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

Abstract

We report here on novel groups of Archaea in the bacterioplankton of a small boreal forest lake studied by the culture-independent analysis of the 16S rRNA genes amplified directly from lake water in combination with fluorescent in situ hybridization (FISH). Polymerase chain reaction products were cloned and 28 of the 160 Archaea clones with around 900-bp-long 16S rRNA gene inserts, were sequenced. Phylogenetic analysis, including 642 Archaea sequences, confirmed that none of the freshwater clones were closely affiliated with known cultured Archaea. Twelve Archaea sequences from lake Valkea Kotinen (VAL) belonged to Group I of uncultivated Crenarchaeota and affiliated with environmental sequences from freshwater sediments, rice roots and soil as well as with sequences from an anaerobic digestor. Eight of the Crenarchaeota VAL clones formed a tight cluster. Sixteen sequences belonged to Euryarchaeota. Four of these formed a cluster together with environmental sequences from freshwater sediments and peat bogs within the order Methanomicrobiales. Five were affiliated with sequences from marine sediments situated close to marine Group II and three formed a novel cluster VAL III distantly 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 rRNA-targeted oligonucleotide probes revealed the presence of Methanomicrobiales in the studied lake. These observations indicate a new ecological niche for many novel`non-extreme' environmental Archaea in the pelagic water of a boreal forest lake. ß

Examining the global distribution of dominant archaeal populations in soil

“…As only the most abundant archaea were recovered by our method, it should be stressed that the phylogenetic tree represents relationships among the most dominant archaea and does not depict the full extent of archaeal diversity in these soils, which is potentially much greater (Fierer et al, 2007). The majority of the archaeal phylotypes (90.9% of all archaeal sequences) were contained within the group 1.1b crenarchaeotal clade (Jurgens et al, 2000), which has been shown previously to be dominant in soils (Auguet et al, 2009).…”

Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea

“…Direct cell count and fluorescent in situ hybridization (FISH) To determine the abundance of bacteria and archaea in collected samples, three oligonucleotide probes were used: EUB338I (Amann et al, 1990), ARCH915 (Amann et al, 1992) and Cren512 (Jü rgens et al, 2000). Filters were fixed on board with formaldehyde (final concentration 4% v/v) for 4 h, washed twice with 1X PBS (phosphate-buffered saline), fixed in 1 ml ethanol : 1X PBS (1:1) and stored at 4 1C until further treatment.…”

Occurrence and distribution of tetraether membrane lipids in soils: Implications for the use of the TEX86 proxy and the BIT index

“…doi: 10.1016/j.orggeochem.2006.07.018 diverse settings such as marine and lacustrine water columns and sediments (e.g. DeLong et al, 1994;MacGregor et al, 1997;Schleper et al, 1997;Vetriani et al, 1999;Jurgens et al, 2000;Karner et al, 2001;Keough et al, 2003), peat bogs, wetlands and soils (e.g. Buckley et al, 1998;Ochsenreiter et al, 2003;Sizova et al, 2003;Kotsyurbenko et al, 2004) and the deep subsurface (Takai et al, 2001).…”