February 28, 2006 - ASM Comments on FY 2007 Budget Request for Microbial Observatories Program at NSF

Dr. James P. Collins
Assistant Director, Biological Sciences Directorate
National Science Foundation
Room 605 N
4201 Wilson Boulevard
Arlington, VA 22230

Dear Dr. Collins,

The American Society for Microbiology (ASM) would like to express its concern with the proposed fiscal year (FY) 2007 funding level for the Microbial Observatories/ Microbial Interactions and Process (MO/MIP) activity supported by the National Science Foundation (NSF) in the Biological Sciences Directorate and the impact that request may have on support for microbiological research. The ASM has received unsolicited comments about MO/MIP from more than 100 individuals representing more than 40 institutions.

The ASM is the premier educational and scientific society dedicated to the advancement of microbiological research and its application for the common good. The Society represents more than 42,000 microbiologists, including scientists in academic, industrial and government institutions, working in a variety of areas, including public health, medical, genomic, molecular, environmental and food microbiology.

MO/MIP was recently housed in Emerging Frontiers in recognition of the need for a distinct emphasis on microbial biology research that cannot be supported adequately in other programs. Transfer of MO/MIP from Emerging Frontiers to the Division of Molecular and Cellular Biosciences (MCB) raises questions about NSF’s emphasis on microbial biology, especially since the transfer appears to have been accompanied by a net loss of $6.52 million for MCB between FY05 and 07.

This is particularly troubling since the pace of astounding discoveries in microbial biology is increasing through applications of genomics and metagenomics. Moreover, losses to MO/MIP appear to be occurring in spite of a 7.9 percent increase in NSF’s budget request to Congress, which includes a 5.4 percent increase for the Biological Sciences Directorate. The ASM is concerned that the MO/MIP program, which contributes directly to American competitiveness, is threatened, while the NSF budget increases in response to the “American Competitiveness Initiative.”

The NSF has a long history of supporting microbial biology. NSF supported, paradigm-changing discoveries about microbes have fueled a revolution in biology itself, not just in microbial biology. Some discoveries have profoundly altered our most basic understanding of the biological world. Others have resulted in dramatic technological advances leading to new energy sources (i.e., biological fuel cells and energy from waste treatment), and improvements in industrial efficiency and remediation of chemical wastes. Advances in microbial biology have spawned numerous innovations with major economic and social impacts. Many other important discoveries lay ahead.

The significance of microbes and microbial biology has been recognized in many ways by NSF and other Federal agencies. The interagency “Microbe Project” provides just one example of a broad consensus that microbial research merits considerable national attention and funding support. NSF’s MO/MIP activity is one of the most successful and significant programs ever developed to promote such research. MO/MIP was created to address gaps in research not covered by other core programs; those gaps would still exist without MO/MIP as a distinct entity.

MO/MIP is significant because it-


• recognizes that microorganisms encompass far greater phylogenetic, biochemical and physiological diversity than all other organisms combined, and provides the first opportunity to systematically explore that diversity using contemporary and still evolving approaches that are transforming microbial biology;

• supports a research emphasis that is unique within the portfolio of federally-sponsored research programs; it is the only national effort for discovery of microbes, and the only program that parallels active discovery efforts supported by other nations;

• integrates state-of-the art, “cutting-edge” research questions and methods from multiple, traditionally distinct disciplines, provides support for an amount of time sufficient to ensure successful integration of these disciplines, and fosters synthetic analyses that create new knowledge about fundamentally important problems;

• promotes innovation through the discovery of novel microbes, through the development and application of new methods, and by promoting interactions among diverse scientific disciplines;

• provides a highly visible programmatic focus on microbial biology that attracts undergraduate and graduate students, and supports training of a new generation of microbial biologists essential for the Nation’s future scientific workforce.

