Does capillary racetrack-based enrichment reflect the diversity of uncultivated magnetotactic cocci in environmental samples?

Jogler

Schüler

et al. 2011

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A targeted metagenomic approach was applied to investigate magnetotactic bacteria (MTB) within the phylum Nitrospirae in Lake Miyun near Beijing, China. Five fosmids containing rRNA operons were identified. Comparative sequence analysis of a total of 172 kb provided new insights into their genome organization and revealed unexpected subgenomic diversity of uncultivated MTB in the phylum Nitrospirae. In addition, affiliation of two novel MTB with the phylum Nitrospirae was verified by fluorescence in situ hybridization. One of them was morphologically similar to "Candidatus Magnetobacterium bavaricum," but the other differed substantially in cell shape and magnetosome organization from all previously described "Ca. Magnetobacterium bavaricum"-like bacteria.

Section: Fig 1 (A)mentioning

confidence: 59%

Metagenomic Analysis Reveals Unexpected Subgenomic Diversity of Magnetotactic Bacteria within the Phylum Nitrospirae

Jogler

Schüler

et al. 2011

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“…Nearly complete 16S rRNA genes were amplified directly from magnetically enriched MTB cells in which MWB-1 was dominant by using the universal bacterial primers 27F (5=-AGAGTTTGATCCTGGCTCAG-3=) and 1492R (5=-GGTTACCTTG TTACGACTT-3=) as described previously (31,34). PCR was performed using a T-Gradient thermocycler (Whatman Biometra, Göttingen, Germany).…”

Section: Methodsmentioning

confidence: 99%

Newly Isolated but Uncultivated Magnetotactic Bacterium of the Phylum Nitrospirae from Beijing, China

Pan

2012

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Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with >6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximumlikelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments. Biomineralization of magnetic minerals has been discovered in a broad range of organisms, including birds, fishes, mollusks, insects, and microorganisms (23,53,55). A typical example of biomineralization is found in magnetotactic bacteria (MTB), a morphologically and phylogenetically diverse group of microorganisms that form special intracellular organelles, called magnetosomes (3, 5). Magnetosomes are membrane-enveloped, nanosized, high-purity crystals of iron oxide magnetite and/or iron sulfide greigite, usually arranged into one or more linear chains (21). These specific organelles help MTB to sense and swim along the earth's magnetic field, a behavior known as magnetotaxis (8). In conjunction with aerotaxis and chemotaxis, magnetotaxis facilitates the location of MTB to their favorable positions in vertical chemical gradients in the oxic-anoxic transition zone (OATZ) (11,40). The ubiquity and abundance of MTB near the OATZ suggest their potentially important roles in the geochemical cycling of iron and sulfur in nature (48). Molecular approaches based on 16S rRNA gene sequencing have provided evidence for the phylogenetic heterogeneity of MTB. Most discovered MTB are affiliated with the Alphaproteobacteria, but MTB belonging to the Gammaproteobacteria, the Deltaproteobacteria, and Nitrospirae have also been described (2, 28).One of the most intriguing examples of MTB is "Candidatus Magnetobacterium bavaricum," a magnetite-producing MTB within the deep-branching bacterial phylum Nitrospirae that was first discovered in Lake Chiemsee in Upper Bavaria, Germany (49, 54). "Ca. Magnetobacterium bavaricum" is a large, rod-shaped bact...

“…The bacterial universal primers 27F (5Ј-AGAGTTTGATCCTGGCTCAG-3Ј) and 1492R (5Ј-GGTTACCTTGTTACGACTT-3Ј) (5) were used to amplify 16S rRNA genes directly from the 20 l of magnetically enriched MTB. PCR amplification and cloning procedures for construction of a 16S rRNA genes clone library were performed as previously reported (22,23). Twenty clones were randomly picked up and subjected to sequencing.…”

Section: Methodsmentioning

confidence: 99%

Uncultivated Magnetotactic Cocci from Yuandadu Park in Beijing, China

Pan

2009

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In the present study, we investigated a group of uncultivated magnetotactic cocci, which was magnetically isolated from a freshwater pond in Beijing, China. Light and transmission electron microscopy showed that these cocci ranged from 1.5 to 2.5 m and contained two to four chains of magnetite magnetosomes, which sometimes were partially disorganized. Overall, the size of the disorganized magnetosomes was significantly smaller than that arranged in chains. All characterized magnetosome crystals were elongated (shape factor ‫؍‬ 0.64) and fall into the single-domain size range (30 to 115 nm). Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the enriched bacteria were a virtually homogeneous population and represented a novel lineage in the Alphaproteobacteria. The closest cultivated relative was magnetotactic coccoid strain MC-1 (88% sequence identity). First-order reversal curve diagrams revealed that these cocci had relatively strong magnetic interactions compared to the single-chain magnetotactic bacteria. Low-temperature magnetic measurements showed that the Verwey transition of them was ϳ108 K, confirming magnetite magnetosomes, and the delta ratio ␦ FC /␦ ZFC was >2. Based on the structure, phylogenetic position and magnetic properties, the enriched magnetotactic cocci of Alphaproteobacteria are provisionally named as "Candidatus Magnetococcus yuandaducum."Magnetotactic bacteria (MTB) can mineralize intracellular nanosized iron oxides or sulfides called magnetosomes, which in most MTB are normally single-domain (SD) magnetite with a narrow range of grain sizes from 30 to 120 nm (3). The chain configuration of magnetosomes renders MTB able to navigate the oxic-anoxic interface in chemically stratified environments by swimming along the Earth's magnetic field (13). Diverse MTB, including coccoid, spirillar, rod-shaped bacteria and multicellular magnetotactic prokaryotes with one, two, or more chains of magnetosomes, thrive in a broad range of aquatic environments, which sometimes even are dominant strains of the microbial biomass in sediment (10, 47). Based on their phylogeny, all currently known MTB can be divided into two taxonomic groups: Proteobacteria and Nitrospira phyla (2).When MTB die, the magnetosomes can be preserved in sediment as fossil magnetosomes (or magnetofossils) (6). Fossil magnetosomes have been found in lacustrine and deep-sea sediments (6,35,43,51), which are stable carriers of natural remanence and may play substantial contributions to the bulk magnetization of sediments due to their SD sizes (6,19,26,32,33). Moreover, since most known MTB are microaerophilic or anaerobic and are concentrated in the oxic-anoxic transition zone, the presence and characteristics of MTB species in vertically stratified sediments can be used as a potential paleoenvironmental proxy (19,44,45). However, how to identify bacterial magnetite or greigite (Fe 3 S 4 ) in sediments is still challenging. Recently, characterizing the magnetic properties of MTB has attracte...