By Professor Rick Cavicchioli

Books

, 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, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000278887900002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Cavicchioli R; Curmi PMG; Siddiqui KS; Thomas T, 2006, '17 Proteins from Psychrophiles', in Methods in Microbiology, Elsevier, pp. 395 - 436, http://dx.doi.org/10.1016/s0580-9517(08)70020-5

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

Williams TJ; Cavicchioli R, 2024, 'Extraction of Proteins from Marine Microbial Communities Sampled by Lab Filters', Methods in molecular biology (Clifton, N.J.), 2820, pp. 1 - 6, http://dx.doi.org/10.1007/978-1-0716-3910-8_1

Pavlopoulos GA; Baltoumas FA; Liu S; Selvitopi O; Camargo AP; Nayfach S; Azad A; Roux S; Call L; Ivanova NN; Chen IM; Paez-Espino D; Karatzas E; Acinas SG; Ahlgren N; Attwood G; Baldrian P; Berry T; Bhatnagar JM; Bhaya D; Bidle KD; Blanchard JL; Boyd ES; Bowen JL; Bowman J; Brawley SH; Brodie EL; Brune A; Bryant DA; Buchan A; Cadillo-Quiroz H; Campbell BJ; Cavicchioli R; Chuckran PF; Coleman M; Crowe S; Colman DR; Currie CR; Dangl J; Delherbe N; Denef VJ; Dijkstra P; Distel DD; Eloe-Fadrosh E; Fisher K; Francis C; Garoutte A; Gaudin A; Gerwick L; Godoy-Vitorino F; Guerra P; Guo J; Habteselassie MY; Hallam SJ; Hatzenpichler R; Hentschel U; Hess M; Hirsch AM; Hug LA; Hultman J; Hunt DE; Huntemann M; Inskeep WP; James TY; Jansson J; Johnston ER; Kalyuzhnaya M; Kelly CN; Kelly RM; Klassen JL; Nüsslein K; Kostka JE; Lindow S; Lilleskov E; Lynes M; Mackelprang R; Martin FM; Mason OU; McKay RM; McMahon K; Mead DA; Medina M; Meredith LK; Mock T; Mohn WW; Moran MA; Murray A; Neufeld JD; Neumann R; Norton JM; Partida-Martinez LP; Pietrasiak N; Pelletier D; Reddy TBK; Reese BK; Reichart NJ; Reiss R; Saito MA; Schachtman DP; Seshadri R, 2023, 'Unraveling the functional dark matter through global metagenomics', Nature, 622, pp. 594 - 602, http://dx.doi.org/10.1038/s41586-023-06583-7

Lappan R; Shelley G; Islam ZF; Leung PM; Lockwood S; Nauer PA; Jirapanjawat T; Ni G; Chen YJ; Kessler AJ; Williams TJ; Cavicchioli R; Baltar F; Cook PLM; Morales SE; Greening C, 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

Le Lay C; Hamm JN; Williams TJ; Shi M; Cavicchioli R; Holmes EC, 2023, 'Viral community composition of hypersaline lakes', Virus Evolution, 9, http://dx.doi.org/10.1093/ve/vead057

Panwar P; Williams TJ; Allen MA; Cavicchioli R, 2022, 'Population structure of an Antarctic aquatic cyanobacterium', Microbiome, 10, http://dx.doi.org/10.1186/s40168-022-01404-x

Fremin BJ; Bhatt AS; Kyrpides NC; Sengupta A; Sczyrba A; Maria da Silva A; Buchan A; Gaudin A; Brune A; Hirsch AM; Neumann A; Shade A; Visel A; Campbell B; Baker B; Hedlund BP; Crump BC; Currie C; Kelly C; Craft C; Hazard C; Francis C; Schadt CW; Averill C; Mobilian C; Buckley D; Hunt D; Noguera D; Beck D; Valentine DL; Walsh D; Sumner D; Lymperopoulou D; Bhaya D; Bryant DA; Morrison E; Brodie E; Young E; Lilleskov E; Högfors-Rönnholm E; Chen F; Stewart F; Nicol GW; Teeling H; Beller HR; Dionisi H; Liao HL; Beman JM; Stegen J; Tiedje J; Jansson J; VanderGheynst J; Norton J; Dangl J; Blanchard J; Bowen J; Macalady J; Pett-Ridge J; Rich J; Payet JP; Gladden JD; Raff JD; Klassen JL; Tarn J; Neufeld J; Gravuer K; Hofmockel K; Chen KH; Konstantinidis K; DeAngelis KM; Partida-Martinez LP; Meredith L; Chistoserdova L; Moran MA; Scarborough M; Schrenk M; Sullivan M; David M; O'Malley MA; Medina M; Habteselassie M; Ward ND; Pietrasiak N; Mason OU; Sorensen PO; Estrada de los Santos P; Baldrian P; McKay RM; Simister R; Stepanauskas R; Neumann R; Malmstrom R; Cavicchioli R; Kelly R; Hatzenpichler R; Stocker R; Cattolico RA; Ziels R; Vilgalys R; Blumer-Schuette S, 2022, 'Thousands of small, novel genes predicted in global phage genomes', Cell Reports, 39, http://dx.doi.org/10.1016/j.celrep.2022.110984

