title: Pond sediment magnetite grains show a distinctive microbial community.
abstract: Formation of magnetite in anaerobic sediments is thought to be enhanced by the activities of iron-reducing bacteria. Geobacter has been implicated as playing a major role, as in culture its cells are often associated with extracellular magnetite grains. We studied the bacterial community associated with magnetite grains in sediment of a freshwater pond in South Korea. Magnetite was isolated from the sediment using a magnet. The magnetite-depleted fraction of sediment was also taken for comparison. DNA was extracted from each set of samples, followed by PCR for 16S bacterial ribosomal RNA (rRNA) gene and HiSeq sequencing. The bacterial communities of the magnetite-enriched and magnetite-depleted fractions were significantly different. The enrichment of three abundant operational taxonomic units (OTUs) suggests that they may either be dependent upon the magnetite grain environment or may be playing a role in magnetite formation. The most abundant OTU in magnetite-enriched fractions was Geobacter, bolstering the case that this genus is important in magnetite formation in natural systems. Other major OTUs strongly associated with the magnetite-enriched fraction, rather than the magnetite-depleted fraction, include a Sulfuricella and a novel member of the Betaproteobacteria. The existence of distinct bacterial communities associated with particular mineral grain types may also be an example of niche separation and coexistence in sediments and soils, which cannot usually be detected due to difficulties in separating and concentrating minerals.
authors.affiliation: Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151, Republic of Korea.
authors.forename: H-K
authors.initials: HK
authors.lastname: Song
authors.forename: S
authors.initials: S
authors.lastname: Sonkaria
authors.forename: V
authors.initials: V
authors.lastname: Khare
authors.forename: K
authors.initials: K
authors.lastname: Dong
authors.forename: H-T
authors.initials: HT
authors.lastname: Lee
authors.forename: S-H
authors.initials: SH
authors.lastname: Ahn
authors.forename: H-K
authors.initials: HK
authors.lastname: Kim
authors.forename: H-J
authors.initials: HJ
authors.lastname: Kang
authors.forename: S-H
authors.initials: SH
authors.lastname: Lee
authors.forename: S P
authors.initials: SP
authors.lastname: Jung
authors.forename: J M
authors.initials: JM
authors.lastname: Adams
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D052203:Ferrosoferric Oxide / Q000032:analysis*; D045302:Geobacter / Q000235:genetics; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology*; D064307:Microbiota / Q000235:genetics*; D008969:Molecular Sequence Data; D061005:Ponds / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D056910:Republic of Korea; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D052203:Ferrosoferric Oxide