This experiment focuses on the factors affecting the diversity of microbial populations in coastal marine sediments. Top-down and bottom-up mechanisms of control were studied by setting up experiments where samples contain environments with different levels of predator exclusion and food sources. Specifically, a mixture of anoxic and sterile sediment were placed in packets of 3 different mesh pore sizes (1, 100, and 250 microns) and exposed to 3 different carbon levels (ambient, 36mg agarose, and 36mg agarose amended with 3 mg tryptone). The level of tryptone was chosen to be above the ambient levels and to be enough to be significant in comparison to agarose levels. The mesh is known to cause predator exclusion from an experiment conducted the previous summer. The anoxic sediment was used because the microbial life forms living in it would die once brought into an oxic enviromnent, thus allowing other life forms to colonize it.

Marina Ermakova1, Lora McGuinness2, and Lee J. Kerkhof2

1 Dept. of Molecular Biology and Biochemistry 2 Institute of Marine and Coastal Sciences, Rutgers University New Brunswick, NJ

Assessing top-down and bottom-up control mechanisms structuring marine microbial communities

Introduction

Conclusion

ReferencesLewin-Jacus, Joshua, L. McGuinness, and L. J. Kerkhof. The Effects of Grazer Exclusion on Sand Colonization by Microbial Communities. American Society of Microbiology; 2010; San Diego, California.Scala, D. J., and L. J. Kerkhof. 1998. Nitrous oxide reductase (nosZ) genespecific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 162: 61–68.

The clusters appear to be structured by temporal effects rather than predator exclusion or carbon sources. There are no apparent clusters based on mesh size. There are some sub-clusters that group carbon sources together. Additionally, the clusters seem to be more coherent for the later time points. Temporal effects seem to be more significant to microbial diversity than either addition of carbon sources or predator exclusion for the time frame in this study. The clusters also imply that carbon sources are more significant than predator exclusion.

MethodsDNA was extracted from sediment samples of each treatment. T-RFLP analysis was used to fingerprint the microbial communities, as described in Scala and Kerkhof (1998).

Left: The diffusion of red food dye out of 6% agarose plugs when enclosed in sediment was teated. The picture shows plugs removed from water at different time points. Right: These bags of mesh containing sediment and a carbon treatment were suspended in a marine environment for 1,2,3, or 4 weeks.

Results

Bray-Curtis cluster with alternating colors indicating groupings

Sorensen's cluster with alternating colors indicating groupings

Future DirectionFollow up experiments may have a longer timeline and more mesh sizes to test these variables more in depth. Additionally, a different slow release matrix from agarose should be used. This matrix should diffuse a carbon source over the course of weeks rather than days and should not be a carbon source itself.

T1 (of 4 time points):

No Carbon Source

Agarose Agarose + Tryptone

1 micron mesh size

Sample T1N1 Sample T1A1 Sample T1T1

100 micron mesh size

Sample T1N100

Sample T1A100

Sample T1T100

250 micron mesh size

Sample T1N250

Sample T1A250

Sample T1T250

T0

T2

T1

T4

T3

1 µ mesh, agarose plug

No Addition

T0

T2

T1

T4

T3

100 µ mesh, no plug

T0

T2

T1

T3

250 µ mesh, tryptone plug

DNA fingerprints of samples

AcknowledgementsWe would like to thank RUMFS for facilitating the deployment of the experiment and the RIOS program for funding.

Experimental Design:

Terminal restriction fragments (bp)

1 µ mesh, agarose plug

1 µ mesh, agarose plug

1 µ mesh, agarose plug

No Addition

100 µ mesh, no plug

100 µ mesh, no plug

100 µ mesh, no plug

No Addition

250 µ mesh, tryptone plug

250 µ mesh, tryptone plug