Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

Speth, Daan R.; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei‐Yuan; Dutilh, Bas E.; Jetten, Mike S. M.

doi:10.1007/s00248-017-0929-7

Cited by 69 publications

(30 citation statements)

References 36 publications

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“…The genome shares less than 90% 16S rRNA sequence identity and 74-81% of genomic ANI (average nucleotide identity) with previously characterized Scalindua species from other marine habitats, including Ca . S. rubra 20 and Ca. S. AMX11 21 from seawater, Ca.…”

Section: Main Textmentioning

confidence: 99%

In situgrowth of anammox bacteria in subseafloor sediments

Zhao

Mogollón

Abby

et al. 2019

Preprint

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The deep biosphere buried in marine sediments was estimated to host an equal number 18 of microbes as found in the above oceans 1 . It has been debated if these cells are alive 19 and active 2 , and their per cell energy availability does not seem to allow for net 20 population growth 3 . Here, we report the growth of anammox bacteria in ~80,000 year 21 old subsurface sediments indicated by their four orders of magnitude abundance 22 increase in the nitrate-ammonia transition zone (NATZ). Their growth coincides with a 23 local increase in anammox power supply. The genome of the dominant anammox 24 bacterium from the NATZ was reconstructed and showed an increased index of 25 replication confirming in situ active growth. The genome belongs to a new Scalindua 26 species so far exclusively found in marine environments, which has the genetic capacity 27 of urea and cyanate utilization and is enriched in genes allowing it to cope with external 28 environmental stressors, such as energy limitation. Our results suggest that specific 29 microbial groups are not only able to survive over geological timescales, but also thrive 30 in the deep subsurface when encountering favorable conditions. 31 32 Main text 33 The global cell numbers of microbes in marine sediments is estimated to be on the order of 34 2.9-5.4×10 29 equaling up to 1/3 rd of the total prokaryotic biomass on Earth 1,4 . A considerable 35 portion of these cells reside beyond the bioturbation zone and constitute the marine deep 36 biosphere 5 . Microbial cells in the subseafloor sediments are sealed off from recruitment of 37 new cells and fresh substrates from the surface, and therefore are thought to suffer severe 38 energy limitations 3 . Despite this, several lines of circumstantial evidence indicate that the 39 deep microbial biosphere is alive 6,7 , but with extremely slow metabolic rates 8,9 and long 40 turnover times of hundreds to thousands of years 2,10 . Although microbial growth (net biomass 41 production) was frequently assumed 10,11 and recently observed in laboratory incubations 12 , 42 concrete evidence of in situ microbial growth in the marine deep biosphere is lacking. 43Energy availability is considered one of the most fundamental factors limiting life, but 44 has not been explicitly demonstrated to control the changes of microbial communities in the 45 deep biosphere 13 . Whereas the deep sedimentary realm is a stable environment with low 46 energy availability, geochemical transition zones such as the sulfate-methane transition 47 growth associated with increased power availabilities in ~ 80,000 year old subsurface 55 sediments. 56 We retrieved four sediment cores (2.0-3.6 meters long) from the seabed of the Arctic 57 Mid-Ocean Ridge (AMOR) at water depths of 1653 -3007 m ( Fig. 1a and Table S1), to 58 perform high vertical resolution geochemical measurements and microbiological analyses. All 59 four cores exhibited similar geochemical profiles ( Fig. 2a-c), summarized as follows: 1) O 2 60 monotonically decreased and was deplet...

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Section: Main Textmentioning

confidence: 99%

In situgrowth of anammox bacteria in subseafloor sediments

Zhao

Mogollón

Abby

et al. 2019

Preprint

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“…S. brodae from a wastewater plant [18], and Ca. S. rubra from a marine brine pool [19]. These large genomes (>4000 genes;~4-5.2 Mbp) contain many genes absent from characterized genomes of other anammox genera, but also vary in gene content among species.…”

Section: Introductionmentioning

confidence: 99%

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

et al. 2018

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Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.

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“…The genomic nitrogen cycling potential in the river sediment was in general low. In this analysis we corrected for sequencing depth and gene length, however we could not correct for gene copy number since for many microorganisms this is not yet known, for example the gene hao can have up to ten different copies in anammox bacteria (Van de Vossenberg et al , 2013; Speth et al , 2017). At the pristine site ammonium oxidation ( amoA, nxr ) and denitrification genes ( nar, nir, nor, nos ) were more abundant N-cycle processes, whereas ammonification ( nrf ) seemed more important in S6.…”

Section: Discussionmentioning

confidence: 99%