Publications


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2015. 

Spain AM, MS Elshahed, FZ Najar, and LR Krumholz 2015. Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism. PeerJ 3:e1259.
http://www.ncbi.nlm.nih.gov/pubmed/26417542

Couger MB, A Hurlbut, CL Murphy, C Budd, DP French, WD Hoff, MS Elshahed, and NH Youssef. Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01. Genome Announc. 3:e01071-15.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574379     

Coveley S, MS Elshahed, and NH Youssef 2015. Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA). PeerJ 3:e1182. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548494

Youssef NH, IF Farag, C Rinke, SJ Hallam, T Woyke, and MS Elshahed. Exploring the metabolic potential and niche specialization of candidate phylum “Latescibacteria” (WS3) using single-cell genomics. PLoS ONE. 10:e0127499.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127499

Najjari, A, MS Elshahed, A. Cherif, and NH Youssef. Patterns and determinants of diversity and community structure of Halophilic Archaea (Class Halobacteria) in Tunisian endorheic salt lakes and sebkhet systems. Appl. Environ. Microbiol. 81: 4432-4441.
http://aem.asm.org/content/81/13/4432.abstract

Youssef NH, MB Couger, AL McCully, AE Guerrero Criado, and MS Elshahed. Assessing the global phylum level diversity within the bacterial domain: A review. J. Adv. Res. 3:269-282.
http://www.sciencedirect.com/science/article/pii/S2090123214001283

Youssef NH, C Rinke, R Stepanauskas, I Farag, T Woyke, and MS Elshahed 2015. Insights into the metabolism, lifestyle, and putative evolutionary history of the novel archaeal phylum Diapherotrites. The ISME J 9:447-460.
http://www.nature.com/ismej/journal/v9/n2/abs/ismej2014141a.html

2014.
Struchtemeyer CG, MB Couger, A. Ranganathan, AS Liggenstoffer, NH Youssef, and MS Elshahed. Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure. Scientific Rep. 4:6892.

http://www.nature.com/srep/2014/141104/srep06892/full/srep06892.html

Gruninger RJ, AK Puniya, TM Callaghan, JE. Edwards, NH Youssef, SS Dagar, K Fliegerova, GW Griffith, R Forster, A Tsang, T McAllister, and MS. Elshahed. Anaerobic Fungi (Phylum Neocallimastigomycota): Advances in understanding of their taxonomy, life cycle, ecology, role, and biotechnological potential. FEMS Microbiol. Ecol. 90:1-17.
http://femsec.oxfordjournals.org/content/90/1/1.long

Liggenstoffer AS, NH Youssef, MR Wilkins, and MS Elshahed. Evaluating the utility of hydrothermolysis pretreatment approaches in enhancing lignocellulosic biomass degradation by the anaerobic fungus Orpinomyces sp. strain C1A. J. Microbiol. Meth. 104:43-48.
http://www.sciencedirect.com/science/article/pii/S0167701214001651

Farag IF, JP Davis, NH Youssef, and MS Elshahed. Global patterns of abundance, diversity and community structure of the Aminicenantes (Candidate phylum OP8). PLoS ONE 9: e92139.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092139

Youssef NH, KN Savage-Ashlock, AL McCully, B Luedtke, EI Shaw, WD Hoff, and M. S. Elshahed. 2014. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. The ISME. J. 8:636-649.
http://www.nature.com/ismej/journal/v8/n3/abs/ismej2013165a.html

CG Struchtemeyer, NH Youssef, and MS Elshahed. Protocols for investigating the microbiology of drilling fluids, hydraulic fracturing fluids, and formations in unconventional natural gas reservoirs. In “Hydrocarbon and Lipid Microbiology Protocols”. Springer Protocols Series. Springer-Verlag Berlin Heidelburg.

NH Youssef and MS. Elshahed. The phylum Planctomycetes in E. Roesenberg, E. Stackebrant, F. Thompson, E. F. DeLong, and S. Lory. The Prokaryotes 4th edition. Springer, New York: New York.

2013
Youssef NH, MB Couger, CG Struchtemeyer, AS Liggenstoffer, RA Prade, FZ Najar, HK Atiyeh, MR Wilkins, and MS. Elshahed. Genome of the anaerobic fungus Orpinomyces sp. C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl. Environ. Microbiol. 79:4620-4634.

http://aem.asm.org/content/79/15/4620.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

2012
Davis JP, Struchtemeyer CG, and MS Elshahed. Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett shale (Texas, USA). Micr. Ecol. 64:942-954.

http://link.springer.com/article/10.1007%2Fs00248-012-0073-3

Struchtemeyer CG, and MS Elshahed. Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA. FEMS Microbiol Ecol. 81:13-25.
http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2011.01196.x/abstract

Struchtemeyer CG, M Morrison, and MS Elshahed. A critical assessment of the efficacy of biocides used during the hydraulic fracturing process in shale natural gas wells. Int. J. Biodeg. Bioremed. 71:15-21.
http://www.sciencedirect.com/science/article/pii/S096483051200073X