MO/MIP has supported numerous highly successful research efforts, that have-

• substantially expanded the diversity of cultured microbes, including the first isolation of marine planktonic archaea and other organisms that play major roles in transformations of carbon, energy and nutrients in terrestrial and aquatic environments;

• isolated an organism (Silicibacter pomeroyi) representative of those that regulate the emission of climate-active sulfur gases from the oceans to the atmosphere, and led to isolation of many other important microbes, the genomes of which are currently being sequenced;

• established the first synoptic molecular ecological analyses of forest fungi (Duke Forest) and the first systematic analyses of aquatic viroplankton (Chesapeake Bay);

• pioneered new concepts and approaches, e.g., metagenomics, for assessing microbial phylogenetic and functional diversity in terrestrial and aquatic environments generally;

• trained more than 100 graduate students, and provided opportunities for research and education for hundreds undergraduates, many of whom have pursued graduate degrees;

• created a variety of educational outreach programs for the K-12 community, including both students and teachers.

The MO/MIP program has very strong, broad-based community support-

• recently, in excess of 100 individuals representing more than 40 institutions have submitted unsolicited letters to ASM expressing their fervent desire for the continuation of a distinct MO/MIP program; excerpts from several of these communications are attached as examples;

• individuals supporting MO/MIP include a wide spectrum of scientists, ranging from graduate students to new assistant professors to senior faculty and administrators; they represent multiple disciplines and research interests, and work with a very broad range of habitats and organisms;

• the USDA has recognized the uniqueness and importance of MO/MIP by committing to participation in a multi-year, jointly funded collaboration to support research on agricultural systems.

Based on the input it has received and its consideration of the importance of MO/MIP, the ASM offers the following recommendations-

1. Retain MO/MIP as a distinct, visible activity and plan a transition from a finite program to a long-term core program.

2. Develop a plan through broad community input for increased funding to take advantage of new opportunities in metagenomics and other emerging technologies.

3. Foster collaborations among the MO/MIP program, the National Ecological Observatory Network (NEON) and Ocean Observing Systems (OOS) to take advantage of and promote synergisms in methodological approaches, database management and other computational resources, and shared scientific questions.


The MO/MIP program has been exemplary. It supports research, training and outreach that are helping to define the future of microbiology and interdisciplinary efforts involving microbes. MO/MIP is thriving and deserves expanded support and long-term commitments from NSF.

The ASM appreciates your consideration of these comments and offers its continued support for NSF’s efforts to advance microbial biology and science in general.


Stanley Maloy, Ph.D.
President, ASM

Gary M. King, Ph.D.
Chair, Committee on Environmental Microbiology, ASM

James Tiedje, Ph.D.
Immediate Past President, ASM

Ruth L. Berkelman, M.D.
Chair, Public and Scientific Affairs Board, ASM

Excerpts from communications submitted to ASM:

Dr. Jo Handelsman, HHMI Professor, Department of Plant Pathology, University of Wisconsin.

“The MO/MIP program has been one of the most dramatic influences on microbiology in my 26 years in the field. It has engendered a new kind of interdisciplinary thinking in the field, new collaborations, and a new type of interaction among PIs. It has fostered the kind of large scale science that is necessary to begin to build the database that will provide the basis for elucidating general principles in microbial ecology.”

Dr. Robert Miller, Regents Professor and Head, Department of Microbiology and Molecular Genetics, Oklahoma State University.

“The unique nature of the interdisciplinary research supported by the Microbial Observatories program will be lost if it is merged with another more traditionally based program. The very features of the program that makes its approach to ecology unique makes it difficult or impossible to administer as a part of a program that has multiple missions and priorities. Work such as we are carrying out at the Great Salt Plains Observatory here in Oklahoma has brought together microbiologists, botanists, biogeologists, biophysicists, evolutionary theorists and many other disciplines in a program of study that has created new paradigms of investigation and thought. Because of this, our university has just expanded it geology department to include an endowed chair in Microbiogeophysics. This new and unfamiliar term, “microbiogeophysics,” itself speaks volumes about the new directions in interdisciplinary science investigations that the MO/MIP programs are supporting and allowing to incubate and mature. It also speaks to the difficulty of combining the program with a “traditional” area of study that is not looking forward to the future of new, interdisciplinary biology.”

