02467.x
    Journal articles | 2011
    2011, 'Life and applications of extremophiles', Environmental Microbiology, 13, pp. 1903 - 1907, http://dx.doi.org/10.1111/j.1462-2920.2011.02512.x
    Journal articles | 2011
    2011, 'Proteomics of extremophiles', Environmental Microbiology, 13, pp. 1934 - 1955, http://dx.doi.org/10.1111/j.1462-2920.2011.02484.x
    Journal articles | 2011
    2011, 'Simple high-throughput annotation pipeline (SHAP)', Bioinformatics, 27, pp. 2431 - 2432, http://dx.doi.org/10.1093/bioinformatics/btr411
    Journal articles | 2011
    2011, 'Temperature-dependent global gene expression in the Antarctic archaeon, Methanococcoides burtonii.', Environmental Microbiology, 13, pp. 2018 - 2038, http://dx.doi.org/10.1111/j.1462-2920.2010.02367.x
    Journal articles | 2011
    2011, 'The RNA polymerase subunits E/F from the Antarctic archaeon, Methanococcoides burtonii bind to specific classes of mRNA.', Environmental Microbiology, 13, pp. 2039 - 2055, http://dx.doi.org/10.1111/j.1462-2920.2010.02385.x
    Journal articles | 2011
    2011, 'Virophage control of Antarctic algal host–virus dynamics', Proceedings of the National Academy of Sciences of the United States of America, 108, pp. 6163 - 6168, http://dx.doi.org/10.1073/pnas.1018221108
    Journal articles | 2010
    2010, 'A chemically modified alpha-amylase with a moltenglobule state has entropically driven enhanced thermal stability', Protein Engineering Design and Selection, 23, pp. 769 - 780, http://dx.doi.org/10.1093/protein/gzq051
    Journal articles | 2010
    2010, 'Analyzing the hydrophobic proteome of the Antarctic archaeon Methanococcoides burtonii using differential solubility fractionation', Journal of Proteome Research, 9, pp. 664 - 676, http://dx.doi.org/10.1021/pr9007865
    Journal articles | 2010
    2010, 'Cold adaptation in the marine bacterium, Sphingopyxis alaskensis assessed using quantitative proteomics.', Environmental Microbiology, 12, pp. 2658 - 2676, http://dx.doi.org/10.1111/j.1462-2920.2010.02235.x
    Journal articles | 2010
    2010, 'Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part I: The effect of growth temperature', Journal of Proteome Research, 9, pp. 640 - 652, http://dx.doi.org/10.1021/pr900509n
    Journal articles | 2010
    2010, 'Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part II: The effect of different methylated growth substrates', Journal of Proteome Research, 9, pp. 653 - 663, http://dx.doi.org/10.1021/pr9005102
    Journal articles | 2010
    2010, 'Influence of growth temperature and starvation state on survival and DNA damage induction in the marine bacterium Sphingopyxis alaskensis exposed to UV radiation.', Journal of Photochemistry and Photobiology B - Biology, 100, pp. 51 - 56, http://dx.doi.org/10.1016/j.jphotobiol.2010.05.001
    Journal articles | 2010
    2010, 'Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica.', ISME Journal, 4, pp. 1002 - 1019, http://dx.doi.org/10.1038/ismej.2010.28
    Journal articles | 2009
    2009, 'A novel approach for enhancing the catalytic efficiency of a protease at low temperature: Reduction in substrate inhibition by chemical modification', Biotechnology and Bioengineering, 103, pp. 676 - 686, http://dx.doi.org/10.1002/bit.22300
    Journal articles | 2009
    2009, 'Carbon and nitrogen substrate utilization in the marine bacterium Sphingopyxis alaskensis strain RB2256', ISME Journal, 3, pp. 1036 - 1052, http://dx.doi.org/10.1038/ismej.2009.52
    Journal articles | 2009
    2009, 'Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling', Molecular and Cellular Proteomics, 8, pp. 2227 - 2242, http://dx.doi.org/10.1074/mcp.M800462-MCP200
    Journal articles | 2009
    2009, 'Remarkable resistance to UVB of the marine bacterium Photobacterium angustum explained by an unexpected role of photolyase', Photochemical and Photobiological Sciences, 8, pp. 1313 - 1320, http://dx.doi.org/10.1039/b902715g
    Journal articles | 2009
    2009, 'The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: The role of genome evolution in cold adaptation', ISME Journal, 3, pp. 1012 - 1035, http://dx.doi.org/10.1038/ismej.2009.45
    Journal articles | 2009
    2009, 'The genomic basis of trophic strategy in marine bacteria', Proceedings of the National Academy of Sciences of the United States of America, 106, pp. 15527 - 15533, http://dx.doi.org/10.1073/pnas.0903507106
    Journal articles | 2009
    2009, 'The response of the marine bacterium Sphingopyxis alaskensis to solar radiation assessed by quantitative proteomics', Environmental Microbiology, 11, pp. 2660 - 2675, http://dx.doi.org/10.1111/j.1462-2920.2009.01992.x
    Journal articles | 2007