Williams TJ; Allen MA; Panwar P; Cavicchioli R, 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

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, 12, pp. 3076, http://dx.doi.org/10.1038/s41467-021-23402-7

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, 9, pp. 136, http://dx.doi.org/10.1186/s40168-021-01084-z

Panwar P; Allen MA; Williams TJ; Haque S; Brazendale S; Hancock AM; Paez-Espino D; Cavicchioli R, 2021, 'Remarkably coherent population structure for a dominant Antarctic Chlorobium species', Microbiome, 9, http://dx.doi.org/10.1186/s40168-021-01173-z

Williams TJ; Allen MA; Berengut JF; Cavicchioli R, 2021, 'Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake', Frontiers in Microbiology, 12, http://dx.doi.org/10.3389/fmicb.2021.741077

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, 12, pp. 674758, http://dx.doi.org/10.3389/fmicb.2021.674758

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; Williams T; Thomas T, 2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, 39, pp. 499 - 509, http://dx.doi.org/10.1038/s41587-020-0718-6

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, 8, pp. 116, http://dx.doi.org/10.1186/s40168-020-00889-8

Roux S; Paul BG; Bagby SC; Allen MA; Attwood G; Cavicchioli R; Chistoserdova L; Hallam SJ; Hernandez ME; Hess M; Liu W-T; O’Malley MA; Peng X; Rich VI; Saleska S; Eloe-Fadrosh EA, 2020, 'Ecology and molecular targets of hypermutation in the global microbiome', , pp. 2020.04.01.020958, http://dx.doi.org/10.1101/2020.04.01.020958

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, 17, pp. 569 - 586, http://dx.doi.org/10.1038/s41579-019-0222-5

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, 21, pp. 1513 - 1528, http://dx.doi.org/10.1111/1462-2920.14611

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, 85, http://dx.doi.org/10.1128/AEM.02935-18

Cavicchioli R, 2019, 'A vision for a ‘microbcentric’ future', Microbial Biotechnology, 12, pp. 26 - 29, http://dx.doi.org/10.1111/1751-7915.13262

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, 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116

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, pp. 113, http://dx.doi.org/10.1186/s40168-018-0495-3

Cavicchioli R, 2018, 'Extreme Excitement about Archaea', Cell, 172, pp. 1153 - 1154, http://dx.doi.org/10.1016/j.cell.2018.02.038

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

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

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

Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, 7, pp. 44480, http://dx.doi.org/10.1038/srep44480

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

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, 45, pp. D457 - D465, http://dx.doi.org/10.1093/nar/gkw1030

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, pp. 37454, http://dx.doi.org/10.1038/srep37454

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, 6, pp. 34639, http://dx.doi.org/10.1038/srep34639

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, pp. e1600492, http://dx.doi.org/10.1126/sciadv.1600492

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, pp. 70, http://dx.doi.org/10.1186/s40793-016-0194-2

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, 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229

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, 6, pp. 24278, http://dx.doi.org/10.1038/srep24278

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

Cavicchioli R, 2016, 'On the concept of a psychrophile', ISME Journal, 10, pp. 793 - 795, http://dx.doi.org/10.1038/ismej.2015.160

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

Cavicchioli R, 2015, 'Microbial ecology of Antarctic aquatic systems', Nature Reviews Microbiology, 13, pp. 691 - 706, http://dx.doi.org/10.1038/nrmicro3549

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

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, 9, pp. 2094 - 2107, http://dx.doi.org/10.1038/ismej.2015.110

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, pp. 7579, http://dx.doi.org/10.1038/ncomms8579

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

Luk AWS; Williams TJ; Erdmann S; Thane Papke R; Cavicchioli R, 2014, 'Viruses of haloarchaea', Life, 4, pp. 681 - 715, http://dx.doi.org/10.3390/life4040681

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, 8, pp. 1645 - 1658, http://dx.doi.org/10.1038/ismej.2014.65

Williams TJ; Cavicchioli R, 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

Siddiqui KS; Ertan H; Charlton T; Poljakc A; Khaled AK; Yang X; Marshall G; Cavicchioli R; Poljak A, 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

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