Select Publications


2007, Archaea: Molecular and Cellular Biology, Cavicchioli R, (ed.), ASM Press, USA

Book Chapters

Woese CR, 2007, 'The Archaea: an Invitation to Evolution', in Cavicchioli R (ed.), ARCHAEA: MOLECULAR AND CELLULAR BIOLOGY, AMER SOC MICROBIOLOGY, pp. 1 - 13,

Cavicchioli R; Curmi PMG; Siddiqui KS; Thomas T, 2006, '17 Proteins from Psychrophiles', in Methods in Microbiology, Elsevier, pp. 395 - 436,

Cavicchioli R; Goodchild A; Raftery M, 2005, 'Proteomics of Archaea', in Microbial Proteomics: Functional Biology of Whole Organisms, pp. 57 - 72,

Journal articles

Roux S; Paul BG; Bagby SC; Nayfach S; Allen MA; Attwood G; Cavicchioli R; Chistoserdova L; Gruninger RJ; Hallam SJ; Hernandez ME; Hess M; Liu WT; McAllister TA; O’Malley MA; Peng X; Rich VI; Saleska SR; Eloe-Fadrosh EA, 2021, 'Ecology and molecular targets of hypermutation in the global microbiome', Nature Communications, vol. 12, pp. 3076,

Shen L; Liu Y; Allen MA; Xu B; Wang N; Williams TJ; Wang F; Zhou Y; Liu Q; Cavicchioli R, 2021, 'Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution', Microbiome, vol. 9, pp. 136,

Williams TJ; Allen MA; Ivanova N; Huntemann M; Haque S; Hancock AM; Brazendale S; Cavicchioli R, 2021, 'Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake', Frontiers in Microbiology, vol. 12,

Nayfach S; Roux S; Seshadri R; Udwary D; Varghese N; Schulz F; Wu D; Paez-Espino D; Chen IM; Huntemann M; Palaniappan K; Ladau J; Mukherjee S; Reddy TBK; Nielsen T; Kirton E; Faria JP; Edirisinghe JN; Henry CS; Jungbluth SP; Chivian D; Dehal P; Wood-Charlson EM; Arkin AP; Tringe SG; Visel A; Abreu H; Acinas SG; Allen E; Allen MA; Alteio LV; Andersen G; Anesio AM; Attwood G; Avila-Magaña V; Badis Y; Bailey J; Baker B; Baldrian P; Barton HA; Beck DAC; Becraft ED; Beller HR; Beman JM; Bernier-Latmani R; Berry TD; Bertagnolli A; Bertilsson S; Bhatnagar JM; Bird JT; Blanchard JL; Blumer-Schuette SE; Bohannan B; Borton MA; Brady A; Brawley SH; Brodie J; Brown S; Brum JR; Brune A; Bryant DA; Buchan A; Buckley DH; Buongiorno J; Cadillo-Quiroz H; Caffrey SM; Campbell AN; Campbell B; Carr S; Carroll JL; Cary SC; Cates AM; Cattolico RA; Cavicchioli R; Chistoserdova L; Coleman ML; Constant P; Conway JM; Mac Cormack WP; Crowe S; Crump B; Currie C; Daly R; DeAngelis KM; Denef V; Denman SE; Desta A; Dionisi H; Dodsworth J; Dombrowski N; Donohue T; Dopson M; Driscoll T; Dunfield P; Dupont CL; Dynarski KA; Edgcomb V; Edwards EA; Elshahed MS; Figueroa I, 2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, vol. 39, pp. 499 - 509,

Panwar P; Allen MA; Williams TJ; Hancock AM; Brazendale S; Bevington J; Roux S; Páez-Espino D; Nayfach S; Berg M; Schulz F; Chen IMA; Huntemann M; Shapiro N; Kyrpides NC; Woyke T; Eloe-Fadrosh EA; Cavicchioli R, 2020, 'Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community', Microbiome, vol. 8, pp. 116,

