Microbial Ecology at Sea : Sampling , Subsampling and Incubation Considerations

Thl' l1larit1l' 1'11vironll1l'nt is the largest contiguous habitat on Earth; hllwl'vl'r, it is fill' frnm bdng homogeneous. Relevant ecological time and SPdL'l' Sl'ilil's span mUrl' than nine orders of magnitude (Figure 2.1; Dickey, ll)l) 1), t!1l'l'l'by contributing to the challenge of adequate and representatin' s.lmpling uf thl~ marine environment. Man;.' distinct marine ecosystems and their microbial assemblages 1\,)\'1.' bl'L'n idl'nlifil'd and studied, ranging from ice-swept polar seas to dt·l'P-SL'.1 hylimtl1l'l'mal wnts. The diversity of microbial habitats is even grL'Iltl'1' th,1l1 ,1lretldy implied, especially considering the fact that microorg,misms lin' in micl'm~nvironments that are defined on space scales of millinwtt'l's tlI' IL'ss. As a result, the environments sensed by individual micl'lllws may bt' quite different from the surrounding bulk fluid. FurthL'l'mOl'e, many microbes Jive in truly protected habitats such as the l'ntl'ric tracks of Ia~ger metazoan organisms; sampling these microbes will I'L'quirl' fllndaml'nt,llly different methods than those used to target 'expllsl'd' mk\'()bial assemblages. In fact, the spectrum of oceanic habitats 1\I1d thl' dh'l'rsilv tlf tlw associated microbial assemblages is so extreme I I1t1t ,lin' bnltld· gl'nL'ralizatillns rl~gnrding sampling, sllbsmnpling and