Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments

Abstract

Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal-rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO2 using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese-oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal-oxidizing genera, Leptothrix of the beta-Proteobacteria and Hyphomicrobium of the alpha-Proteobacteria, and a Fe(III)-reducing group related to the Magnetospirillum genus of the alpha-Proteobacteria. Groups related to the metal-reducing delta-Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments.

Molecular Characterization of the Archaeal Community in an Amazonian Wetland Soil and Culture-Dependent Isolation of Methanogenic Archaea

“…The sequences classified by RDP Classifier as members of the class Methanosarcinales, showed similarity by BLAST to sequences found in freshwater sediments, namely AY652476.1 [52], AF293016.1 and AF293017.1 [53].…”

Microbial DNA extraction and analyses of soil iron–manganese nodules

“…The two bacteria, as the model Mn(II)-oxidizing bacteria belong to Firmicutes and b-proteobacteria lineages, have been well studied (Tebo et al, 2004). The clone DQ537531 in a-proteobacteria lingeage was 92% similar to an uncultured bacteria clone from Green Bay ferromanganous micronodule (Stein et al, 2001). The high sequence similarity reveals the presence of some organisms related to the known Mn(II)-oxidizing bacteria from aquatic environment and they may play significant role in the formation of soil Fe-Mn nodules.…”

Characterization of biofilm and corrosion of cast iron pipes in drinking water distribution system with UV/Cl2 disinfection

“…The compositions of bacteria related with iron cycling underwent great changes in different ARs and different stages. In the AR with UV/Cl 2 , at stage I, the relative abundance of nitrate-reducing bacteria (NRB) was 9.9%, and among them, 3.9% NRB were related to redox cycling of iron, such as Hyphomicrobium (3.7%) (Stein et al, 2001), and 6% NRB produced siderophores, including Sphingomonas (Duckworth et al, 2009), Brucella (Roop, 2012), Acinetobacter (Proschak et al, 2013) and Azospirillum (Loaces et al, 2011). The ironrespiring bacteria were 11.7%, predominantly including ironreducing bacteria (IRB) Acidobacterium (10.2%) (Nancucheo and Johnson, 2010) and iron-oxidizing bacteria (IOB) Pedomicrobium (1.3%) (Braun et al, 2009).…”