Cavicchioli R; Ripple WJ; Timmis KN; Azam F; Bakken LR; Baylis M; Behrenfeld MJ; Boetius A; Boyd PW; Classen AT; Crowther TW; Danovaro R; Foreman CM; Huisman J; Hutchins DA; Jansson JK; Karl DM; Koskella B; Mark Welch DB; Martiny JBH; Moran MA; Orphan VJ; Reay DS; Remais JV; Rich VI; Singh BK; Stein LY; Stewart FJ; Sullivan MB; van Oppen MJH; Weaver SC; Webb EA; Webster NS, 2019, 'Scientists’ warning to humanity: microorganisms and climate change', Nature Reviews Microbiology, vol. 17, pp. 569 - 586,

Timmis K; Cavicchioli R; Garcia JL; Nogales B; Chavarría M; Stein L; McGenity TJ; Webster N; Singh BK; Handelsman J; de Lorenzo V; Pruzzo C; Timmis J; Martín JLR; Verstraete W; Jetten M; Danchin A; Huang W; Gilbert J; Lal R; Santos H; Lee SY; Sessitsch A; Bonfante P; Gram L; Lin RTP; Ron E; Karahan ZC; van der Meer JR; Artunkal S; Jahn D; Harper L, 2019, 'The urgent need for microbiology literacy in society', Environmental Microbiology, vol. 21, pp. 1513 - 1528,

Williams TJ; Allen MA; Liao Y; Raftery MJ; Cavicchioli R, 2019, 'Sucrose metabolism in haloarchaea: Reassessment using genomics, proteomics, and metagenomics', Applied and Environmental Microbiology, vol. 85,

Cavicchioli R, 2019, 'A vision for a ‘microbcentric’ future', Microbial Biotechnology, vol. 12, pp. 26 - 29,

Hamm JN; Erdmann S; Eloe-Fadrosh EA; Angeloni A; Zhong L; Brownlee C; Williams TJ; Barton K; Carswell S; Smith MA; Brazendale S; Hancock AM; Allen MA; Raftery MJ; Cavicchioli R, 2019, 'Unexpected host dependency of Antarctic Nanohaloarchaeota', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, pp. 14661 - 14670,

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, vol. 6,

2018, 'Extreme Excitement about Archaea', Cell, vol. 172, pp. 1153 - 1154,

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, vol. 2, pp. 1446 - 1455,

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, vol. 19, pp. 2210 - 2227,

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, vol. 57, pp. 131 - 140,

Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, vol. 7,

Williams TJ; Allen M; Tschitschko B; Cavicchioli R, 2017, 'Glycerol metabolism of haloarchaea', Environmental Microbiology, vol. 19, pp. 864 - 877,

Paez-Espino D; Chen IMA; Palaniappan K; Ratner A; Chu K; Szeto E; Pillay M; Huang J; Markowitz VM; Nielsen T; Huntemann M; Reddy TBK; 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, vol. 45, pp. D457 - D465,

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, vol. 6,

Liao Y; Williams TJ; Walsh JC; Ji M; Poljak A; Curmi PMG; Duggin IG; Cavicchioli R, 2016, 'Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Investigating acetamidase gene function', Scientific Reports, vol. 6,

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, vol. 2,

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, vol. 11,

Taha ; Siddiqui KS; Campanaro S; Najnin T; Deshpande N; Williams TJ; Aldrich-Wright J; Wilkins M; Curmi PMG; Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental microbiology, vol. 18, pp. 2810 - 2824,

Najnin T; Siddiqui KS; Taha ; Elkaid N; Kornfeld G; Curmi PMG; Cavicchioli R, 2016, 'Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii', Scientific Reports, vol. 6,

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, vol. 150, pp. 671 - 680,

Cavicchioli R, 2016, 'On the concept of a psychrophile', ISME Journal, vol. 10, pp. 793 - 795,

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, vol. 82, pp. 3165 - 3173,

Cavicchioli R, 2015, 'Microbial ecology of Antarctic aquatic systems', Nature Reviews Microbiology, vol. 13, pp. 691 - 706,

