Mark Silby


Faculty picture - Mark SilbyMark Silby

Associate Professor

Ph.D. University of Canterbury, New Zealand
Bacterial genetics and genomics, environmental microbiology

Phone: 508-999-8365 
Office: Science and Engineering, Room 335

Silby Lab Website

My research interests are in microbial activities in natural environments such as soil. Most of what we know about bacteria has been discovered using laboratory cultures of single species. Unlike traditional laboratory conditions, in complex environments such as soil bacteria need to respond to fluctuating environmental parameters, and must interact with a large number of other microbial species. We have found that in the presence of multiple bacterial species and while dwelling in soil, bacteria behave in ways which have never been observed in laboratory culture experiments.


Using the model bacterium Pseudomonas fluorescens, we are interested in addressing two aspects of life in natural environments. First, we are focused on understanding mechanisms that enable persistence and competitive fitness, and adaptation to environmental fluctuations which occur during growth in soil. Second, my laboratory used co-culture of multiple bacterial species to explore communication among soil bacteria resulting in multiple responses including the production of an antimicrobial compound.


Long term goals include developing an understanding of the dynamics of microbial communities in natural environments, using microbial systems as sensors of environmental contamination, and improving the use of bacteria in biological control of plant pathogens and in the bioremediation of oil spills.


In our research we use massively parallel DNA sequencing technology alongside established genetic, molecular biology, and microbiological tools.


 Recent Publications | Graduate Students |  Courses

Current Projects

1. Determination of transcriptome response of Pseudomonas fluorescens to perturbation of the soil environment and genetic analysis of specific stress response pathways.

2. Transcriptome analysis of Pseudomonas fluorescens and the plant pathogen Xanthomonas campestris during interactions in laboratory media and on plant surfaces.

3. Dissecting the mechanisms of interspecies chemical communication between Pseudomonas fluorescens and the soil bacterium Pedobacter sp. V48 (collaboration with Netherlands Institute for Ecology).


Publications (pubmed search

  • Silby MW, Nicoll JS & Levy SB (2012) Regulation of Polyphosphate Kinase Production by Antisense RNA in Pseudomonas fluorescens Pf0-1. Applied and Environmental Microbiology 78: 4533-4537.
  • Mastropaolo MD, Silby MW, Nicoll JS & Levy SB (2012) Novel Genes Involved in Motility and Biofilm Formation in Pseudomonas fluorescens Pf0-1. Applied and Environmental Microbiology 78: 4318-4329.
  • Garbeva P, Silby MW, Raaijmakers JM, Levy SB & de Boer W (2011) Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME J 5: 973-985.
  • Garbeva P, Tyc O, Remus-Emsermann MNP, van der Wal A, Vos M, Silby M & de Boer W (2011) No Apparent Costs for Facultative Antibiotic Production by the Soil Bacterium Pseudomonas fluorescens Pf0-1. PLoS ONE 6: e27266.
  • Silby MW, Winstanley C, Godfrey SAC, Levy SB & Jackson RW (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiology Reviews 35: 652-680.
  • Silby MW, Nicoll JS & Levy SB (2009) Requirement of Polyphosphate by Pseudomonas fluorescens Pf0-1 for Competitive Fitness and Heat Tolerance in Laboratory Media and Sterile Soil. Appl. Environ. Microbiol. 75: 3872-3881.
  • Silby MW, Cerdeno-Tarraga AM, Vernikos GS, et al. (2009) Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10: R51.
  • Kim W, Silby MW, Purvine SO, et al. (2009) Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1. PLoS ONE 4: e8455.
  • Silby MW & Levy SB (2008) Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1. PLoS Genetics 4: e1000094.
  • Silby MW, Ferguson GC, Billington C & Heinemann JA (2007) Localization of the plasmid-encoded proteins TraI and MobA in eukaryotic cells. Plasmid 57: 118-130.
  • Silby MW, Giddens SR & Mahanty HK (2005) Mutation of a LysR-type regulator of antifungal activity results in a growth advantage in stationary phase phenotype in Pseudomonas aureofaciens PA147-2. Appl. Environ. Microbiol. 71: 569-573.
  • Silby MW & Levy SB (2004) Use of IVET to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: discovery of expressed sequences with novel genetic organization. Journal of Bacteriology 186: 7411-7419.
  • Silby MW, Rainey PB & Levy SB (2004) IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150: 518-520.
  • Robleto EA, Lopez-Hernandez I, Silby MW & Levy SB (2003) Genetic analysis of the AdnA regulon in Pseudomonas fluorescens: nonessential role of flagella in adhesion to sand and biofilm formation. Journal of Bacteriology 185: 453-460.
  • Silby MW (2002) A theory can be falsified or tested. Faith cannot. Nature 416: 785.

Recent Graduate Students

John Lafleur, Ph.D candidate (BMEBT program).

Reducing biofilm development by enzymatic disruption of quorum sensing.

Adam Bitzer Ph.D candidate (BMEBT program).

How does interspecies interaction trigger a cooperative surface locomotion?

Doug Marshall, M.S candidate (Biology program).

Determining the genome-wide response of Pseudomonas fluorescens to dehydration stress in soil.

Kendall Murray, M.S candidate (Biology program).

Deciphering the interplay between Pseudomonas fluorescens and Xanthomonas campestris on plant surfaces.



Courses Professor Silby has taught include:

BIO 321 General Microbiology (Fall)
BIO 333 General Genetics lab (Spring)
BIO 411/511 Seminar in Microbial Genetics (Spring)
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