Publications
RECENT HIGHLIGHTS
Diversity 13(11): 525 (2021)
The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species
The complete genome of Clostridium clariflavum DSM 19732
Standards in Genomic Sciences 6(1):104-115
Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated from thermophilic anaerobic sludge (Shiratori et al, 2009). This species is of interest because of its similarity to the model cellulolytic organism Clostridium thermocellum and for the ability of environmental isolates to break down cellulose and hemicellulose. Here we describe features of the 4,897,678 bp long genome and its annotation, consisting of 4,131 protein-coding and 98 RNA genes, for the type strain DSM 19732.
COMPLETE LIST OF PUBLICATIONS
Boss, B.L., A.E.Wanees, A.E., S.J. Zaslow, T.G. Normile, J.A. Izquierdo (2022). Comparative Genomics of the Plant Growth-Promoting Bacterium Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata. BMC Genomics 23:508
Boss, B.L., B.R. Charbonneau, J.A. Izquierdo (2021). Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats. Diversity 13(11), 525.
Wanees, A.E., S.J. Zaslow, S.J. Potter, B.P. Hsieh, B.L. Boss, J.A. Izquierdo (2018). Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata. Genome Announcements 6 (21), e00410-18
Lee, L.L., S.E Blumer-Schuette, J.A Izquierdo, J.V Zurawski, A.J. Loder, J.M. Conway, J.G. Elkins, M. Podar, A. Clum, P.C. Jones, M.J. Piatek, D.A. Weighill, D.A. Jacobson, M.W.W. Adams, R.M. Kelly (2018). Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis. Appl Environ Microbiol 84:e02694-17.
Zurawski, J.V., J.M. Conway, L.L. Lee, H.J. Simpson, J.A. Izquierdo, S. Blumer-Schuette, I. Nookaew, M.W.W. Adams and R.M. Kelly (2015). Comparative analysis of extremely thermophilic Caldicellulosiruptor species reveals common and unique cellular strategies for plant biomass utilization. Appl Environ Microbiol 81(20): 7159-7170
Rooney, E.A., K.T. Rowe, A. Guseva, M. Huntemann, J.K. Han, A. Chen, N.C. Kyrpides, K. Mavromatis, V.M. Markowitz, K. Palaniappan, N. Ivanova, A. Pati, K. Liolios, H.P. Nordberg, M.N. Cantor, S.X. Hua, N. Shapiro, T. Woyke, L.R. Lynd, J.A. Izquierdo (2015). Draft genome sequence of the cellulolytic and xylanolytic thermophile Clostridium clariflavum Strain 4-2a. Genome Announc 3(4): e00797-15
Lee, L.L., J.A. Izquierdo, S.E. Blumer-Schuette, J.V. Zurawski, J.M. Conway, R. W. Cottingham, M. Huntemann, A. Copeland,I-Min A. Chen, N. Kyrpides, V. Markowitz, K. Palaniappan, N. Ivanova, N. Mikhailova, G. Ovchinnikova, E. Andersen, A. Pati, D. Stamatis, T.B.K. Reddy, N. Shapiro, H.P. Nordberg, M.N. Cantor, S. X. Hua, T. Woyke, and R. M. Kelly (2015). Complete genome sequences of Caldicellulosiruptor sp. strain Rt8.B8, Caldicellulosiruptor sp. strain Wai35.B1, and "Thermoanaerobacter cellulolyticus". Genome Announc. 3(3):e00440-15
Izquierdo, J.A. and K. Nüsslein (2015). Variation in diazotrophic community structure in forest soils reflects land use history. Soil Biol Biochem 80:1-8
Keller, M., A. Loder, M. Basen, J.A. Izquierdo, R.M. Kelly and M.W.W. Adams (2014). Production of lignofuels and electrofuels by extremely thermophilic microbes. Biofuels 5(5): 499-515
Izquierdo, J.A., S. Pattathil, A. Guseva, M.G. Hahn, L.R. Lynd (2014). Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material. Biotechnology for Biofuels 7:136
Van Houdt, R., D. Van der Lelie, J.A. Izquierdo, A. Aertse, J. Masschelein, R. Lavigne, C.W. Michiels, S. Taghavi (2014). Genome sequence of Serratia plymuthica RVH1, isolate from a raw vegetable-processing line. Genome Announc. 2(1):e00021-14
Reed, PT., J.A. Izquierdo, L.R. Lynd (2014). Growth of Clostridium thermocellum and an environmental consortium in automated repetitive batch fermentation. Biores Biotechnol 155:50-56
Dykstra, A.B., L. St. Brice, M. Rodriguez, B. Raman, J.A. Izquierdo, K.D. Cook, L.R. Lynd, R.L. Hettich (2014). Development of a multi-point quantitation method to simultaneously measure enzymatic and structural components of the Clostridium thermocellum cellulosome protein complex. J Proteome Res 13(2):692-701
StBrice, L., X. Shao, J.A. Izquierdo, L.R. Lynd (2014). Optimization of affinity digestion for isolating cellulase from Clostridium thermocellum. Prep Biochem Biotechnol 44(2):206-216
Taghavi, S., J.A. Izquierdo, D. van der Lelie (2013). Complete genome sequence of Clostridium sp. DL-VIII, a novel solventogenic clostridium isolated from anaerobic sludge. Genome Announc 1(4):e00605-13
Li, L.L., S. Taghavi, J.A. Izquierdo, D. van der Lelie (2012). Complete genome sequence of Clostridium sp. strain BNL1100, a cellulolytic mesophile isolated from corn stover. J Bacteriol 194(24):6982-6983
Mearls E.B., J.A. Izquierdo, L.R. Lynd (2012). Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms. BMC Microbiol 12:180
Izquierdo, J.A., L. Goodwin, K. Davenport, H. Teshima, D. Bruce, C. Detter, R.Tapia, S. Han, M. Land, L. Hauser, J. Han, S. Pitluck, M.Nolan, A. Chen, M. Huntemann, K.Mavromatis, N. Mikhailova, K. Liolios, T. Woyke, L.R. Lynd (2012). The complete genome of Clostridium clariflavum DSM 19732. Stand Genomic Sci 6(1):104-115
Sizova, M.V., J.A. Izquierdo, N. Panikov, and L.R. Lynd (2011). Thermophilic anaerobic bacteria from biocompost able to degrade cellulose and xylan. Appl Environ Microbiol 77(7):2282–2291
Izquierdo, J.A., M.V. Sizova, L.R. Lynd (2010). Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl Environ Microbiol 76(11): 3545-3553
Izquierdo, J.A. and K. Nüsslein (2006). Distribution of extensive nifH gene diversity across physical soil microenvironments. Microb Ecol 51(4): 441-452