Tschitschko B; Williams TJ; Allen MA; Páez-Espino D; Kyrpides N; Zhong L; Raftery MJ; Cavicchioli R, 2015, 'Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation', The ISME Journal, vol. 9, pp. 2094 - 2107,

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, vol. 6,

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, vol. 113, pp. 1 - 8,

Cavicchioli R; Erdmann S, 2015, 'The discovery of Antarctic RNA viruses: A new game changer', Molecular Ecology, vol. 24, pp. 4809 - 4811,

Luk AWS; Williams TJ; Erdmann S; Thane Papke R; Cavicchioli R, 2014, 'Viruses of haloarchaea', Life, vol. 4, pp. 681 - 715,

Williams TJ; Allen MA; DeMaere MZ; Kyrpides NC; Tringe SG; Woyke T; Cavicchioli R, 2014, 'Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea', ISME JOURNAL, vol. 8, pp. 1645 - 1658,

Williams TJ; Cavicchioli R, 2014, 'Marine metaproteomics: Deciphering the microbial metabolic food web', Trends in Microbiology, vol. 22, pp. 248 - 260,

Siddiqui KS; Ertan H; Charlton T; Poljakc A; Khaled AK; Yang X; Marshall G; Cavicchioli R, 2014, 'Versatile peroxidase degradation of humic substances: Use of isothermal titration calorimetry to assess kinetics, and applications to industrial wastes', Journal of Biotechnology, vol. 178, pp. 1 - 11,

Demaere MZ; Williams TJ; Allen MA; Brown MV; Gibson JAE; 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, vol. 110, pp. 16939 - 16944,

Wilkins D; Van sebille E; Rintoul S; Lauro FM; Cavicchioli R, 2013, 'Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects', Nature communications, vol. 4, pp. 2457,

Wilkins D; Lauro FM; Williams TJ; De Maere M; Brown MV; Hoffman JM; Andrews-Pfannkoch C; McQuaid J; Riddle M; Rintoul S; Cavicchioli R, 2013, 'Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics', Environmental Microbiology, vol. 15, pp. 1318 - 1333,

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, vol. 8, pp. 115 - 125,

Wilkins D; Yau S; Williams TJ; Allen MA; Brown MV; Demaere MZ; Lauro FM; Cavicchioli R, 2013, 'Key microbial drivers in Antarctic aquatic environments', FEMS Microbiology Reviews, vol. 37, pp. 303 - 335,

Yau S; Lauro FM; Williams TJ; Brown MV; Demaere MZ; Rich J; Gibson J; Cavicchioli R, 2013, 'Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake', ISME Journal, vol. 7, pp. 1944 - 1961,

Swan B; Tupper B; Sczyrba A; Lauro FM; Martinez-Garcia M; González J; Luo H; Wright J; Landry Z; Hanson N; Thompson B; Poulton N; Schwientek P; Acinas S; Giovannoni S; Moran MA; Hallam S; Cavicchioli R; Woyke T; Stepanauskas R, 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, vol. 110, pp. 11463 - 11468,

Siddiqui KS; Williams TJ; Wilkins D; Yau S; Allen MA; Brown MV; Lauro FM; Cavicchioli R, 2013, 'Psychrophiles', Annual Review of Earth and Planetary Sciences, vol. 41, pp. 87 - 115,

Matallana Surget S; Cavicchioli R; Fauconnier C; Wattiez R; Joux F; Leroy B; Raftery MJ; Lebaron P, 2013, 'Shotgun redox proteomics: Identification and Quantitation of Carbonylated Proteins in the UVB-Resistant Marine Bacterium, Photobacterium angustum S14', PLoS ONE, vol. 8, pp. 1 - 15,

Williams TJ; Wilkins D; Long E; Evans FF; De Maere MZ; Raftery MJ; Cavicchioli R, 2013, 'The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics', Environmental Microbiology, vol. 15, pp. 1302 - 1317,

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