Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

Abstract

Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-010-9734-2) contains supplementary material, which is available to authorized users.

A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer

“…Frozen 0.2-m filters were cut aseptically into small pieces (10-cm 2 total filter area per sample) that were processed using PowerSoil DNA isolation kits (MO BIO Laboratories Inc., Carlsbad, CA) as per the manufacturer's instructions. Bacterial and archaeal 16S rRNA gene amplicons for pyrosequencing were generated from DNA samples according to Vishnivetskaya et al (45) and Porat et al (34), respectively. PCR amplicons were purified using an Agencourt AMPure system (Beckman Coulter Inc., Brea, CA) according to the manufacturer's instructions, and a portion of each product was evaluated for size and purity using an Agilent 2100 bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).…”

Characterization of the Deltaproteobacteria in contaminated and uncontaminated stream sediments and identification of potential mercury methylators

“…Recent studies have investigated the overall bacterial and archaeal community structures in streams of East Tennessee contaminated with mercury and other heavy metals (Porat et al 2010, Vishnivetskaya et al 2011. The goal of the present study was to further these efforts and concentrate on the known guild of methylating bacteria by characterizing the distribution of Deltaproteobacteria in the anthropogenically contaminated surface sediments of streams within the Oak Ridge Reservation.…”

Application of Metagenomics in Environmental Anaerobic Technology

“…); (2)(Wang and Qian 2009;; (3)(Vanwonterghem et al 2014;Baker et al 2003); (4)(Yu et al 2005;Sundberg et al 2013); (5)(Tiao et al 2012;Tyson et al 2004); (6)(Kozich et al 2013); (7)(Claesson et al 2010;Ju et al 2013); (8)(Ibarbalz et al 2013;Ha et al 2012); (9)(Porat et al 2010); (10)(Baker et al 2003); (11)(Gantner et al 2011).…”