@article {rand_parasite_2023,
	title = {Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system},
	journal = {Molecular Ecology},
	volume = {32},
	year = {2023},
	pages = {5028{\textendash}5041},
	abstract = {Manipulation of host phenotypes by parasites is hypothesized to be an adaptive strategy enhancing parasite transmission across hosts and generations. Characterizing the molecular mechanisms of manipulation is important to advance our understanding of host{\textendash}parasite coevolution. The trematode (Levinseniella byrdi) is known to alter the colour and behaviour of its amphipod host (Orchestia grillus) presumably increasing predation of amphipods which enhances trematode transmission through its life cycle. We sampled 24 infected and 24 uninfected amphipods from a salt marsh in Massachusetts to perform differential gene expression analysis. In addition, we constructed novel genomic tools for O. grillus including a de novo genome and transcriptome. We discovered that trematode infection results in upregulation of amphipod transcripts associated with pigmentation and detection of external stimuli, and downregulation of multiple amphipod transcripts implicated in invertebrate immune responses, such as vacuolar ATPase genes. We hypothesize that suppression of immune genes and the altered expression of genes associated with coloration and behaviour may allow the trematode to persist in the amphipod and engage in further biochemical manipulation that promotes transmission. The genomic tools and transcriptomic analyses reported provide new opportunities to discover how parasites alter diverse pathways underlying host phenotypic changes in natural populations.},
	keywords = {amphipod, differential expression, ecological genomics, host{\textendash}parasite co-evolution, infection response, Orchestia grillus, parasite manipulation, population genetics, trematode},
	issn = {1365-294X},
	doi = {10.1111/mec.17093},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.17093},
	author = {Rand, David M. and Nunez, Joaquin C. B. and Williams, Shawn and Rong, Stephen and Burley, John T. and Neil, Kimberly B. and Spierer, Adam N. and McKerrow, Wilson and Johnson, David S. and Raynes, Yevgeniy and Fayton, Thomas J. and Skvir, Nicholas and Ferranti, David A. and Zeff, Maya Greenhill and Lyons, Amanda and Okami, Naima and Morgan, David M. and Kinney, Kealohanuiopuna and Brown, Bianca R. P. and Giblin, Anne E. and Cardon, Zoe G.}
}
@article {8775,
	title = {Peat Decomposition and Erosion Contribute to Pond Deepening in a Temperate Salt Marsh},
	journal = {Journal of Geophysical Research: Biogeosciences},
	volume = {128171052},
	year = {2023},
	month = {Jan-02-2023},
	issn = {2169-8953},
	doi = {10.1029/2022JG007063},
	url = {https://onlinelibrary.wiley.com/doi/10.1029/2022JG007063},
	author = {Luk, Sheron and Eagle, Meagan J. and Mariotti, Giulio and Gosselin, Kelsey and Sanderman, Jonathan and Spivak, Amanda C.}
}
@article {vallino_phytoplankton_2020,
	title = {Phytoplankton {Temporal} {Strategies} {Increase} {Entropy} {Production} in a {Marine} {Food} {Web} {Model}},
	journal = {Entropy},
	volume = {22},
	number = {11},
	year = {2020},
	month = {nov},
	pages = {1249},
	abstract = {We develop a trait-based model founded on the hypothesis that biological systems evolve and organize to maximize entropy production by dissipating chemical and electromagnetic free energy over longer time scales than abiotic processes by implementing temporal strategies. A marine food web consisting of phytoplankton, bacteria, and consumer functional groups is used to explore how temporal strategies, or the lack thereof, change entropy production in a shallow pond that receives a continuous flow of reduced organic carbon plus inorganic nitrogen and illumination from solar radiation with diel and seasonal dynamics. Results show that a temporal strategy that employs an explicit circadian clock produces more entropy than a passive strategy that uses internal carbon storage or a balanced growth strategy that requires phytoplankton to grow with fixed stoichiometry. When the community is forced to operate at high specific growth rates near 2 d-1, the optimization-guided model selects for phytoplankton ecotypes that exhibit complementary for winter versus summer environmental conditions to increase entropy production. We also present a new type of trait-based modeling where trait values are determined by maximizing entropy production rather than by random selection.},
	issn = {1099-4300},
	doi = {10.3390/e22111249},
	url = {https://www.mdpi.com/1099-4300/22/11/1249},
	author = {Vallino, Joseph J. and Tsakalakis, Ioannis}
}
@inbook {PIE392,
	title = {Perspectives on a 30-Year Career of Salt Marsh Research},
	booktitle = {Long-Term Environmental Research: Changing the Nature of Scientists},
	year = {2015},
	note = {PI Synthesis},
	publisher = {Oxford University Press},
	organization = {Oxford University Press},
	chapter = {33},
	keywords = {ecology, long-term, LTER-PIE, research funding},
	isbn = {9780199380213},
	author = {Morris, J.T.},
	editor = {Willig, M.R. and Walker, L.R.}
}
@article {PIE345,
