Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation - PubMed (original) (raw)

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

Barbara Bayer et al. ISME J. 2016 May.

Abstract

Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Phylogenetic tree of concatenated 16S–23S rRNA genes from cultivated Thaumarchaeota with sequenced genomes (16 organisms) showing the affiliation of strains D3C and NF5. Full-length gene sequences were aligned with MAFFT (L-INS-I method) based on Archaea-specific structurally accurate seed alignments (1474 and 3026 aligned positions for 16S and 23S rRNA genes, respectively), and unreliable positions were filtered from the resulting alignments with TCS before concatenation (4443 aligned positions in the concatenated alignment). The tree was calculated by maximum likelihood with IQ-Tree based on the GTR+I+Γ4 model, with ultrafast bootstrap (UFBoot) and SH-aLRT support values inferred from 1000 replicates each (see Supplementary materials and methods for details). Support values ⩾85% are represented on the respective branches by semi-circles color-coded as indicated on the figure.

Figure 2

Figure 2

Transmission electron microscopy (a, b) and scanning electron microscopy (c, d) images of strains NF5 (left) and D3C (right).

Figure 3

Figure 3

Typical growth curve of strains D3C (a) and NF5 (b) in medium containing 1 m

m

NH4Cl. Triangles: NH4+ concentrations, full circles: NO2− concentrations, open circles: cell abundances. Error bars represent standard deviations of measurements from triplicate cultures.

Figure 4

Figure 4

Growth of strains D3C and NF5 in medium supplemented with 0.5 m

m

urea. Open circles: cell abundances, full circles: NO2− production. Error bars represent standard deviations of measurements from triplicate cultures.

Similar articles

Cited by

References

    1. Abraham W-R, Rohde M. (2014). The family Hyphomonadacaea. In: The Prokaryotes. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). Springer-Verlag: Berlin, Heidelberg, 4: 283–297.
    1. Alonso-Saez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL et al. (2012). Role for urea in nitrification by polar marine Archaea. Proc Natl Acad Sci USA 109: 17989–17994. - PMC - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215: 403–410. - PubMed
    1. Aoshima M, Ishii M, Igarashi Y. (2004. a). A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol Microbiol 52: 751–761. - PubMed
    1. Aoshima M, Ishii M, Igarashi Y. (2004. b). A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol Microbiol 52: 763–770. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources