Bacteriology Committee Meeting 2005 (APS Meeting, Austin, TX)

Immediate Past Chair: Gwyn Beattie

Chair:  Sheng Yang He

Vice-chair:  Don Kobayashi

Vice-chair elect: Amy Charkowski

Current Members: A. Bogdanove; M. Brodhagen; A. Charkowski, W. Chun, J. Jones, L. Keith, K. Newman, J. Norelli, N. Schaad, G. Sundin, S. von Bodman

Members beginning term (8/3/06): J. Barak, J. Kers, R. Loria, S. Lu, Y. Zhao

Members ending term (8/3/06): G. Beattie, W. Fuqua, I.-M. Lee

Attendance (based on sign-in sheet):  R. Allende-Molar, A. Alvarez, S. Blumer, M. Brodhagen, C. Bull, G. Burnett, A. Charkowski, J. Clifford, D. Gross, T. Denny, K. Everett, Z. Flores, R. Gitaitis, J. Graham, R. Hernandez, M. Irey, J. Jackobs, K. Jahob, J. Jones, S.H. Kim, J. Loper, R. Loria, F. Louws, S. Lu, G. Luo, M. Miller, M. Nakhla, J. Palumbo, A. Records, R. Reedy, L. Renick, T. Riley, G. Sundin, L. Triplett, A. Vidaver, S. von Bodman, N. Wang, L. Wanner, P. Wechter, J. White

Sheng Yang He, presiding

Meeting called to order at 7:00 pm

Current business:

1.  Approval of 2004 Minutes:

A motion to approve to 2004 Minutes was moved, seconded and approved unanimously.

2.  Transport of bacterial isolates.  Jim White (Virologist) from APHIS spoke on the issue of moving bacteria across state lines (APHIS PPQ Form 526).  Generally speaking, processing permit applications can be quick (within 60 days), with delayed approval of permits resulting primarily from missing information on applications.  Domestic transfer requests are generally not a problem; however, international import requests are more difficult.  A major impediment to application processing involves problems associated with taxonomic changes of the requested organism. 

Development and maintenance of the widely prevalent bacterial pathogen list can facilitate the process of pathogen transport requests.  Funds are available (up to $5000/yr) to support efforts in generating the list for participating states, which should be updated every other year.  Any remaining funds can default to general use by the Bacteriology Committee.  It is expected that electronic submissions of the generated/updated list can be expected in the near future.  A web-based list of pathogen names must be chosen for this purpose.  J. White indicated that his office is currently using the DZM list, which was met with some opposition, since alternative, more appropriate lists are available, such as the ISPP list.  There are currently 31 states (currently listed on the APHIS website) with widely prevalent lists (states are not required to participate). 

Jim White emphasized that he is open to phone calls and emails to assist people with their requests.  Jim White contact information:  301 734-8713; James.l.white@aphis.usda.gov

3.  Ad hoc committee reports:

A.  Genomics (Joyce Loper)

Goal: Priority listing of bacteria for genome sequencing.

(J. Loper, Chair, G. Beattie, R. Davis, S. Hogenhout, C. Kado, D. Kobayashi, L. Thomashow, S. von Bodman.  Post meeting note -- new members:  C. Bull, A. Charkowski, R. Loria and A. Records)

Up to 10 strains can be listed in the immediate priority category and up to 25 strains can be listed in the high priority category.  The current list contains highlighted strains, which refer to strains thought to be in the process of being sequenced).  There are still spots available on both the bacterial pathogens and beneficial microbes lists, for both immediate priority and high priority categories, emphasizing a need for the committee to address and update both lists.  To date, email has not worked well, since there have been few responses using this format.

Carolee Bull initiated a discussion on the need to sequence type strains, primarily for comparative purposes, especially at the taxonomic/phylogenic level (type strains at the species and subspecies/pathovar levels).  A discussion ensued regarding the biological relevance of type strains, and the importance of genome sequencing with respect to taxonomy versus biological relevance.  It was agreed upon that biological differences between closely related strains have yielded very interesting differences.

A second discussion ensued regarding an email from Jan Leach about utilizing DOE (JGI) as a sequencing source.  Tim Denny questioned the DOE sequencing priority of plant pathogens.  However, Joyce stated JGI is involved in sequencing plant pathogens, especially in terms of comparative genomics.

B. Ralstonia solanacearum race 3

Goal: To address the appropriateness of listing this organism on the select agent list.

(Caitlyn Allen, Chair, A. Alvarez, T. Denny, J. Jones, A. Kelman)

C. Allen was not present at the meeting.  Tim Denny stated that the final rules were released, and R. solanacearum race 3 was still on select agent list, closing the case on the issue.  There remains the problem that research on the organism is restricted, since BL3 containment is required and few labs have BL3 status (very costly to obtain).

C. Bacterial taxonomy (Carolee Bull) 

Goal: To develop an interactive website on phytobacteriology taxonomy.

A discussion ensued regarding taxonomic issues and the International Union of Microbiological Societies, International Committee on Systematics of Prokaryotes. Carolee stated she recently attended a meeting and there has been no APS representative for last 15 yrs.  (ISPP has representation at ICSP, and Carolee currently serves on the ISPP taxonomy committee.)  Recognizing the need, Carolee was nominated to represent APS for this purpose, and the committee unanimously approved the nomination.

Carolee brought up two issues regarding taxonomy.  The first involved the process of naming of new species, which is outlined in the ICPS minutes.  Naming requires depositing strains in 2 different culture collections.   The second involved material transfer agreements that are now required by certain collections, e.g., ATCC.  Carolee proposed that type material should be non restrictive in terms of research (see discussions on need for national repository and interstate transport).

There was a discussion on developing a drop down list of prevalent bacteria, stating that the ISPP list should be used, but Anne Alvarez cautioned that it is not easy to interpret.  The hope is to be able to link synonyms, as well as linking all DOI documents on a single bacterial species (i.e., rDNA, etc to give history of a given species/strain).  There was some discussion on the formation of a new taxonomy subcommittee, which included Carolee Bull, Frank Lowes, and Ann Alvarez.  Frank suggested others should be considered, such as S. DeBoer.

D. Listing of prevalent phytopathogenic bacteria in the US

Goal:  To provide a reference tool for APHIS in their regulation of importation and exportation of research isolates of microorganisms between researchers.  The intent is to expedite the APHIS permit process.

(N. Schaad, Chair, A. Alvarez, T. Burr, A. Chatterjee, W. Chun, E. Civerolo, C. Ishimaru, J. Jones, F. Louws, G. Sundin, A. Vidaver)

There was no formal report from this ad hoc committee, although the topic was addressed in previous discussions during the committee meeting.

E. APS press publication related to bacteriology (Anne Alvarez)

Update of bacterial disease images on CD (organized like a compendium).  Anne stated that images of key diseases associated with a given species/pathovar are still missing, and is requesting help in obtaining these images.  Sheng Yang suggested that a highlighted email request should be sent for images still being sought. Approximately $4000 let over from the prevalent bacteria list effort were previously designated to support this effort, as discussed in the previous year’s committee meeting; however, Anne has not received any funds to date.

F. Bacteriology web site:  (Wes Chun).  There was no report/discussion regarding this topic (W. Chun was not in attendance).

G. Need for National Plant Pathogenic Bacteria Repository:  (Carolee Bull). Because a national repository does not exist, many strains reported in the literature have been lost.  Carolee Bull is requesting the development of a good strategy for establishing a repository within the US.  She emphasized the need to have an equivalent group to the Europeans, who are currently dictating nomenclature for plant pathogens.  Amy Charkowski stated that NSF has a program to support repositories of this sort, with funding as much as $500,000.  Sheng Yang mentioned he has the application information that is needed for this.

4.  Centennial Committee: APS Press Illustrations Committee together with the Centennial Committee are planning to compile a list of historical events, people and discoveries over the last 100 years as part of the APS centennial celebration in 2008.  This list will be displayed at the 2008 APS meeting in Minneapolis, MN.  There were no volunteers for the project; however, several names were suggested as potential contributors, including Bob Stall, Arthur Kelman, Ken Starr, Luis Sequeira, Chris Hayward, Eugene Nester; and Milt Schroth.

New business

Nomination of new members/new officers:

Amy Charkowski was nominated by Ann Alvarez; Sheng Yang He seconded the nomination; The committee unanimously approved the nomination.

Committees are now subjected to unlimited membership, with postdoctorates and graduate students encouraged to join.  The only criterion is that committee members must be also be an APS member.  As a result, there were many volunteers for committee membership, which were listed on the attendance sheet.  In addition, four nominations (Frank White, Jim Alfano, Chris Smart, and Brion Duffy) were made prior to the meeting.

This year’s sponsored special session:

Functional Genomics Meets Bacterial Diseases, Part II: Erwinia Genomics

Organizers: A. Charkowski and B. Schroeder

Co-sponsored sessions:

The Nature and Application of Biocontrol Microbes III: Pseudomonas spp.

Organizers: B. Jacobsen and B. McSpadden Gardener.

Endophytes: An emerging tool for biological control

Organizers: P. Backman and R. Sikora.

Retropathology: Disease for control of weeds

Organizer: D. Sands

Proposed special session topics for 2006 meeting:

I.  Role of type III effectors in bacterial virulence

Organizers:  Frank White and Xiayan Tan

Potential speakers: Mary Beth Mudgett; Frank White; David Mackey; Jianmin Zhou; Sheng-Yang He

(Received 24 votes)

II. Cross domain bacterial pathogens

Organizers: N. Schaad and J. Barak:

This proposal was resubmitted from the previous year, which has strong support from the committee.  Unfortunately, however, it was not approved by the program committee.  The proposal was resubmitted this year, but there was no representation by the organizers.  Therefore, it received little support from the committee.

III. Functional Genomics Meets Bacterial Diseases III: Xanthomonas and Xylella

Organizers:  Frank Loews and Jeff Jones

Potential Speakers:  G. Lacy; U. Bonas; F. White; D. Hopkins; 2 additional speakers for Xylella

(Received 24 votes from the committee)

IV. Evolution of virulence in Gram-positive bacteria

(emphasis will be on comparative genomics, which is different from the previous symposium presented at the 2004)

Organizer: Rosemary Loria

Potential speakers: S. Gill; C. Ishimaru; R Loria; J. Vivanco

(Received 12 votes from the committee)

Committee co-sponsor requests:

Molecular signaling in the phyllosphere (Phyllosphere Microbiology Committee) 

Alternative taxa in Biocontrol (Biocontrol Committee)

Meeting Adjourned at 8:30