Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment

Wang, Zong-Jie; Xie, Zhihong; Wang, Chao; Du, Zong‐Jun; Chen, Guanjun

doi:10.1007/s10482-014-0232-2

Cited by 18 publications

(5 citation statements)

References 27 publications

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“…Izemoplasma (Supplementary Table 6 and Supplementary Information ). All other DNA-degraders identified in this study belong to bacterial groups that do not require supplementation of nucleic acid building blocks to growth media and therefore have capacity to synthesize their own nucleotides 28 , 36 – 38 .…”

Section: Resultsmentioning

confidence: 99%

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

et al. 2021

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Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse ‘Candidatus Izemoplasma’, Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse ‘Candidatus Izemoplasmatales’ (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.

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Section: Resultsmentioning

confidence: 99%

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

et al. 2021

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“…Table 4) (see Supporting information for descriptions). All other DNA-degraders identified in this study belong to bacterial groups that do not require supplementation of nucleic acid building blocks to growth media 29, 38-40 .…”

Section: Resultsmentioning

confidence: 96%

DNA-foraging bacteria in the seafloor

Wasmund

Pelikan

Watzka

et al. 2019

Preprint

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17Extracellular DNA is a major macromolecule in global element cycles, and is a particularly 18 crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor. 19Nevertheless, the identities, ecophysiology and genetic features of key DNA-foraging 20 microorganisms in marine sediments are completely unknown. Here we combined 21 microcosm experiments, stable isotope probing and genome-centric metagenomics to study 22 microbial catabolism of DNA and its sub-components in anoxic marine sediments. 13 C-DNA 23 added to sediment microcosms was degraded within ten days and mineralised to 13 CO2. 24Stable isotope probing showed that diverse Candidatus Izemoplasma, Lutibacter, Shewanella, 25Fusibacteraceae and Nitrincolaceae incorporated DNA-derived 13 C-carbon. Genomes 26representative of the 13 C-labelled taxa were recovered and all encoded enzymatic repertoires 27 for catabolism of DNA. Comparative genomics indicated that DNA can be digested by 28 diverse members of the order Candidatus Izemoplasmatales (former Tenericutes), which 29 appear to be specialised DNA-degraders that encode multiple extracellular nucleases. 30Fusibacteraceae lacked genes for extracellular nucleases but utilised various individual 31 purine-and pyrimidine-based molecules, suggesting they 'cheated' on liberated sub-32 components of DNA. Close relatives of the DNA-degrading taxa are globally distributed in 33 marine sediments, suggesting that these poorly understood taxa contribute widely to the key 34 ecosystem function of degrading and recycling DNA in the seabed. 35 36 37 DNA compared to 12 C-DNA, from several time points, i.e., days 4, 10 and 13 (Supp. Fig. 5). 130Later time points showed no elevated 16S rRNA gene abundances in heavy fractions and 131 therefore subsequent analyses focused on the first three time points, and thus, largely on the 132 primary DNA degraders. 133

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“…Sediment was collected from the continental shelf regions of the Aoshan Bay, Jimo, PR China (36°22′08″N 120°41′56″E) by the enrichment method devised by Wang et al [5]. The enrichment medium was made as described previously [6].…”

Section: Methodsmentioning

confidence: 99%

Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment

Zhao

Wang

Song

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two novel, designated strains 29W222T and 2943T, were isolated from the marine sediment from Aoshan Bay, Jimo, PR China. Growth was observed at pH 6.0–8.5 (optimum, pH 7.5) for strain 29W222T, and pH 5.5–8.5 (pH 7.0) for strain 2943T. Both strains displayed growth in 0.5–6 % NaCl with an optimum at 1 % for 29W222T; 0.5 % for 2943T. Both strains grew optimally at 33 °C. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that 29W222T and 2943T represented members of the genus Fulvivirga and strain 29W222T was most closely related to Fulvivirga kasyanovii KMM 6220T (97.9 % sequence similarity) and Fulvivirga imtechensis AK7T (95.0 %), and 2943T to Fulvivirga imtechensis AK7T (95.7 %) and Fulvivirga kasyanovii KMM 6220T (94.8 %). The genomic DNA G+C contents of 29W222T and 2943T were 39.9 and 37.7 mol%, respectively. The results of chemotaxonomic analysis indicated that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acid was iso-C15 : 0 for both strains. Average nucleotide identity and average amino acid identity values between strain 29W222T and Fulvivirga kasyanovii KMM 6220T were 78.9 and 83.6 %, respectively; the corresponding values between 2943T and Fulvivirga imtechensis AK7T were 69.8 and 63.6 %, respectively. Therefore, strains 29W222T and 2943T represent to two novel species of the genus Fulvivirga , for which the names Fulvivirga marina sp. nov. (29W222T=KCTC 62848T=MCCC 1K05194T) and Fulvivirga sediminis sp. nov. (2943T=KCTC 62847T= MCCC 1K05144T) are proposed, respectively.

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Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment

Cited by 18 publications

References 27 publications

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

DNA-foraging bacteria in the seafloor

Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment

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