Schoch CL, KA Seifert, S Huhndorf, V Robert, JL Spouge, CA Levesque, W Chen; et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA 109:6241-6246.
http://www.pnas.org/content/109/16/6241

Youssef NH, B Steidley, and MS Elshahed. Novel high-rank phylogenetic diversities within a sulfur spring (Zodletone spring, Oklahoma, USA) revealed using a combined pyrosequencing/Sanger approach. Appl. Environ. Microbiol. 78: 2677-2688.
http://aem.asm.org/content/78/8/2677.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Youssef NH, KN Savage-Ashlock, and MS Elshahed. Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats. Applied Environmental Microbiology. Appl. Environ. Microbiol. 78: 1332-1344.
http://aem.asm.org/content/78/5/1332.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

2011
Youssef NH, PC Blainey, SR Quake, and MS Elshahed. A partial genome assembly from a candidate division OP11 single cell from an anoxic spring (Zodletone spring, OK, USA). Appl. Environ. Microbiol. 77: 7804-7814.

http://aem.asm.org/content/77/21/7804.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Sheik CS, WH Beasley, MS Elshahed, X Zhou, Y Luo, and LR Krumholz. Effect of warming and drought on grassland microbial communities. The ISME Journal 5:1692-1700.
http://www.nature.com/ismej/journal/v5/n10/abs/ismej201132a.html

Struchtemeyer CG, JP Davis, MS Elshahed. Influence of the Drilling Mud Formulation Process on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale Appl. Environ. Microbiol. 77: 4744-4753.
http://aem.asm.org/content/77/14/4744.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Bühring SI, SM Sievert, HM Jonkers, T Ertefai, MS Elshahed, LR Krumholz, and K-U Hinrichs. Insights into the chemotaxonomic composition and carbon cycling in phototrophic microbial mats in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analogue for ancient microbial mat systems. Geobiology 9:166-179.
http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4669.2010.00268.x/abstract

MS Elshahed and NH Youssef. Novelty and uniqueness patterns of rare members of the soil biosphere In F. de Bruijn (editor) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Wiley/Blackwell Publishing CO.

2010
Liggenstoffer AS, NH Youssef, MB Couger, and MS Elshahed. Phylogenetic diversity and community structure of anaerobic fungi (Phylum Neacallymastigales) in ruminant and non-ruminant herbivores. The ISME J. 4:1225–1235.
http://www.nature.com/ismej/journal/v4/n10/abs/ismej201049a.html

Youssef NH, MB Couger, and MS Elshahed. Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone spring, OK, USA): the role of the rare biosphere PLoS ONE 5:e12414. 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012414

Savage KN, LR Krumholz, LM Gieg, VA Parisi, JM Suflita, J Allen, RP Philp, and MS Elshahed. Biodegradation of low molecular weight alkanes under mesophilic, sulfate-reducing conditions: evidence, metabolic intermediates, and community patterns. FEMS Microbiol. Ecol. 72:485-495.
http://femsec.oxfordjournals.org/content/72/3/485.long

MS Elshahed* 2010 Microbiological aspects of biofuel production: current status and future directions. J. Adv. Res. 1:103-111.
http://www.sciencedirect.com/science/article/pii/S2090123210000329

SR Heise, MS Elshahed, and SE Little. Bacterial diversity in Amblyomma americanum with a focus on members of the genus Rickettsia. J. Med. Entymol. 47: 258-268.
http://jme.oxfordjournals.org/content/47/2/258.abstract

2009
Youssef NH, C Sheik, LR Krumholz, FZ Najar, BA Roe, and MS Elshahed. A Comparative study of species richness estimates obtained using near complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl. Environ. Microbiol. 75: 5227-5236.

http://aem.asm.org/content/75/16/5227.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Davis JP, NH Youssef, and MS Elshahed. Assessment of the diversity, abundance, and ecological distribution of candidate division SR1 reveals a high phylogenetic, but a limited morphotypic diversity. Appl. Environ. Microbiol. 75: 4139-4148.
http://aem.asm.org/content/75/12/4139.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Spain, AM, LR Krumholz, and MS Elshahed. Abundance, composition, diversity, and novelty of soil Proteobacteria. The ISME J. 3: 992-1000.
http://www.nature.com/ismej/journal/v3/n8/abs/ismej200943a.html

Youssef NH, MS Elshahed, and MJ McInerney. Microbially-mediated processes in oil fields: culprits, problems, and opportunities. Adv. Appl. Microbiol. 66:141-251.
http://www.sciencedirect.com/science/article/pii/S006521640800806X

Youssef NH, and MS Elshahed. Diversity rankings among bacterial lineages in soil. The ISME J. 3: 305-313.
http://www.nature.com/ismej/journal/v3/n3/abs/ismej2008106a.html

2008
Elshahed MS, NH Youssef, AM Spain, C. Sheik, FZ Najar, LO Sukharnikov, BA Roe, JP Davis, PD Schloss, VL Bailey, and LR Krumholz. Novelty and uniqueness patterns within rare members of the soil biosphere. Appl. Environ. Microbiol. 74: 5422-5428.

