Fate of Heterotrophic Microbes in Pelagic Habitats: Focus on Populations

Abstract

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a “Gleasonian” perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed

Planktonic food webs: microbial hub approach

“…the individual cells cease to exist), whereas in our model bacterial lysis or consumption by grazers is reflected in a modification of the existing flows from the bacterial compartment. More generally, each food-web compartment is an (Fuhrman et al 2006), biogeographical distributions (Martiny et al 2006), and nutritional strategies (Cottrell & Kirchman 2000, Malmstrom et al 2004, Pernthaler & Amann 2005. However, although our incomplete knowledge of bacterial phylotypes does not allow associating most of them to specific biogeochemical or ecological functions, some key functional characteristics of bacteria at the community level (e.g.…”

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

“…Some metabolic guilds of bacteria carry rRNA signatures (e.g. sulphate-reducing bacteria, methanotrophs, nitrifiers), but most metabolic or physiological functions have yet to be linked to clearly delineated phylogenetic groups (Pernthaler & Amann 2005). Thus to identify cohesive ecological populations in clone libraries, two basic approaches appear possible.…”

A Guide to the Natural History of Freshwater Lake Bacteria

“…Since this early recognition of the critical role of bacteria in regenerating and mobilizing nutrients in freshwater food webs, it has become clear that aquatic bacteria drive transformations and the cycling of most biologically active elements in these ecosystems. This key position held in essentially all biogeochemical cycles does not merely stem from the role of bacteria as the principal degraders and min-eralizers of organic compounds to their inorganic constituents (30,36) but also results from their biomass production and trophic coupling to eukaryote predators, which, by fueling the food web, has a profound impact on elemental fluxes and water quality in the ecosystem (154). Given the facts that lakes and other inland waters play a more critical role in the global carbon budget than previously recognized (31) and that lakes have been described as early indicators (i.e., sentinels) of both regional and global environmental change (133,228), the role of microbes in these processes is of renewed interest.…”