Dr. Mary Lidstrom, Jungers Professor of Engineering and Microbiology, HHMI Professor and Vice-Provost for Research, University of Washington.

“In my own project we have microbiologists, biochemists, bioinformaticists, ecologists, analytical chemists, chemical engineers, physicists, and electrical engineers, as well as a genomics group in another institution, most of whom have never been involved with site-based studies before. We have opened up a whole new world to this group and to their colleagues, and my project is just one example in which such partnerships are changing the way we do science.”

Dr. Holly Pinkart, Associate Professor, Department of Biological Sciences, Central Washington University.

“At our MO, we have discovered that over half of the organisms we culture from [a] haloalkaline lake are previously undescribed genera. This contribution alone adds much to our knowledge of genetic diversity. Additionally, these isolates have demonstrated novel metabolisms, from new degradative pathways to the ability to induce formation of minerals. Other programs at NSF may address parts of this research, but none … would allow for the scope of this project. The other current program areas at NSF, such as Geobiology and Biotic Surveys and Inventories, do not address specifically the role of microorganisms in the environment (whatever that environment may be) while addressing questions of biodiversity. In addition to bringing together established scientists in a variety of fields (microbiologists, geochemists, chemical engineers, oceanographers) in a way that few other programs do, the MO/MIP program has also been extremely effective for attracting new scientists to the field of microbiology. Our MO has trained close to 40 undergraduate students, many of whom have gone on to graduate school. Additionally, the organism-centered, integrative approaches engendered by the MO/MIP program has driven development of genomic and other molecular tools, as well as novel cultivation strategies that target the uncultivated majority of organisms that reside within the biosphere.”

Dr. Andreas Teske, Associate Professor, Department of Marine Sciences, University of North Carolina.

“I mention just one example of many, the recent cultivation of MG-1 archaea, one of the dominant prokaryotes in the ocean, and their physiological identification as nitrifyers - with major implications for nitrogen cycling in the world's oceans. The PIs of this project, John Waterbury and David Stahl, are members of the Plum Island Microbial Observatory, which co-funded this groundbreaking study (Koenneke et al. 2005. Nature 437:543-546). At a recent workshop hosted by the NASA Astrobiology Institute (NAI) last November, the MO/MIP program was discussed by NASA officials as a model for NASA to emulate - to get NAI-funded scientists to work on a number of carefully chosen "analog" sites for potential extraterrestrial biospheres; such analog sites should be chosen for their significance in biogeochemistry, extremophilic microbiology, and origin of life research.”

Ms. Ashley Shade plus 49 graduate students in the Microbiology Doctoral Training Program, University of Wisconsin.

“We perceive the removal of MO/MIP as a drastic setback in the field of microbiology, and specifically the cutting-edge and expanding sub-disciplines of microbial ecology, environmental microbiology, and microbial interactions. Previously, these essential sub-disciplines have been emphasized for their interdisciplinary efforts and encouraged with NSF support. MDTP students would like this support to continue fully as we strive to become excellent researchers and future principal investigators.”

Dr. Jean Brenchley, Professor of Microbiology and Biotechnology, Penn State University, and past-President, American Society for Microbiology.

“Microbiology as a discipline differs from others, not just by its subject material, but also by its methods, relevance, and inclusive thinking. Funding and featuring the MO/MIP program by NSF has been, and I hope will continue to be, critical for supporting the innovative and extraordinary advances arising from research in microbial biology. The disappearance of this program will be destructive to the excellent ongoing research while further diminishing the visibility of microbiology at a time when molecular tools are enabling extraordinary advances and applications.”