Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic Sediments

Abstract

In this report, we describe the selective cloning of large DNA fragments from magnetotactic metagenomes from various aquatic habitats. This was achieved by a two-step magnetic enrichment which allowed the mass collection of environmental magnetotactic bacteria (MTB) virtually free of nonmagnetic contaminants. Four fosmid libraries were constructed and screened by end sequencing and hybridization analysis using heterologous magnetosome gene probes. A total of 14 fosmids were fully sequenced. We identified and characterized two fosmids, most likely originating from two different alphaproteobacterial strains of MTB that contain several putative operons with homology to the magnetosome island (MAI) of cultivated MTB. This is the first evidence that uncultivated MTB exhibit similar yet differing organizations of the MAI, which may account for the diversity in biomineralization and magnetotaxis observed in MTB from various environments.

Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branchingNitrospiraphylum

“…In Magnetospirillum gryphiswaldense most genes implicated in magnetosome synthesis were identified within several operons of a genomic magnetosome island (MAI) (15), which encodes functions in magnetosome membrane biogenesis, magnetosomal iron uptake, and control of magnetite crystallization (8,10). Because of their conservation in other cultivated α-proteobacterial MTB (16,17), it has been suggested that the MAI may have been transferred horizontally, which was further corroborated by the recent discovery of homologous gene clusters in metagenomic clones (18) and the δ-proteobacterial Desulfovibrio magneticus RS-1 (19). However, the limited genetic information about magnetosome formation that has been confined to a few cultivated MTB mainly of the α-Proteobacteria, is in striking disparity to the fact that MTB are a noncoherent and phylogenetically heterogeneous group.…”

“…To identify putative magnetosome genes, we initially attempted a similar approach as was successfully used for the identification of MAI clusters from metagenomic large-insert libraries (18). However, screening of more than 10,000 clones from six independently constructed fosmid libraries based on magnetically highly enriched Mbav cells failed to detect any clones harboring genes with similarity to known magnetosome proteins.…”

“…Pyrosequencing generated a total of 118. (18,21) were PCR screened. Five clones, which previously had escaped our initial screening because of the lack of endsequence similarities, were identified from which either identical sequences of mamE (1 clone), or mamP (1 clone), or both (3 clones) could be amplified.…”

“…Sediment sample collection, magnetic Mbav enrichment, DNA extraction and fosmid library construction was performed as previously described (18,21). Six fosmid libraries were screened via endsequencing and PCR as previously described (18,21).…”

Common ancestry of iron oxide- and iron-sulfide-based biomineralization in magnetotactic bacteria

“…Magnetite magnetosome formation in the Alphaproteobacteria has been extensively characterized in some cultured species (Jogler and Schü ler, 2009) and briefly studied in uncultured organisms from environmental samples (Jogler et al, 2009b). The genes responsible for magnetite biomineralization, the mam and mms genes, make up the mamAB, mamGFDC, mamXY and mms6 operons (Jogler and Schü ler, 2009) in a genomic island known as the magnetosome island (MAI; Schü ler, 2004).…”