http://aem.asm.org/content/74/17/5422.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Youssef NH, and MS Elshahed. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias. J. Microbiol. Meth. 75:86-91.
http://www.sciencedirect.com/science/article/pii/S0167701208001772

Savage KN, LR Krumholz, A Oren, and MS Elshahed. Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon isolated from Zodletone spring in southwestern Oklahoma. Int. J. Syst. Evol. Microbiol. 58: 856-860.
http://ijs.sgmjournals.org/content/58/4/856.abstract

2007
Elshahed MS, NH Youssef, Q Luo, FZ Najar, BA Roe, TM Sisk, SI Buhring, K-U Hinrichs, and LR Krumholz. Phylogenetic and metabolic diversity of Planctomycetes from anaerobic sulfide- and sulfur-rich Zodletone spring, OK. Appl. Environ. Microbiol. 73:4707-4716.

http://aem.asm.org/content/73/15/4707.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Spain AM, AD Peacock, J Istook, MS Elshahed, FZ Najar, BA Roe, DC White, and LR Krumholz. Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer. Appl. Environ. Microbiol. 73:4892-4904.
http://aem.asm.org/content/73/15/4892.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Savage KN, LR Krumholz, A Oren and MS Elshahed. Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, high-sulfide spring. Int. J. Syst. Evol. Microbiol. 57:19-24.
http://ijs.sgmjournals.org/content/57/1/19.full

2006-2001
Elshahed MS
, FZ Najar, M Aycock, C Qu, BA Roe, and LR Krumholz 2005. Metagenomic analysis of the microbial community at Zodletone spring: Insights into the genome of novel Candidate division OD1. Appl. Environ. Microbiol. 71: 7958-7962.
http://aem.asm.org/content/71/11/7598.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Luo Q, LR Krumholz, FZ Najar, BA Roe, AD Peacock, DC White, and MS Elshahed. Diversity of the microeukaryotic community in sulfide-rich Zodletone spring. 71:6175-6184.
http://aem.asm.org/content/71/10/6175.abstract?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Struchtemeyer CG, MS Elshahed, KE Duncan, and MJ McInerney. Evidence for Acetoclastic Methanogenesis in the Presence of Sulfate in a Gas Condensate-Contaminated Aquifer. Appl. Environ. Microbiol. 71:5348-5355.
http://aem.asm.org/content/71/9/5348.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Elshahed MS, KN Savage, A Ventosa, M Carmen-Gutierrez, A Oren, and LR Krumholz. Haloferax sulfurifontissp. nov., a halophilic archaeon isolated from a sulfide and sulfur-rich spring. Int. J. Syst. Evol. Microbiol. 54:2275-2279.
http://ijs.sgmjournals.org/content/54/6/2275.full?sid=d89ddd2b-afc6-490e-832d-69d234feb67e

Senko JM, BS Campbell, JR Henricksen, MS Elshahed, TA Dewers, and LR Krumholz. Barite deposition mediated by phototrophic sulfide oxidizing bacteria. Geochem. Cosmochem. Acta. 68:773-780.
http://www.sciencedirect.com/science/article/pii/S0016703703005556

Elshahed MS, FZ Najar, BA Roe, A Oren, TA Dewers, and LR Krumholz. Survey of archaeal diversity reveals abundance of halophilic Archaea in a low-salt, anaerobic sulfur spring. Appl. Environ. Microbiol. 70:2230-2239.
http://aem.asm.org/content/70/4/2230.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Elshahed MS, JM Senko, FZ Najar, SM Kenton, BA Roe, TA Dewers, JR Spear, and LR Krumholz.Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl. Environ. Microbiol. 69:5609-5621.
http://aem.asm.org/content/69/9/5609.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Elshahed MS, and MJ McInerney 2001.Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in absence of hydrogen-utilizing microorganisms. Appl. Environ. Microbiol. 67:5520-5525.
http://aem.asm.org/content/67/12/5520.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Elshahed MS, VK Bhupathiraju, NQ Wofford, MA Nanny, and MJ McInerney 2001. Metabolism of benzoate, cyclohex-1-ene carboxylate and cyclohexane carboxylate by Syntrophus aciditrophicus strain SB in syntrophic association with H2-using microorganisms. Appl. Environ. Microbiol. 67:1728-1738. 
http://aem.asm.org/content/67/4/1728.full?sid=e0672c6b-d6d7-463f-91d1-ba0aea38a70e

Elshahed MS, and MJ McInerney 2001. Is interspecies hydrogen transfer needed for toluene degradation under sulfate-reducing conditions? FEMS Microbiol. Ecol. 35:163-169.
http://femsec.oxfordjournals.org/content/35/2/163.long

Elshahed MS, LM Gieg, MJ McInerney, and JM Suflita 2001. Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments. Environ. Sci. and Technol. 35:682-689.
http://pubs.acs.org/doi/full/10.1021/es001571u