DNA-foraging bacteria in the seafloor

Abstract

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

Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology

“…contribute to the biogeochemical cycling of deep biosphere 4,15 . Unfortunately, up to date, there is no any available pure culture of Izimaplasma bacteria, which seriously hinders the accurate determination of their features such as growth, metabolism, physiology and ecology.…”

“…5e and 5f), which might be due to the deficiency of organic nutrients in the deep-sea environment. Instead, strain zrk13 could be able to maintain a good growth status mainly by digesting DNA to obtain energy for supporting growth given its strong DNA degradation capability and the ubiquitous existence of extracellular DNA in the deep-sea sediments 15,23 .…”

“…Among the free-living Tenericutes identified in the marine environments, Candidatus Izimaplasma was mainly studied based on the enrichment and corresponding assembled genomes given the absence of pure cultures 4,15 . Candidatus Izimaplasma was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes 4 , and an intermediate in the reductive evolution from Firmicutes to Mollicutes 4 .…”

“…Candidatus Izimaplasma was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes 4 , and an intermediate in the reductive evolution from Firmicutes to Mollicutes 4 . Members of the Izimaplasma are thought to be heterotrophs engaging primarily in fermentative metabolism 4 , and thereby producing lactate and possibly other small molecules such as acetate or ethanol, which in turn may be utilized by other members of the cold seep 15 . Notably, based on their genomic analysis, Candidatus Izimaplasma bacteria are believed to be important DNA degraders 4,15 .…”

“…Members of the Izimaplasma are thought to be heterotrophs engaging primarily in fermentative metabolism 4 , and thereby producing lactate and possibly other small molecules such as acetate or ethanol, which in turn may be utilized by other members of the cold seep 15 . Notably, based on their genomic analysis, Candidatus Izimaplasma bacteria are believed to be important DNA degraders 4,15 . Recent studies have shown high concentrations of extracellular DNA in marine sediments from shallow depths down to the abyssal floor 16–18 .…”