    Cavicchioli R, 2007, 'Antarctic metagenomics', Microbiology Australia, 28, pp. 98 - 103
    Journal articles | 2007
    2007, 'Integration of genomics and proteomics into marine microbial ecology', Marine Ecology Progress Series, 332, pp. 291 - 299, http://dx.doi.org/10.3354/meps332291
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    2007, 'Isolation and characterisation of marine oligotropic bacteria', Journal de la Societe de Biologie, 201, pp. 41 - 50, http://dx.doi.org/10.1051/jbio:2007005
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    2007, 'Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers', BioEssays, 29, pp. 11 - 14, http://dx.doi.org/10.1002/bies.20519
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    2007, 'Structure and function of cold shock proteins in archaea', Journal of Bacteriology, 189, pp. 5738 - 5748, http://dx.doi.org/10.1128/JB.00395-07
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    2006, 'Cold-adapted Archaea', Nature Reviews Microbiology, 4, pp. 331 - 343, http://dx.doi.org/10.1038/nrmicro1390
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    2006, 'Cold-adapted enzymes', Annual Review of Biochemistry, 75, pp. 403 - 433, http://dx.doi.org/10.1146/annurev.biochem.75.103004.142723
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    2006, 'Proteomic and computational analysis of secreted proteins with type 1 signal peptides from the antarctic archaeon Methanococcoides burtonii', Journal of Proteome Research, 5, pp. 2457 - 2464, http://dx.doi.org/10.1021/pr060220x
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    2006, 'Role of lysine versus arginine in enzyme cold-adaptation: Modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis', Proteins - Structure Function and Bioinformatics, 64, pp. 486 - 501, http://dx.doi.org/10.1002/prot.20989
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    2006, 'Terrestrial models for extra terrestrial life: methanogens and halophiles at Martian temperatures', International Journal of Astrobiology, 5, pp. 89 - 97, http://dx.doi.org/10.1017/S1473550406002916
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    2005, 'Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT', Journal of Proteome Research, 4, pp. 473 - 480, http://dx.doi.org/10.1021/pr049760p
    Journal articles | 2005
    2005, 'Improved thermal stability and activity in the cold-adapted lipase B from Candida antarctica following chemical modification with oxidized polysaccharides', Extremophiles, 9, pp. 471 - 476, http://dx.doi.org/10.1007/s00792-005-0464-1
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    2005, 'Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii', Journal of Proteome Research, 4, pp. 464 - 472, http://dx.doi.org/10.1021/pr049797+
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    2005, 'Role of disulfide bridges in the activity and stability of a cold-active alpha-amylase', Journal of Bacteriology, 187, pp. 6206 - 6212, http://dx.doi.org/10.1128/JB.187.17.6206-6212.2005
    Journal articles | 2005
    2005, 'The active site is the least stable structure in the unfolding pathway of a multidomain cold-adapted alpha-amylase', Journal of Bacteriology, 187, pp. 6197 - 6205, http://dx.doi.org/10.1128/JB.187.17.6197-6205.2005
    Journal articles | 2004
    Siddiqui KS; Poljak A; Cavicchioli R, 2004, 'Improved activity and stability of alkaline phosphatases from psychrophilic and mesophilic organisms by chemically modifying aliphatic or amino groups using tetracarboxy-benzophenone derivatives', Cellular and Molecular Biology, 50, pp. 657 - 667
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    2004, 'A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii', Molecular Microbiology, 53, pp. 309 - 321, http://dx.doi.org/10.1111/j.1365-2958.2004.04130.x
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    2004, 'An online database for the detection of novel archaeal sequences inhuman ESTs', Bioinformatics, 20, pp. 2361 - 2362, http://dx.doi.org/10.1093/bioinformatics/bth249
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    2004, 'Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry', Journal of Proteome Research, 3, pp. 1164 - 1176, http://dx.doi.org/10.1021/pr0498988
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    2004, 'Cold adaptation in the Antarctic archaeon Methanococcoides burtonii involves membrane lipid unsaturation', Journal of Bacteriology, 186, pp. 8508 - 8515, http://dx.doi.org/10.1128/JB.186.24.8508-8515.2004
    Journal articles | 2004
    2004, 'Cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis', Proteomics, 4, pp. 1779 - 1788, http://dx.doi.org/10.1002/pmic.200300695
