Freshwater microbial communities

Abstract

Freshwaters provide essential commodities and services to society and they act as regulators of carbon cycling and of local and global climate. Prokaryotic microbes in lacustrine ecosystems are centrally involved in various biogeochemical cycles, for example, they are responsible for a considerable fraction of global methane and carbon dioxide production. Freshwater systems comprise a diverse set of habitats hosting contrasting microbial assemblages. Subsurface environments such as groundwater and hyporheic corridors harbor various types of chemolithotrophic bacteria, as well as microbes from exotic phyla without a single cultured representative. The microbial assemblages in large rivers exhibit distinct longitudinal transformations related to the gradually changing supply of organic carbon in lotic environments, and abrupt shifts in community composition are induced by discontinuities, for example, impoundments or point sources of organic matter. Riverine and stream biofilms may be regarded as “landscapes” of microbial assemblages which appear to be more shaped by extrinsic factors, particularly the velocity and direction of the water flow, than by immigration of waterborne bacteria. Lakes and ponds offer a range of habitats to specialized prokaryotic assemblages, including the air-water interface, the chemocline and anoxic realms, the benthic layer, or the aufwuchs (periphyton) on littoral macrophytes. The prokaryotic assemblages in the euphotic zone of standing and running waters harbor both, oxygenic and anoxygenic autotrophic microbes, and various lineages of bacteriorhodopsin-bearing photoheterotrophs. If categorized according to growth strategy and cell size, microbes in freshwater pelagic habitats can be roughly divided into free-living ultramicrobacteria, opportunistically growing bacteria that often exhibit a dual lifestyle (planktonic and surface attached), and filamentous bacteria that resist protistan grazing. Apart from the biotic interactions that affect prokaryotes in all biomes, such as competition with other pro- and eukaryotes, predation, and parasitism, there are specific properties of lacustrine ecosystem that may be responsible for the establishment of typical and unique microbial assemblages: On the one hand, there are indications for the importance of regional factors in shaping freshwater microbial assemblages, such as local climate, biogeochemical interaction with the catchment area, and the massive introduction of bacteria into lakes with low hydrological retention times. On the other hand, freshwaters are discontinuous habitats, and intrinsic factors, such as internal variability, lake trophic state, pH, organic matter composition, phytoplankton, and food web structure, may all codetermine microbial community structure by selecting for or against particular ecotypes.