Chapter 7 : Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments

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One of the major challenges in studying microorganisms from natural habitats is the inability to cultivate many of them in the laboratory. Recently, the complete genome sequence of was determined from a metagenomic library providing further insights into the potential physiological properties of uncultured ammonia-oxidizing archaea (AOA). The genes of ammonia-oxidizing bacteria (AOB) and AOA are distantly related, and molecular approaches to study the distribution and diversity of ammonia oxidizers rely on specific PCR primers that amplify the archaeal A or the bacterial A variant. Nitrification is an important process in sedimentary biogeochemistry and particularly in estuarine sediments, which can be exposed to high loads of nutrients from agricultural runoff. There is now unambiguous evidence for the occurrence of AOA in environments of elevated temperature. The mechanisms by which soil pH influences the growth and activity of many microbial functional groups have been determined through a combination of physiological and soil microcosm studies. With their involvement in ammonia oxidation, the majority of mesophilic crenarchaeota (or thaumarchaeota) are most likely major players in biogeochemical cycling. Most studies that attempted to evaluate the actual activity of AOA (and bacteria) seem to reveal that there could, in fact, be an ecological niche differentiation between AOA and AOB.

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 1

Phylogenetic analysis of crenarchaeal 16S rRNA gene sequences recovered from marine and terrestrial environments together with cultivated AOA and hyperthermophiles. Sequence names in bold represent cultivated organisms or genomic fragments containing both 16S rRNA and AMO subunit genes. Lineages with a bold arc represent those known to have associated AMO subunit genes. Dashed lines at multifurcating nodes indicate manual adjustment reflecting low bootstrap support for any relative branching order. The scale bar represents an estimated 0.05 changes per nucleotide position, and numbers at nodes indicate the most conservative value of bootstrap support from three treeing methods.

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 2

Phylogenetic analysis showing the diversity of AMO subunit A genes associated with archaea and the environments from which they were obtained. The height and length of each triangle is proportional to the number of taxa included in this analysis and maximum individual branch length, respectively. The scale bars represent an estimated 0.05 changes per nucleotide position, and numbers at nodes indicate the most conservative value of bootstrap support from three treeing methods. (From , with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 3

Analysis of a soil depth profile of a sandy ecosystem (Rotböll, Darmstadt, Germany). Absolute numbers of genes of archaea and bacteria quantified by qPCR and phylogenetic analysis illustrating the relatedness of AOA sequences retrieved from two depths (0 to 10 and 60 to 70 cm) are shown. The clustering of sequences from the same depth demonstrates the presence of populations adapted to specific conditions within the soil profile. (Adapted from data obtained by Leininger et al., 806–809, 2006, with permission from Macmillan Publishers, Ltd.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 4

Distribution of inorganic nitrogen, ammonia oxidation rates, and archaeal and 16S rRNA genes in a 100 m vertical profile in Guaymas Basin, Gulf of California. Areas of active nitrification and correlation with crenarchaeal/AOA numbers and NH ammonia oxidation rates are highlighted between dotted lines. (From Beman et al., 429–441, 2008, with permission from Macmillan Publishing, Ltd.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 5

Growth of acetylene-sensitive AOA in nitrifying soil microcosms. (A) Denaturing gradient gel electrophoresis (DGGE) analysis of AOA communities after PCR amplification of genes. Each lane represents an individual microcosm. The arrow indicates the growth of a specific population of AOA in control microcosms only (no acetylene). (B) Demonstration of complete inhibition of ammonia-oxidizing activity in microcosms with a 10 Pa acetylene headspace partial pressure. (C) qPCR assay specific for the AOA population highlighted in the DGGE profile. Growth of the AOA occurred only in those microcosms with active nitrification. (Adapted from data obtained by Offre et al., 99–108, 2009, with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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Image of FIGURE 6

Abundances of AOB and AOA in nitrifying soil mesocosms amended with fertilizer and various amounts of the antibiotic sulfadiazine. genes were quantified by qPCR. Dark gray bars, 0 mg of sulfadiazine (kg of soil) added; light gray bars, 10 mg kg added; open bars, 100 mg kg added. While both AOA and AOB communities increased in size upon fertilization, the AOA population was less sensitive to sulfadiazine and thus was probably responsible for most of the ammonia oxidation measured after antibiotic treatment. Note the large numbers of archaea compared with AOB (different scales in the figure). (From Schauss et al., 446–456, 2009, with permission.)

Citation: Nicol G, Leininger S, Schleper C. 2011. Distribution and Activity of Ammonia-Oxidizing Archaea in Natural Environments, p 157-178. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch7
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