	title = {Predicting microbial nitrate reduction pathways in coastal sediments},
	journal = {Aquatic Microbial Ecology},
	volume = {71},
	year = {2014},
	note = {PI Plum Data},
	pages = {223-238},
	keywords = {coastal sediments, estuaries, inorganic nutrients, LTER-PIE, microbes, nitrate reduction},
	doi = {10.3354/ame01678},
	author = {Algar, C.K. and Vallino, J.J.}
}
@article {,
	title = {The production of urban vacant land: relational placemaking in Boston, MA neighborhoods.},
	journal = {Cities and the Environment},
	volume = {35},
	year = {2013},
	note = {PI Plum Data},
	pages = {156-163},
	keywords = {civil society organization, community gardens, LTER-PIE, neighborhood perception, relational place-making, urban governance, urban vacant land},
	doi = {10.1016/j.cities.2013.06.012.},
	author = {Foo, K. and Martin, D. and Wool, C. and Polsky, C.}
}
@mastersthesis {PIE282,
	title = {Population-level responses of the mummichog, Fundulus heteroclitus, to chronic nutrient enrichment in a New England salt marsh},
	volume = {M.S.},
	year = {2011},
	note = {Grad},
	pages = {75},
	school = {Louisiana State University},
	type = {mastersthesis},
	address = {Baton Rouge, LA},
	keywords = {disturbance, Fundulus heteroclitus, inorganic nutrients, LTER-PIE, population dynamics, salt marsh},
	author = {Lockfield, K.}
}
@article {PIE173,
	title = {Plant nitrogen dynamics in fertilized and natural New England saltmarshes: a paired 15N tracer study},
	journal = {Marine Ecology Progress Series},
	volume = {354},
	year = {2008},
	note = {PD Plum Data},
	pages = {35-46},
	keywords = {eutrophication, inorganic nitrogen, LTER-PIE, marsh ecosystem, nitrogen cycling, nitrogen isotopes, organic matter, plant ecophysiology, primary production, Spartina alterniflora, Spartina patens},
	doi = {10.3354/meps07170},
	author = {Drake, D.C. and Peterson, B.J. and Deegan, L.A. and Harris, L.A. and Miller, E.E. and Warren, R.S.}
}
@article {PIE93,
	title = {Patterns of sedimentation in a salt marsh-dominated estuary.},
	journal = {Biological Bulletin},
	volume = {205},
	year = {2003},
	note = {REU},
	pages = {239-241},
	keywords = {estuary, LTER-PIE, salt marsh, sedimentation},
	doi = {10.2307/1543274},
	author = {Cavatorta, J. and Johnston, M. and Hopkinson, C.S. and Valentine, V.}
}
@article {PIE111,
	title = {Phosphorus Limitation of Coastal Ecosystem Processes},
	journal = {Science},
	volume = {299},
	number = {563-565},
	year = {2003},
	note = {PI Coastal},
	keywords = {LTER-PIE, nutrient limitation, phosphorus, salt marsh},
	doi = {10.1126/science.1079100},
	author = {Sundareshwar, P.V. and Morris, J.T. and Koepfler, E.K. and Fornwalt, B.}
}
@article {PIE99,
	title = {Pre-industrial and contemporary fluxes of nitrogen through rivers: A global assessment based on typology},
	journal = {Biogeochemistry},
	volume = {68},
	year = {2003},
	note = {PI Synthesis},
	pages = {1-35},
	keywords = {anthropogenic loading, global, inorganic nutrients, LTER-PIE, nitrogen, nitrogen budget, nitrogen yields, rivers, watershed},
	doi = {10.1023/B:BIOG.0000025742.82155.92},
	author = {Green, P.A. and Vorosmarty, C.J. and Meybeck, M. and Galloway, J.N. and Peterson, B.J. and Boyer, E.W.}
}
@article {PIE113,
	title = {Processing watershed-derived nitrogen in a well-flushed New England estuary.},
	journal = {Limnology and Oceanography},
	volume = {48},
	number = {5},
	year = {2003},
	note = {PD Coastal},
	pages = {1766-1778},
	keywords = {estuary, LTER-PIE, nitrogen, watershed},
	doi = {10.4319/lo.2003.48.5.1766},
	author = {Tobias, C.R. and Cieri, M. and Peterson, B.J. and Deegan, L.A. and Vallino, J. and Hughes, J.}
}
@article {PIE25,
	title = {Population size and summer home range of the green crab, <i>Carcinus maenus</i>, in salt marsh tidal creeks},
	journal = {Biological Bulletin},
	volume = {197},
	year = {1999},
	note = {REU},
	pages = {292-299},
	keywords = {LTER-PIE, population size, salt marsh, green crab},
	doi = {10.2307/1542662},
	author = {Young, T. and Komarow, S. and Deegan, L. and Garritt, R.}
}
@techreport {PIE1,
	title = {The Plum Island Sound/River ecosystem: Current status and future management},
	year = {1998},
	note = {PI Plum Data},
	pages = {311},
	institution = {Plum Island Sound Minibay Project, Massachusetts Bays Program},
	keywords = {ecosystem, PIE LMER, water quality},
	author = {Buchsbaum, R. and Cooper, A. and LeBlanc, J.}
}
@article {PIE8,
	title = {Population size and site fidelity of <i>Fundulus heteroclitus</i> in a macrotidal saltmarsh creek},
	journal = {Biological Bulletin},
	volume = {195},
	year = {1998},
	note = {REU},
	pages = {238-239},
	keywords = {fish population, Fundulus, LTER-PIE, mummichog, population dynamics, saltmarsh creek, site fidelity},
	doi = {10.2307/1542858},
	author = {Sweeney, J. and Deegan, L. and Garritt, R.}
}
@article {PIE7,
	title = {A preliminary evaluation of sedimentation rates and species distribution in Plum Island estuary, Massachusetts},
	journal = {Biological Bulletin},
	volume = {195},
	year = {1998},
	note = {REU},
	pages = {232-233},
	keywords = {estuary, LTER-PIE, organic matter, salt marsh, sedimentation},
	doi = {10.2307/1542855},
	author = {Schmitt, C. and Weston, N.B. and Hopkinson, C.}
}
