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Bioindication has become an indispensable part of water quality monitoring in most countries of the

world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for

biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in

routine assessments, although they have been recognized for their importance in environmental pro-

cesses. Recently, the use of molecular methods has revealed unexpected diversity within known func-

tional groups and novel metabolic pathways that are particularly important in energy and nutrient cy-

cling. In various habitats, microbial communities respond to eutrophication, metals, and natural or an-

thropogenic organic pollutants through changes in diversity and function. In this review, we evaluated

the common trends in these changes, documenting that they have value as bioindicators and can be used

not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, com-

munity structures and diversity, as well as functional genes, in novel monitoring programs. These micro-

bial community measures can also be combined into biotic indices, improving the resolution of individual

bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic

analysis, as these are the most promising with respect to detailed bioindication value. We conclude that

microbial community dynamics are a missing link important for our understanding of rapid changes in

the structure and function of aquatic ecosystems, and should be addressed in the future environmental

monitoring of freshwater ecosystems.