The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium
Citations
946 citations
Cites background from "The metagenome of the marine anammo..."
...…study (20 sequences out of 21) were part of one cluster (cluster 1, Figure 3) closely related to nirS sequences of “Candidatus Scalindua profunda” (van de Vossenberg et al., 2013), and of uncultured bacteria obtained from continental margin sediment of the Arabian Sea (Sokoll et al., 2012) and…...
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430 citations
Cites background from "The metagenome of the marine anammo..."
...Meanwhile, the partial genome of B. fulgida was described (Gori et al., 2011), followed by the recent publication of the genome of the marine species S. profunda (Van de Vossenberg et al., 2012)....
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...In the S. profunda assembly (4664 ORFs), for instance, only 693 genes had significant BLASTN hits with K. stuttgartiensis (Van de Vossenberg et al., 2012)....
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...Within these biofilm aggregates, the microorganisms are associated with a variety of other very diverse species (e.g. Strous et al., 2006; Van de Vossenberg et al., 2012)....
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...On the other hand, the S. profunda genome contains two putative citrate synthase genes (scal03477 and scal01583) (Van de Vossenberg et al., 2012)....
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...In striking contrast, NirS is one of the most abundant proteins in S. profunda (Van de Vossenberg et al., 2012)....
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369 citations
Cites background from "The metagenome of the marine anammo..."
...Transcripts of these aerobic organisms, however, are essentially absent in the core of the open-ocean AMZ at 200 m, where sequences matching the anammox bacterium “Candidatus Scalindua profunda” (30) are prominent (Fig....
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284 citations
Cites background from "The metagenome of the marine anammo..."
...…and John Wiley & Sons Ltd, Environmental Microbiology ‘Ca. Kuenenia’ (Strous et al., 2006; Speth et al., 2012), ‘Ca. Brocadia’ (Gori et al., 2011; Oshiki et al., 2015), ‘Ca. Jettenia’ (Hira et al., 2012; Hu et al., 2012b) and ‘Ca. Scalindua’ (van de Vossenberg et al., 2013; Speth et al., 2015)....
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...Genes responsible for the TCA cycle are also species specific, and a complete gene set, including citrate synthase and citrate lyase, was only found in the ‘Ca. Scalindua profunda’ and ‘Ca. Scalindua brodae’ genomes (van de Vossenberg et al., 2013; Speth et al., 2015)....
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269 citations
References
63,427 citations
"The metagenome of the marine anammo..." refers methods in this paper
..., 2005), CLUSTALW (Thompson et al., 1994) and Muscle (Edgar, 2004)....
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...Alignments of proteins were done with ProbCons (Do et al., 2005), CLUSTALW (Thompson et al., 1994) and Muscle (Edgar, 2004)....
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37,524 citations
"The metagenome of the marine anammo..." refers methods in this paper
...Alignments of proteins were done with ProbCons (Do et al., 2005), CLUSTALW (Thompson et al., 1994) and Muscle (Edgar, 2004)....
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9,397 citations
"The metagenome of the marine anammo..." refers methods in this paper
...Data obtained by additional metagenome sequencing and de novo assemblies with different programs and parameters, and automated annotated with RAST (Aziz et al., 2008), were used to confirm gene sequences and lengths....
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6,757 citations
"The metagenome of the marine anammo..." refers methods in this paper
...The arb package was used to accurately determine the phylogenetic position of assembled rRNA sequences longer than 1200 bp (Ludwig et al., 2004)....
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6,492 citations
"The metagenome of the marine anammo..." refers methods in this paper
...The S. profunda genome has four genes encoding transporter proteins from the Formate/Nitrite Transporter (FNT) family (Saier Jr et al., 1999), FocA/NirC, with six predicted membrane spanning helices, but no apparent predicted signal peptide (SignalP)....
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...Signal peptides were predicted with SignalP (Bendtsen et al., 2004), transmembrane helices with TMHMM (Sonnhammer et al., 1998)....
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