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    2004, 'Response to William Martin`s letter: Pathogenic archaebacteria: do they not exist because archaebacteria usedifferent vitamins? Response to William Martin`s letter', BioEssays, 26, pp. 593 - 593, http://dx.doi.org/10.1002/bies.20044
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    2004, 'Serpins in unicellular Eukarya, Archaea, and Bacteria: Sequence analysis and evolution', Journal of Molecular Evolution, 59, pp. 437 - 447, http://dx.doi.org/10.1007/s00239-004-2635-6
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    2003, 'Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [Topt], 23oC) and Stetteria hydrogenophila (Topt,95oC)', Journal of Bacteriology, 185, pp. 5483 - 5490, http://dx.doi.org/10.1128/JB.185.18.5483-5490.2003
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    2003, 'Life under Nitrient Limitation in Oligotrophic Marine Environments: An Eco/Physiological Perspective of Sphingopyxis alaskensis (Formerly Sphingomonas alaskensis)', Microbial Ecology, 45, pp. 203 - 217, http://dx.doi.org/10.1007/s00248-002-3008-6
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    2003, 'Mechanisms of Thermal Adaptation Revealed from the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii', Genome Research, 13, pp. 1580 - 1588, http://dx.doi.org/10.1101/gr.1180903
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    2003, 'Pathogenic archaea: do they exist?', BioEssays, 25, pp. 1119 - 1128, http://dx.doi.org/10.1002/bies.10354
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    2002, 'Cold adaptation of archaeal Elongation Factor 2 (EF-2) proteins', Current Protein and Peptide Science, 3, pp. 223 - 230, http://dx.doi.org/10.2174/1389203024605359
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    2002, 'Extremophiles and the Search for Extraterrestrial Life', Astrobiology, 2, pp. 281 - 292, http://dx.doi.org/10.1089/153110702762027862
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    2002, 'Low-temperature extremophiles and their applications', Current Opinion in Biotechnology, 13, pp. 253 - 261, http://dx.doi.org/10.1016/S0958-1669(02)00317-8
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    2002, 'Thermodynamic activation properties of elongation factor 2 (EF-2) proteins from psychrotolerant and thermophilic Archaea', Extremophiles, 6, pp. 143 - 150, http://dx.doi.org/10.1007/s007920100237
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    2001, 'Effects of ribosomes and intracellular solutes on activities and stabilities of elongation factor 2 proteins from psychrotolerant and thermophilic methanogens', Journal of Bacteriology, 183, pp. 1974 - 1982, http://dx.doi.org/10.1128/JB.183.6.1974-1982.2001
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    2001, 'Specific growth rate plays a critical role in hydrogen peroxide resistance ofr the marine oligotrophic ultramicrobacterium Sphingomonas alaskensis Strain RB2256', Applied and Environmental Microbiology, 67, pp. 1292 - 1299, http://dx.doi.org/10.1128/AEM.67.3.1292-1299.2001
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    2001, 'Sphingomonas alaskensis Strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific', Applied and Environmental Microbiology, 67, pp. 4945 - 4954
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    2000, 'Cold stress response in Archaea', Extremophiles, 4, pp. 321 - 331, http://dx.doi.org/10.1007/s007920070001
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    2000, 'Effect of temperature on the stability and activity of the elongation factor 2 proteins from low-temperature adapted and thermophilic methanogens', Journal of Bacteriology, 182, pp. 1328 - 1332, http://dx.doi.org/10.1128/JB.182.5.1328-1332.2000
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    2000, 'Low temperature regulated DEAD-box RNA Helicase from the Antarctic Archaeon, Methanococcoides burtonii', Journal of Molecular Biology, 297, pp. 553 - 567, http://dx.doi.org/10.1006/jmbi.2000.3585
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    2000, 'Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. Strain RB2256', Applied and Environmental Microbiology, 66, pp. 2037 - 2044, http://dx.doi.org/10.1128/AEM.66.5.2037-2044.2000
    Journal articles | 2000
    2000, 'Structural analysis of the elongation factor G protein from the low-temperature-adapted bacterium Arthrobacter globiformis S155', Extremophiles, 4, pp. 123 - 130, http://dx.doi.org/10.1007/s007920050146
