306 Estuarine Ecosystems accidental, reflecting patterns in salinity, hydrology, and geometry of the estuarine basin, tidal stream channels and meanders, and other basin-wide factors Reefs also influence estuarine development, sedimentation, and water clarity, and thus the formation of other habitats (e.g., submerged aquatic vegetation, marshes, soft bottoms, and hard bottoms) for a host of organisms And as climatic, interannual, and interseasonal changes mobilize variable hydrologic conditions, the role of rooted and cemented estuarine habitats such as oyster reefs, seagrasses, and marshlands together play interdependent roles in providing shelter, stability, and predictable habitat This may be of fundamental importance to functional development of the estuarine land–seascape In sum, the eastern oyster appears to be a classic example of a ‘‘foundation’’ species at the level of the estuarine ecosystem Similarly, the role of fish communities must not be overlooked Another type of functional feedback concerns the fact that many species exist in a number of separate populations, either as young or as adults, that mix together seasonally especially in nonreproductive periods A common pattern of estuarineassociated fishes, for example, is estuarine or coastal spawning followed by juvenile egress from estuaries or larval ingress into estuaries with settlement by juveniles in nursery habitats As estuarine-associated species use a diversity of habitats for reproduction, growth, and recruitment, these patchy populations at other times assemble as metapopulations or contingent memberships (Secor and Rooker, 2005; Secor, 1999) For example, an estuary-dependent species such as menhaden, which is distributed patchily among individual estuaries as juveniles, assembles over the shelf to form one or more metapopulations as adults (Figure 3) These shelf metapopulations join those of other species to become part of the shelf ‘‘metacommunity.’’ It follows that fluctuations of any one metapopulation within any one estuary will affect the total ‘‘metacommunity’’ to a greater or lesser extent (Ray, 1997) This form of large-scale biodiversity centers on community composition, not necessarily on the presence or absence of individual species, but may be strongly affected by functional alterations of estuaries Observing the collection of species in patterns of communities leads to the conclusion that at the scale of the large, regional ecosystem, each estuary with its community components may be conceived in terms of connectivities to the sum total of estuaries responsible, to a greater or lesser degree, for the overall functional dynamics of the biogeographic region This large-scale perspective fuses scientific concepts of landscape ecology with metapopulation theory The concepts presented in the case of the Chesapeake Bay suggest controls and feedbacks among organisms and the environment at several scales One fundamental factor seems clear: east coast estuaries have been perturbed in many ways, and one of the most dramatic for the Chesapeake Bay has been the depletion of oyster reefs and some fishes, for example, shad, and the practical eradication of their functional ecosystem roles Although data are lacking to explain beyond doubt what changes have been perpetrated by these biodiversity losses, it seems apparent that at the very least they have left a marked effect on the entire Bay system Furthermore, it may be that these effects have cascaded up-scale to affect the adjacent continental shelf Estuarine community Oyster Oyster patches metapopulation Region Estuary Estuary − shelf fish metacommunities Estuary Figure The concept of estuarine metapopulations and shelf metacommunities Oyster reef metapopulations influence estuarine morphometrics and biodiversity Consequently, the fish biota of various estuaries influence the fish metacommunity of the shelf Future Challenges We make three points in conclusion The first concerns the need for greatly increased attention to the natural histories of estuarine and shelf species, which underlie both theory and management practice The minimal requirements for informed conservation and management are descriptions of species’ life histories in the context of their environmental relationships Second, many estuarine organisms range widely and form metapopulations over the shelf, as components of estuary–shelf communities Thus, the minimal scale for sustainability of biodiversity becomes that of the biogeographic region Quantitative, landscape-level descriptions of the regional coastal zone, including estuarine habitats, are a necessary prerequisite for conservation and management Third, it has become a truism in ecology that no one scale adequately describes ecosystem phenomena Rather, the interaction among phenomena on different scales must become the centerpiece of research and management This strongly suggests that explanations for fluctuations in biodiversity, including those within biotic communities and at regional scales, will continue to be obscure until multiscale ecosystem functions are better understood Ecosystem-based management is the logical outcome of interdisciplinary, multiscale knowledge This recognizes that understanding the