Urban Ecology

In highly populated areas, such as New York City, a new environment is built and surrounding area heavily influenced. While this creates a challenge to preserve the natural environment from the many anthropogenic stressors it also creates a built environment that very little is known about.  My research on the coastal environment has adapted to this even greater urban environment by understanding the Jamaica Bay ecosystem as well as describe the built environment at a microbial scale.

I hope to apply what I learn from the aquatic metagenome of Jamaica Bay to the assessment of ecosystem health and inform future management strategies. Check out this brief video about my recent work in Jamaica Bay!

Authentic Research Experience in Microbiology – AREM

A major element of my work in New York City has been to manage the AREM program, which provides classroom research opportunities to undergraduate students.  The students are encouraged to OBSERVE, PARTICIPATE, and DISCOVER more about their environmental microbiome.

This work has now expanded beyond New York City!  I have been able to reach more than 40 faculty and 2000 students in less than 3 years!  Through student surveys, the program impact is assessed and results show that students gain more of an understanding and appreciation for science!

(Paper in preparation for publication)

Coral and Sponge Microbiome

The microbial communities of corals and sponges make up much of what a coral or sponge is and their processes.  For this reason, I focus my work around the holobiont concept.  This concept acknowledges that coral colonies cannot be studied without taking into account the many symbionts within and around a polyp.  This concept also applies to sponges and is important for studying both coral and sponge diseases.  I am also relate my research to the field of Oceans and Human Health, through the use of benthic organisms as indicators for environmental contamination, particularly human sewage.

The pathogenic relationship between Serratia marcescens and Acropora palmata was initially identified as White Pox Disease. Repeated challenge experiments illustrate how the bacterium alone can cause White Pox Disease.

(Sutherland, K.P., Shaban, S., Joyner, J.L., Porter, J.W., Lipp, E.K., 2011. Human Pathogen Shown to Cause Disease in the Threatened Elkhorn Coral Acropora palmata. Plos One 6, e23468.)

However continued field research has shown that the role of S. marcescens is not as discrete in the coral reef ecosystem.  S. marcescens is regularly found in the coastal environment and as part of many coral mucus bacterial communities, multiple species in addition to healthy and diseased A. palmata.

(Joyner, J.L., Sutherland, K.P., Kemp, D., Berry, B., Griffin, A., Porter, J.W., Broome, M., Noren, H., Lipp, E.K. Systematic analysis of white pox disease in Acropora palmata of the Florida Keys and the role of Serratia marcescens. Applied Environmental Microbiology, 81(13).)

Further work is being done to investigate the pathogenesis of S. marcescens to A. palmata and the etiology of White Pox Disease.  Using next generation sequencing the complete bacterial community of A. palmata mucus paired with water for multiple colonies was sequenced.  Tagged colonies allowed following community shifts through seasons and comparisons between reefs, this is one of the first environmental microbiome projects that has replication to make general conclusions about the coral mucus bacterial community as well as effect from environmental stressors.

(Papers in preparation for publication)


Dry Tortugas Water Quality

The Dry Tortugas National Park (DTNP) is a remote marine park with few known sources of human fecal contamination, but has seen an increase in coral disease that could be attributed to water quality. This study examines the DTNP coastal environment for evidence and sources of contamination.  Fecal indicator bacteria, Serratia marcescens and human enteric viruses were evaluated quarterly for one year at four stations.  Bacterial levels were low throughout the study, but commonly detected at the docks and beach.  Fecal coliform bacteria and enterococci were most often detected, whereas S. marcescens was rarely detected.  During a 42-h beach and bather study, both fecal coliform bacteria and S. marcescens levels were significantly correlated with bather/beachgoer density.  Human recreational activities directly contribute to enteric bacteria introduction in this remote environment; while unlikely to pose a significant human health risk it may serve as a potential threat to the surrounding ecosystem.

(Paper in preparation for publication)


Serratia marcescesns qPCR Detection

The coastal environment in the Florida Keys is regularly faced with sewage contamination through poorly treated human waste (septic systems and injection wells).  Through human waste the bacterium Serratia marcescens was introduced into marine waters and is now a cause for disease (white pox) in the threatened coral species Acropora palmata.  Using quantitative real-time PCR, gene regions were investigated for an assay specific for detecting S. marcescens.  An assay for the LuxS gene region was developed and applied to coastal water and sewage treatment plant influent where S. marcescens was rapidly detected.  S. marcescens was identified from other Serratia species with a reliable limit of detection.  Compared to traditional culture detection methods for environmental samples, this qPCR assay reliably detects environmental S. marcescens in complex Key Largo sewage influent samples and Florida Key’s residential canals.  This detection assay has both rapid quantitative abilities and sensitivity, which are key components for water quality monitoring and detecting potential pathogens.

(Joyner, J.L., Wanless, D.W., Sinigalliano, C., Lipp, E.K., 2014. Use of Quantitative Real-Time PCR for Direct Detection of Serratia marcescens in Marine and Other Aquatic Environments. Applied Environmental Microbiology, 80(5):1679.)

Serratia marcescens Virulence Characteristics

Ongoing work is to discern differences in virulence between known pathogenic and non-pathogenic strains of S. marcescens against A. palmata. While the mode of S. marcescens pathogenesis is not yet known for corals, its virulence in a C. elegans model has been attributed to the expression of at least three key genes.  Conventional PCR was used to screen strains of S. marcescens from marine and environmental sources for homologues of wzm  (LPS biosynthesis), vibC  (iron transport) and shlB  (hemolysin).  This analysis indicated that these genes do not have the same role among environmental strains.

Digital Camera


Dissertation Research Summary