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    1999, 'An assessment of protein profiles from the marine oligotrophic ultramicrobacterium, Sphingomonas sp. strain RB2256', Electrophoresis, 20, pp. 2094 - 2098, http://dx.doi.org/10.1002/(SICI)1522-2683(19990701)20:10<2094::AID-ELPS2094>3.0.CO;2-E
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    1999, 'Sphingomonads from marine environments', Journal of Industrial Microbiology and Biotechnology, 23, pp. 268 - 272, http://dx.doi.org/10.1038/sj.jim.2900732
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    1998, 'Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, mesophilic and thermophilic proteins', FEBS Letters, 439, pp. 281 - 286, http://dx.doi.org/10.1016/S0014-5793(98)01375-1
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    1998, 'Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp., strain RB2256', Applied and Environmental Microbiology, 64, pp. 4433 - 4438
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    1997, '`Locked-on` and `locked-off` signal transduction mutants of Escherichia coli NarQ and NarX sensors for nitrate and nitrite: role of the P-box element', Molecular Microbiology, 24, pp. 1049 - 1060, http://dx.doi.org/10.1046/j.1365-2958.1997.4131779.x
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    1996, 'Characterization of the aegA locus of Escherichia coli: control of gene expression in response to anaerobiosis and nitrate', Journal of Bacteriology, 178, pp. 6968 - 6974, http://dx.doi.org/10.1128/jb.178.23.6968-6974.1996
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    1996, 'Responses to stress and nutrient availability by the marine ultramicrobacterium Sphingomonas sp strain RB2256', Applied and Environmental Microbiology, 62, pp. 1287 - 1294
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    1996, 'Role of the periplasmic domain of the Escherichia coli NarX sensor-transmitter protein in nitrate-dependent signal transduction and gene regulation', Molecular Microbiology, 21, pp. 901 - 911, http://dx.doi.org/10.1046/j.1365-2958.1996.491422.x
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    1995, 'The NarX and NarQ sensor-transmitter proteins of Escherichia coli each require two conserved histidines for nitrate-dependent signal transduction to NarL', Journal of Bacteriology, 177, pp. 2416 - 2424, http://dx.doi.org/10.1128/jb.177.9.2416-2424.1995
    Journal articles | 1994
    1994, 'Phosphorylation and dephosphorylation of the NarQ, NarX and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli', Journal of Bacteriology, 176, pp. 4985 - 4992, http://dx.doi.org/10.1128/jb.176.16.4985-4992.1994
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    1992, 'Identification and characterisation of narQ, a second nitrate sensor for nitrate-dependent gene regulation in Escherichia coli', Molecular Microbiology, 6, pp. 1913 - 1923, http://dx.doi.org/10.1111/j.1365-2958.1992.tb01364.x
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    1992, 'Physical map location of the narQ gene of Escherichia coli', Journal of Bacteriology, 174, pp. 7882 - 7882, http://dx.doi.org/10.1128/jb.174.23.7882.1992
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    1991, 'FSendA, a novel family E endoglucanase gene from Fibrobacter succinogenes AR1', Journal of Bacteriology, 175, pp. 3265 - 3268, http://dx.doi.org/10.1128/jb.173.10.3265-3268.1991
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    1991, 'Molecular cloning, expression and characterisation of endoglucanase genes from Fibrobacter succinogenes AR1', Applied and Environmental Microbiology, 57, pp. 359 - 365
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    1991, 'The involvement of transcriptional read through from internal promoters in the expression of a novel endoglucanase gene FSendA, from Fibrobacter succinogenes AR1', Nucleic Acids Research, 19, pp. 1661 - 1669, http://dx.doi.org/10.1093/nar/19.7.1661
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    1986, 'Loss of heat shock acquisition of thermotolerance in yeast is not correlated with the loss of heat shock proteins', FEBS Letters, 207, pp. 149 - 152, http://dx.doi.org/10.1016/0014-5793(86)80030-8
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    1984, 'Mitochondrial and cytoplasmic protein syntheses are not required for heat shock acquisition of ethanol and thermotolerance in yeast', FEBS Letters, 172, pp. 299 - 302, http://dx.doi.org/10.1016/0014-5793(84)81145-X
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    1983, 'Acquisition of ethanol tolerance in yeast cells by heat shock', Biotechnology Letters, 5, pp. 683 - 688, http://dx.doi.org/10.1007/BF01386362
  • Preprints | 2023
    2023, The intracellular lifestyle of an archaeal symbiont, , http://dx.doi.org/10.1101/2023.02.24.529834