SBI Newsletter Header

June  2012
Read the newsletter online or link to past newsletters: 

Last Issue of SBI Newsletter

This is the last issue of the SBI newsletter, but you will still be able to use the SBI Website to access

  • Feature articles on SBI research
  • Bibliography of  nearly 280 SBI-related journal articles by OSU researchers
  • News archive of SBI-related news stories
  • Abstracts and agendas from the five summer workshops
  • Posters or PowerPoint presentations by SBI interns over the six years of the program
  • Program background

Upcoming Events

Monday, June 4 4:00pm. The Influence of the Forest Floor Moss Cover on Ectomycorrhizal Abundance in the Oregon Cascades (Part of the Crop & Soil Science Seminar Series). Presented by: Jed Cappellazzi Held on campus at ALS 4000. FMI:

Wednesday, June 6 - Friday, June 8. Ocean Crust Processes and Consequences for Life (Dark Energy Biosphere Institute (DEBI) Research Coordination Network (RCN)). Theme: Processes in the ocean crust, from formation to subduction, and consequences for ocean-crust exchange budgets and subseafloor life. S Held at University of Bremen, Germany. FMI: Wolfgang Bach

Friday, June 15 12-12:45pm. Viral Manipulation of the Genetic Landscape of Deep Subsurface Microbial Communities (C-DEBI Networked Speaker Series. See Website for how to connect.). Presentation on metagenomic tools developed to assess the nature and impact of the viral community in hydrothermal systems; ongoing comparative metagenomics studies to determine whether viruses are transferring genes between archaeal and bacterial hosts. Held at Online. FMI: Rosalynn Lee Sylvan. .

Saturday, June 16 - Tuesday, June 19. American Society for Microbiology General Meeting. ASM's General Meeting focuses on the following broad categories: diagnostic microbiology and epidemiology; pathogenesis and host response mechanisms; general and applied microbiology (including environmental microbiology); and molecular microbiology, physiology, and virology. Held at San Francisco, CA. FMI:

Sunday, July 8 - Friday, July 13. 14th International Working Meeting on Soil Micromorphology. Held at l’Institut d’Estudis Catalans, Barcelona, Spain. FMI: .

Sunday, August 5 - Friday, August 10. Workshop: Answering Ecological Questions with Metagenomic Sequencing (2012 Ecological Society of America Annual Meeting). Held at Oregon Convention Center, Portland, OR. FMI: David Myrold

Sunday, October 21 - Wednesday, October 24. Symposium on Soil Metagenomics (2012 Soil Science Society of America Annual Meeting). Held at Cincinnati, Ohio. FMI: David Myrold

Latest OSU SBI-Related Publications

Publications from 2012

Chong, Lauren S.; Prokopenko, Maria G.; Berelson, William M.; Townsend-Small, Amy; McManus, James. 2012.  Nitrogen cycling within suboxic and anoxic sediments from the continental margin of Western North America. Marine Chemistry 128   p. 13-25 OSU author: McManus

Grace, Peter R.; Antle, John A.; Aggarwal, P. K.; Ogle, Stephen; Paustian, Keith; Basso, Bruno. 2012.   Soil carbon sequestration and associated economic costs for farming systems of the Indo-Gangetic Plain: A meta-analysis Agricultural Ecosystems and Environment, 146 (1)  137-146. OSU author: Antle

Jennings, Tara N.; Smith, Jane E.; Cromack, Kermit, Jr.; Sulzman, Elizabeth W.; McKay, Donaraye, Caldwell, Bruce A., Beldin, Sarah I. 2012.  Impact of postfire logging on soil bacterial and fungal communities and soil biogeochemistry in a mixed-conifer forest in central Oregon. Plant and Soil  350  (1-2) 393-411. OSU authors: Jennings, Cromack, Sulzman, Caldwell

Yan, Guiping; Smiley, Richard W.; Okubara, Patricia A. 2012.  Detection and Quantification of Pratylenchus thornei in DNA Extracted from Soil Using Real-Time PCR.  Phytopathology 102 (1 )  14-22. OSU authors: Yan, Smiley

Vajrala, Neeraja; Sayavedra-Soto, Luis A.; Bottomley, Peter J.; Arp, Daniel J. 2012. Global analysis of the Nitrosomonas europaea iron starvation stimulon. Archives of Microbiology  194 (4)  305-313 OSU authors: all

Publications from 2011

Sierra, Carlos A.; Harmon, Mark E.; Perakis, Steven S. 2011.  Decomposition of heterogeneous organic matter and its long-term stabilization in soils  Ecological Monographs 81 (4)   619-634 OSU authors:  Sierra, Harmon

Richter Daniel deB; Bacon Allan R.; Mobley Megan L.; et al. 2011.  Human-Soil Relations are Changing Rapidly: Proposals from SSSA's Cross-Divisional Soil Change Working Group. Soil Science Society of America Journal 75 (6)  2079-2084 OSU author: Lajtha

Paszczynski Andrzej J.; Paidisetti Ravindra; Johnson Andrew K.; et al. 2011.  Proteomic and targeted qPCR analyses of subsurface microbial communities for presence of  methane monooxygenase Biodegradation 22 (6) 1045-1059. OSU author: Colwell

Schmidt Michael W. I.; Torn Margaret S.; Abiven Samuel; et al. 2011.  Persistence of soil organic matter as an ecosystem property  Nature  478 (7367) 49-56. OSU author:  Kleber

