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Chapter 12 : Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria

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Abstract:

A comprehensive biological understanding of nitrite-oxidizing bacteria (NOB) will be important to improve the functional stability of wastewater treatment systems and to reduce detrimental effects of nitrification in agriculture. The first part of this chapter provides an overview of the phylogenetic diversity and distribution of NOB in the environment and in engineered systems. Subsequently, the chapter focuses on the ecophysiology and ecological niche differentiation of the genera and . The third part of this chapter addresses most recent insights into the biology of , which are based on the first sequenced genome from this genus. Future research should clarify whether strains indeed are ecophysiologically different and how their diversity influences ecosystem functioning. The chapter also provides an overview of selected metabolic characteristics of ‘’ Nitrospira defluvii’’ as derived from the genomic data. Nevertheless, the microbial genome could be sequenced by using an environmental genomics approach that had been developed for sequencing an uncultured anaerobic ammonium-oxidizing bacterium. Although the phylogeny, might be blurred by past lateral gene transfer events, it is tempting to speculate that the aerobic nitrite-oxidizing system of was derived from an anaerobic protein complex and that the ancestor of was adapted to life under hypoxic conditions. The distant relationship between the NxrA forms of and those of and suggests that the use of nitrite as an energy source was invented more than once in the course of bacterial evolution.

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12

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Image of FIGURE 1
FIGURE 1

Phylogenetic tree, based on 16S rRNA gene sequences, showing the phylogenetic affiliations of the currently known NOB to selected ammonia-oxidizing and nonnitrifying bacteria. Names of nitrite oxidizers are printed bold. Database accession numbers are indicated for all 16S rRNA gene sequences. Arcs delimit bacterial phyla. The inset shows the phylogeny within the genus , which is condensed to a single branch in the large tree. The stippled line at the branch indicates the uncertain phylogenetic affiliation of this genus. The tree topology was determined by maximum likelihood analysis of the sequences and by using a 50% sequence conservation filter for the . The scale bars indicate 0.1 (large tree) or 0.01 (inset) estimated change per nucleotide.

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
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Image of FIGURE 2
FIGURE 2

Phylogenetic tree, based on 16S rRNA gene sequences, showing the phylum . Shaded regions delimit the nitrite-oxidizing sublineages I to VI and the non-nitrifying and - groups. Unshaded sequences between sublineage IV and cannot yet be assigned to any genus, and the physiology of the respective organisms is unknown. Unshaded sequences within the genus cannot be assigned to one of the sublineages by using the criteria proposed by . Database accession numbers are indicated for all 16S rRNA gene sequences. The tree topology was determined by maximum likelihood analysis of the sequences and by using a 50% sequence conservation filter for the genus . The scale bar indicates 0.1 estimated change per nucleotide.

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
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Image of FIGURE 3
FIGURE 3

Numbers of sequence reads that were obtained from the metagenome of a nitrifying activated sludge and had a high sequence similarity to genomes of nitrifying bacteria. The number of reads indicated for the includes all reads obtained for plus the reads obtained for other members of the (refer to the main text for details). Note that the scaling of the axis is logarithmic.

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
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Image of FIGURE 4
FIGURE 4

Phylogenetic tree, based on protein sequences, showing selected alpha subunits from the DMSO reductase family of molybdopterin-containing enzymes. Sequences of nitrite oxidoreductase alpha subunits (NxrA) of NOB are printed in boldface. Database accession numbers are indicated for all protein sequences. The tree topology was determined by maximum likelihood analysis of the sequences of the molybdopterin- and [Fe-S]-binding domains and by excluding N-terminal signal peptides. Protein subunit names indicate the functions of the respective enzymes: NarG, dissimilatory membrane-bound nitrate reductase; NxrA, nitrite oxidoreductase; PcrA, perchlorate reductase; SerA, selenate reductase; ClrA, chlorate reductase; DdhA, dimethyl sulfide dehydrogenase; EdbH, ethylbenzene dehydrogenase; put., putative; n.d., function not determined. (Figure courtesy of Frank Maixner.)

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
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Image of FIGURE 5
FIGURE 5

Phylogenetic tree, based on protein sequences, showing ribulose-1,5-bisphosphate carboxylase (RubisCO) of selected organisms. Arcs delimit RubisCO forms I to IV. Black dots indicate a high parsimony bootstrap support (>90%, 100 iterations) for the respective tree branches. Names of nitrifying bacteria are printed in boldface. The tree topology was determined by Fitch-Margoliash analysis of the sequences (with global rearrangement and randomized input order [seven jumbles]). The scale bar indicates 0.1 estimated changes per residue.

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
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Tables

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TABLE 1

Selected characteristics of known sublineages

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12
Generic image for table
TABLE 2

Selected features of the “ Nitrospira defluvii” genome

Citation: Daims H, Lücker S, Le Paslier D, Wagner M. 2011. Diversity, Environmental Genomics, and Ecophysiology of Nitrite-Oxidizing Bacteria, p 295-322. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch12

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