@article {gourgue_biogeomorphic_2022,
	title = {Biogeomorphic modeling to assess the resilience of tidal-marsh restoration to sea level rise and sediment supply},
	journal = {Earth Surface Dynamics},
	volume = {10},
	year = {2022},
	pages = {531{\textendash}553},
	abstract = {There is an increasing demand for the creation and restoration of tidal marshes around the world, as they provide highly valued ecosystem services. Yet restored tidal marshes are strongly vulnerable to factors such as sea level rise and declining sediment supply. How fast the restored ecosystem develops, how resilient it is to sea level rise, and how this can be steered by restoration design are key questions that are typically challenging to assess due to the complex biogeomorphic feedback processes involved. In this paper, we apply a biogeomorphic model to a specific tidal-marsh restoration project planned by dike breaching. Our modeling approach integrates tidal hydrodynamics, sediment transport, and vegetation dynamics, accounting for relevant fine-scale flow{\textendash}vegetation interactions (less than 1 m2) and their impact on vegetation and landform development at the landscape scale (several km2) and in the long term (several decades). Our model performance is positively evaluated against observations of vegetation and geomorphic development in adjacent tidal marshes. Model scenarios demonstrate that the restored tidal marsh can keep pace with realistic rates of sea level rise and that its resilience is more sensitive to the availability of suspended sediments than to the rate of sea level rise. We further demonstrate that restoration design options can steer marsh resilience, as they affect the rates and spatial patterns of biogeomorphic development. By varying the width of two dike breaches, which serve as tidal inlets to the restored marsh, we show that a larger difference in the width of the two inlets leads to higher biogeomorphic diversity in restored habitats. This study showcases that biogeomorphic modeling can support management choices in restoration design to optimize tidal-marsh development towards sustainable restoration goals.},
	issn = {2196-6311},
	doi = {10.5194/esurf-10-531-2022},
	url = {https://esurf.copernicus.org/articles/10/531/2022/},
	author = {Gourgue, Olivier and van Belzen, Jim and Schwarz, Christian and Vandenbruwaene, Wouter and Vanlede, Joris and Belliard, Jean-Philippe and Fagherazzi, Sergio and Bouma, Tjeerd J. and van de Koppel, Johan and Temmerman, Stijn}
}
@article {bogdan_biological_2022,
	title = {Biological {Networks} across {Scales}{\textemdash}{The} {Theoretical} and {Empirical} {Foundations} for {Time}-{Varying} {Complex} {Networks} that {Connect} {Structure} and {Function} across {Levels} of {Biological} {Organization}},
	journal = {Integrative and Comparative Biology},
	volume = {61},
	number = {6},
	year = {2022},
	month = {feb},
	pages = {1991{\textendash}2010},
	abstract = {Abstract Many biological systems across scales of size and complexity exhibit a time-varying complex network structure that emerges and self-organizes as a result of interactions with the environment. Network interactions optimize some intrinsic cost functions that are unknown and involve for example energy efficiency, robustness, resilience, and frailty. A wide range of networks exist in biology, from gene regulatory networks important for organismal development, protein interaction networks that govern physiology and metabolism, and neural networks that store and convey information to networks of microbes that form microbiomes within hosts, animal contact networks that underlie social systems, and networks of populations on the landscape connected by migration. Increasing availability of extensive (big) data is amplifying our ability to quantify biological networks. Similarly, theoretical methods that describe network structure and dynamics are being developed. Beyond static networks representing snapshots of biological systems, collections of longitudinal data series can help either at defining and characterizing network dynamics over time or analyzing the dynamics constrained to networked architectures. Moreover, due to interactions with the environment and other biological systems, a biological network may not be fully observable. Also, subnetworks may emerge and disappear as a result of the need for the biological system to cope with for example invaders or new information flows. The confluence of these developments renders tractable the question of how the structure of biological networks predicts and controls network dynamics. In particular, there may be structural features that result in homeostatic networks with specific higher-order statistics (e.g., multifractal spectrum), which maintain stability over time through robustness and/or resilience to perturbation. Alternative, plastic networks may respond to perturbation by (adaptive to catastrophic) shifts in structure. Here, we explore the opportunity for discovering universal laws connecting the structure of biological networks with their function, positioning them on the spectrum of time-evolving network structure, that is, dynamics of networks, from highly stable to exquisitely sensitive to perturbation. If such general laws exist, they could transform our ability to predict the response of biological systems to perturbations{\textemdash}an increasingly urgent priority in the face of anthropogenic changes to the environment that affect life across the gamut of organizational scales.},
	issn = {1540-7063, 1557-7023},
	doi = {10.1093/icb/icab069},
	url = {https://academic.oup.com/icb/article/61/6/1991/6281074},
	author = {Bogdan, Paul and Caetano-Anoll{\'e}s, Gustavo and Jolles, Anna and Kim, Hyunju and Morris, James and Murphy, Cheryl A and Royer, Catherine and Snell, Edward H and Steinbrenner, Adam and Strausfeld, Nicholas}
}
@article {liu_biotic_2022,
	title = {Biotic and abiotic factors control the geomorphic characteristics of channel networks in salt marshes},
	journal = {Limnology and Oceanography},
	volume = {67},
	number = {1},
	year = {2022},
	month = {jan},
	pages = {89{\textendash}101},
	issn = {0024-3590, 1939-5590},
	doi = {10.1002/lno.11977},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/lno.11977},
	author = {Liu, Zezheng and Gourgue, Olivier and Fagherazzi, Sergio}
}
@article {mori_biodiversityproductivity_2021,
	title = {Biodiversity{\textendash}productivity relationships are key to nature-based climate solutions},
	journal = {Nature Climate Change},
	volume = {11},
	number = {6},
	year = {2021},
	month = {jun},
	pages = {543{\textendash}550},
	issn = {1758-678X, 1758-6798},
	doi = {10.1038/s41558-021-01062-1},
	url = {http://www.nature.com/articles/s41558-021-01062-1},
	author = {Mori, Akira S. and Dee, Laura E. and Gonzalez, Andrew and Ohashi, Haruka and Cowles, Jane and Wright, Alexandra J. and Loreau, Michel and Hautier, Yann and Newbold, Tim and Reich, Peter B. and Matsui, Tetsuya and Takeuchi, Wataru and Okada, Kei-ichi and Seidl, Rupert and Isbell, Forest}
}
@article {wittyngham_biotic_2021,
	title = {Biotic {Recovery} {Following} {Ice}-{Rafting} in a {Salt} {Marsh}},
	journal = {Estuaries and Coasts},
	year = {2021},
	month = {nov},
	issn = {1559-2723, 1559-2731},
	doi = {10.1007/s12237-021-01023-z},
	url = {https://link.springer.com/10.1007/s12237-021-01023-z},
	author = {Wittyngham, Serina S. and Pant, Manisha and Mart{\'\i}nez-Soto, Kayla and Johnson, David S.}
}
@article {PIE437,
	title = {Bottom-up control of parasites},
	journal = {Ecosphere},
	volume = {8},
	number = {10},
	year = {2017},
	note = {PI Plum Data},
	keywords = {coastal wetlands, disease ecology, disturbance, eutrophication, fertilizer, host traits, inorganic nutrients, intertidal, LTER-PIE, population dynamics},
	doi = {10.1002/ecs2.1885},
	author = {Johnson, D.S. and Heard, R.}
}
@article {PIE385,
	title = {Behavior-based aggregation of land categories for temporal change analysis},
	journal = {International Journal of Applied Earth Observation and Geoinformation},
	volume = {35},
	year = {2015},
	note = {PI Plum Data},
	pages = {229-238},
	keywords = {disturbance, GIS, land change, LTER-PIE},
	doi = {10.1016/j.jag.2014.09.007},
	author = {Aldwaik, S.Z. and Onsted, J.A. and Pontius, R.G., Jr.}
}
@article {PIE342,
	title = {Beaver dams maintain native fish biodiversity by increasing habitat heterogeneity throughout a low-gradient stream network.},
	journal = {Freshwater Biology},
	volume = {58},
	year = {2013},
	note = {Grad},
	pages = {1523 - 1538},
	keywords = {beaver, disturbance, ecosystem engineer, fish assemblage, habitat heterogeneity, LTER-PIE, population dynamics, riverscape scale},
	doi = {10.1111/fwb.12153},
	author = {Smith, J.M. and Mather, M.E.}
}
@article {PIE340,
	title = {Brinson Review: Perspectives on the influence of nutrients on the sustainability of coastal wetlands},
	journal = {Wetlands},
	volume = {33},
	year = {2013},
	note = {PI Plum Data},
	pages = {975-988},
	keywords = {inorganic nutrients, LTER-PIE, primary production, salt marsh, wetland sustainability},
	doi = {10.1007/s13157-013-0480-3},
	author = {Morris, J.T. and Shaffer, J.A. and Nynam, J.A.}
}
@article {PIE289,
	title = {Beyond {\textquoteright}Lawn People{\textquoteright}: The role of emotions in suburban yard management practices},
	journal = {The Professional Geographer},
	year = {2012},
	note = {PI Plum Data},
	keywords = {disturbance, emotion, land use, lawn, LTER-PIE, Massachusetts, primary production, suburbs, yard},
	doi = {10.1080/00330124.2012.681586},
	author = {Harris, E.M. and Martin, D.G. and Polsky, C. and Denhardt, L. and Nehring, A.}
}
@phdthesis {PIE295,
	title = {Beaver dams maintain native fish biodiversity via altered habitat heterogeneity in a coastal stream network: evaluating gear, quantifying fish assemblages, and testing ecological hypotheses with empirical data.},
	volume = {Ph.D.},
	year = {2011},
	note = {Grad},
	school = {University of Massachusetts},
	type = {phdthesis},
	address = {Amherst, MA},
	keywords = {beaver dam, coastal streams, disturbance, habitat alteration, LTER-PIE, population dynamics},
	author = {Smith, J.M.}
}
@article {PIE176,
	title = {The biogeochemical influences of nitrate, dissolved oxygen, and dissolved organic carbon on stream nitrate uptake.},
	journal = {Journal of the North American Benthological Society},
	volume = {28},
	number = {4},
	year = {2009},
	note = {Grad},
	pages = {894-907},
	keywords = {dissolved organic carbon, dissolved oxygen, inorganic nutrients, LTER-PIE, net nutrient uptake, nitrate, nitrate uptake, organic matter, priming effect, solute addition},
	doi = {10.1899/08-183.1},
	author = {Thouin, J.A. and Wollheim, W.M. and Vorosmarty, C.J. and Jacobs, J. and McDowell, W.H.}
}
@mastersthesis {PIE204,
	title = {The biogeochemical influences of nitrate, dissolved oxygen, and dissolved organic carbon on stream nitrate uptake},
	volume = {M.S.},
	year = {2008},
	note = {Grad},
	school = {University of New Hampshire},
	type = {mastersthesis},
	address = {Durham, NH},
	keywords = {carbon, inorganic nutrients, LTER-PIE, nitrate, nitrogen, oxygen},
	author = {Thouin, J.}
}
@article {PIE197,
	title = {Biophysical controls on organic carbon fluxes in fluvial networks},
	journal = {Nature Geoscience},
	volume = {1},
	year = {2008},
	note = {PI Synthesis},
	pages = {95-100},
	keywords = {ecosystem metabolism, estuaries, fluvial networks, heterotrophy, inorganic nutrients, LTER-PIE, organic matter, primary production, rivers},
	doi = {10.1038/ngeo101},
	author = {Battin, T.J. and Kaplan, L. and Findlay, S. and Hopkinson, C. and Marti, E. and Packman, A. and Newbold, J.D. and Sabater, F.}
}
@article {PIE229,
	title = {Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers},
	journal = {Biogeosciences},
	volume = {3},
	year = {2006},
	note = {Collab Plum Data},
	pages = {175-185},
	keywords = {bacteria, biomarkers, coastal sediments, LTER-PIE, organic matter, stable isotopes},
	doi = {10.5194/bg-3-175-2006},
	author = {Bouillon, S. and Boschker, H.T.S.}
}
@article {PIE102,
	title = {Building a database of historic land cover to detect landscape change.},
	journal = {Biological Bulletin},
	volume = {205},
	year = {2003},
	note = {REU},
	pages = {257-258},
	keywords = {land use, landscape, LTER-PIE},
	doi = {10.2307/1543283},
	author = {Holden, M and Lippitt, C. and Pontius, R.G., Jr. and Williams, C.}
}
@article {PIE83,
	title = {Bacterioplankton Community Composition in Flowing Waters of the Ipswich River Watershed},
	journal = {Biological Bulletin},
	volume = {203},
	year = {2002},
	note = {REU},
	pages = {251-252},
	keywords = {bacterioplankton community, Ipswich River, LTER-PIE, watershed},
	doi = {10.2307/1543425},
	author = {Levine, U.Y. and Crump, B.C.}
}
@article {PIE59,
	title = {Benthic metabolism and nutrient regeneration on the continental shelf off eastern Massachusetts, USA},
	journal = {Marine Ecology Progress Series},
	volume = {224},
	year = {2001},
	note = {PI Coastal},
	pages = {1-19},
	keywords = {benthic metabolism, LTER-PIE, nutrient regeneration},
	doi = {10.3354/meps224001},
	author = {Hopkinson, C. S. and Giblin, A.E. and Tucker, J.}
}
@article {PIE49,
	title = {Bacterial consumption of DOC during transport through a temperate estuary},
	journal = {Aquatic Microbial Ecology},
	volume = {22},
	year = {2000},
	note = {PD Coastal},
	month = {2000},
	pages = {1-12},
	keywords = {carbon export, Chesapeake Bay, dissolved organic carbon (DOC), heterotrophy, LTER-PIE, Mid-atlantic bight, York River},
	doi = {10.3354/ame022001},
	author = {Raymond, P.A. and Bauer, J.E.}
}
@proceedings {PIE35,
	title = {Bird use of <i>Phragmites australis</i> in coastal marshes of northern Massachusetts.},
	journal = {Proceedings of the 1st National Conference on Marine Bioinvasions},
	volume = {Jan 24-27, 1999},
	year = {2000},
	note = {PI Plum Data},
	pages = {232-240},
	publisher = {MIT Sea Grant},
	address = {Cambridge, MA},
	keywords = {birds, coastal marsh, LTER-PIE, Phragmites},
	author = {Holt, E. and Buchsbaum, R.},
	editor = {J. Pederson}
}
@article {PIE16,
	title = {Benthic metabolism and nutrient cycling along an estuarine salinity gradient.},
	journal = {Estuaries},
	volume = {22},
	number = {4},
	year = {1999},
	note = {PI Plum Data},
	pages = {825-843},
	keywords = {benthic metabolism, estuary, LTER-PIE},
	doi = {10.2307/1353067},
	author = {Hopkinson, C. S. and Giblin, A.E. and Tucker, J. and Garritt, R.H.}
}