Porter Mark L.; Valdes-Parada Francisco J.; Wood Brian D. 2011.  Multiscale modeling of chemotaxis in homogeneous porous media Water Resources Research 47 . OSU authors: Porter, Wood

Kluber Laurel A.; Smith Jane E.; Myrold David D. 2011.  Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi Soil Biology & Biochemistry 43 (5) 1042-1050. OSU authors: Kluber, Myrold

Davit Y.; Iltis G.; Debenest G.; et al. 2011.  Imaging biofilm in porous media using X-ray computed microtomography Journal of Microscopy 242 (1) 15-25 OSU author: Iltis, Wildenschild

Nachshon Uri; Weisbrod Noam; Dragila Maria I.; et al. 2011.  Combined evaporation and salt precipitation in homogeneous and heterogeneous porous media Water Resources Research 47 (Article W03513) OSU author: Dragila

Vajrala Neeraja; Sayavedra-Soto Luis A.; Bottomley Peter J.; et al.  2011.  Role of a Fur homolog in iron metabolism in Nitrosomonas europaea  BMC Microbiologhy 11 (37). OSU authors: all

Myrold David D.; Pett-Ridge Jennifer; Bottomley Peter J. 2011.  Nitrogen Mineralization and Assimilation at Millimeter Scales. Editor(s): Klotz MG; Stein LY  PT B  Book Series: Methods in Enzymology  496 p. 91-114 OSU authors:all

Radniecki Tyler S.; Lauchnor Ellen G.  2011.  Investigating Nitrosomonas europaea Stress Biomarkers in Batch, Continuous Culture, and Biofilm Reactors PT B Book Series: Methods in Enzymology 496 p.217-246 OSU authors: all

Sierra C. A.; Harmon M. E.; Thomann E.; et al. 2011.  Amplification and dampening of soil respiration by changes in temperature variability Biogeosciences 8 (4) 951-961 OSU authors: Sierra, Harmon

Sayavedra-Soto Luis A.; Vajrala Neeraja; Arp Daniel J.  2011.  Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea Book Series: Methods in Enzymology  486  p. 403-428  OSU authors: all

Sayavedra-Soto Luis A.; Stein Lisa Y. 2011. Genetic Transformation of Ammonia-Oxidizing Bacteria Book Series: Methods in Enzymology 486 p. 389-402   OSU authors: all

Skantar A. M.; Handoo Z. A.; Zasada I. A.; Ingham, R. E.; Carta, L. K.; Chitwood, D. J. 2011.  Morphological and Molecular Characterization of Globodera Populations from Oregon and Idaho Phytopathology 101 (4) 480-491. OSU author: Ingham

Yin Jun; Haggerty Roy; Stoliker Deborah L.;  Kent, Douglas B.; Istok, Jonathan; Greskowiak, Janek;  Zachara, John M. 2011.  Transient groundwater chemistry near a river: Effects on U(VI) transport in laboratory column experiments Water Resources Research 47. OSU authors: Haggerty, Istok

Thorpe Andrea S.; Callaway, Ragan M. 2011.  Biogeographic differences in the effects of Centaurea stoebe on the soil nitrogen cycle: novel weapons and soil microbes Biological Invasions 13 (6) 1435-1445. OSU author: Thorpe

Bertagnolli, A. D.; Treusch, A. H.; Mason, O. U.; Stingl, U.; Vergin, K. L.; Chan, F.; Beszteri, B.; Giovannoni, S. J. 2011.  Bacterial diversity in the bottom boundary layer of the inner continental shelf of Oregon, USA.  Aquatic Microbial Ecology 64 (1): 15-25. OSU authors: Mason, Giovannoni

Argerich, Alba; Marti, Eugenia; Sabater, Francesc; Haggerty, Roy; Ribot, Miquel. 2011.  Influence of transient storage on stream nutrient uptake based on substrata manipulation.  Aquatic Sciences 73 (3): 365-376. OSU author: Haggerty

Opportunities for Students

(listed by due date)

NSF Earth Sciences Postdoctoral Fellowships (EAR-PF) - The research and education plans of each fellowship must address scientific questions within the scope of EAR disciplines. The program supports researchers for a period of up to 2 years with fellowships that can be taken to the institution or national facility of their choice. Applications due July 2, 2012.

The Camille & Henry Dreyfus Foundation, Inc. Postdoctoral Program in Environmental Chemistry 2011 Funding Opportunity -  The Postdoctoral Program in Environmental Chemistry provides a principal investigator with an award of $120,000 over two years to appoint a Postdoctoral Fellow in environmental chemistry. Example topics include but are not limited to the chemistry associated with: the climate, the atmosphere, aquatic or marine settings, toxicology, soil or groundwater. Contact Martha Coleman, Director of Foundation Relations, OSU Foundation for more information. Application due August 20, 2012.

Looking for a summer internship? Visit to look through over 100 internships (and counting!) already uploaded to the platform. You can apply directly through the New Environmental Internship Clearinghouse Portal.

Think ahead for fall! Many fellowships and post-docs have a fall deadlines. The NSF Graduate Research Fellowships page has a thorough list of funding opportunities to check out.

NSF Opportunities for Faculty

(listed by due date)

August 2012

 Newsletters are also available on the Web at