Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization

We report hele on novel groups of Archaea in the bacterioplankton of a smal l boreal forest lake studied by the culture-independent analysis of the 16S rRNA genes amplified directly from lake water in combination with fluoresc ent in situ hybridization (FISH). Polymerase chain reaction products were c loned and 28 of the 160 Archaea clones with around 900-bp-long 16S rRNA gen e inserts, were sequenced. Phylogenetic analysis, including 642 Archaea seq uences, confirmed that none of the freshwater clones were closely affiliate d with known cultured Archaea. Twelve Archaea sequences from lake Valkea Ko tinen (VAL) belonged to Group I of uncultivated Crenarchaeota and affiliate d with environmental sequences from freshwater sediments, rice roots and so il as well as with Sequences From an anaerobic digestor. Eight of the Crena rchaeota VAL clones formed a light cluster. Sixteen sequences belonged to E uryarchaeota. Four of these formed a cluster together with environmental se quences from freshwater sediments and peat bogs within the order Methanomir cobiales. Five were affiliated with sequences from marine sediments situate d close to marine Group II and three formed a novel cluster VAL III distant ly related to the order Thermoplasmales. The remaining four clones formed a distinct clade within a phylogenetic radiation characterized by members of the orders Methanosarcinales and Methanomicrobiales on the same branch as rice cluster I, detected recently on rice roots and in anoxic bulk soil of flooded rice microcosms. FISH with specifically designed rRN4-targeted olig onucleotide probes revealed the presence of Methanomicrobiales in the studi ed lake. These observations indicate a new ecological niche for many novel 'non-extreme' environmental Archaea in the pelagic water of a boreal forest lake. (C) 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.