Skip to main content

Advertisement

Ecological Processes
Ecological Processes Cover Image

You are viewing the new article page. Let us know what you think. Return to old version

Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands

Ecological Processesvolume 2, Article number: 9 (2013) | Download Citation

Abstract

Introduction

Biological soil crusts (BSCs) can dominate surface cover in dry lands worldwide, playing an integral role in arid land biogeochemistry, particularly in N fertilization through fixation and cycling. Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself. The contribution of ammonia-oxidizing bacteria (AOB) in BSCs has been shown, but the role and extent of the recently discovered ammonia-oxidizing archaea (AOA) have not.

Methods

We sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene, which codes for the ammonia monooxygenase enzyme, universally present in ammonia-oxidizing microbes.

Results

All archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota (Nitrososphaera associated Group I.1b). Sequences from the Sonoran Desert, Colorado Plateau, and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert. Based on amoA gene abundances, archaeal and bacterial ammonia oxidizers were ubiquitous in our survey, but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern, cooler deserts to archaeally dominated in southern, warmer deserts.

Conclusions

Archaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling. Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB, possibly driven by temperature.

Introduction

Plant inter-spaces in arid lands are typically colonized by biological soil crusts (BSCs), which in some areas can cover large portions of the landscape (Belnap1995; Pointing and Belnap2012). Pioneering cyanobacteria, such as Microcoleus vaginatus, initiate the formation of BSCs by stabilizing loose soils (Garcia-Pichel and Wojciechowski2009), allowing a succession that involves other bacteria (Garcia-Pichel et al.2001; Gundlapally and Garcia-Pichel2006; Nagy et al.2005), archaea (Soule et al.2009), and fungi (Bates and Garcia-Pichel2009; Bates et al.2012), as well as lichens and mosses in well-developed crusts (Belnap and Lange2003). Functional roles for the majority of nonphototrophic microbes inhabiting BSCs are not known, however, and remain to be established experimentally.

BSC topsoil assemblages are considered “mantles of fertility” (Garcia-Pichel et al.2003) as they play important roles in biogeochemical processes within arid ecosystems (Belnap and Lange2003; Evans and Johansen1999; Strauss et al.2012), fixing an estimated 0.1 Pg of C and 10 Tg of N annually across the globe (Elbert et al.2012). Nitrification (with ammonia oxidation as its rate-limiting step) mediated by BSC microbes is another important component of arid land nutrient cycling that directly impacts soil fertility and rivals N-fixation in its magnitude (Johnson et al.2005). Nitrifiers, such as Nitrosospira, have been recovered from BSCs in molecular surveys, and most probable number assessments suggest ammonia-oxidizing bacteria (AOB) are numerically abundant in BSCs (Gundlapally and Garcia-Pichel2006; Johnson et al.2005). Although archaea are likely important soil ammonia oxidizers (Leininger et al.2006; Zhang et al.2010; Bates et al.2011; Stahl and de la Torre2012) and sizable archaeal populations have been reported from BSCs (Soule et al.2009), little is known about the role of archaea in the arid land N-cycle.

Recent research has improved our understanding of factors that drive the dynamics between archaeal and bacterial ammonia oxidizers in soils. For example, alkaline soils and lower NH4+ concentrations may favor some ammonia-oxidizing archaea (AOA) over their bacterial counterparts (Gubry-Rangin et al.2011; Martens-Habbena et al.2009). Although desert soils are typically characterized by these conditions, few studies have specifically examined AOA in BSCs or the factors that structure communities of N-cycling microbes in arid lands (e.g., Johnson et al.2005,2007; Marusenko et al.2013). As approximately one-third of the terrestrial surface is arid or semi-arid land, and BSC cover can be substantial, understanding the dynamics of nitrification mediated by crust microbes has relevance to the global N-cycle.

Considering the potential for archaea to play an important role in arid land nitrification as ammonia oxidizers, we assessed the diversity and abundance of archaeal amoA genes in BSCs within four biogeographically distinct deserts in the western United States. For comparison, we quantified the abundance of bacterial amoA genes and estimated the portion of AOA and AOB in these BSC microbial communities using published determinations of archaeal 16S rRNA genes from the same samples (Soule et al.2009). We also examined the role of environmental factors, particularly those associated with latitudinal gradients, in structuring these communities of crust ammonia oxidizers.

Methods

Sampling and DNA extraction

We sampled different crust types (e.g., those dominated by cyanobacteria, lichen, or moss) in a variety of geographically dispersed sites (Figure 1, Additional file1) across four distinct desert systems in the western United States, including the Great Basin, Colorado Plateau, Chihuahuan Desert, and Sonoran Desert (listed in order of increasing temperature; Belnap and Lange2003). The mean annual temperature across the four desert regions sampled ranged from 4°C to 22°C. These crust samples were previously characterized for archaeal diversity (Soule et al.2009) based on 16S rRNA genes. For sampling, the bottom portion of a 55 mm Petri plate was used to excise a circular portion of the crust matrix (to a depth of ~ 1 cm) after wetting with a mist of sterile ultra-pure milli-Q water in order to make the crust supple to facilitate collection. All samples were allowed to air-dry, given a unique identification number, sealed in Zip-lock plastic bags for transport, and then stored dry in the lab’s repository at room temperature, as recommended for arid land soil samples (Campbell et al.2009), until DNA extraction. Approximately 1 g of the crust matrix was aseptically transferred to microcentrifuge vials of the Ultra Clean Soil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA), and standard protocols were used in DNA extraction following the kit instructions. All extracts were stored at −80°C until use in downstream applications.

Figure 1
figure1

Map of study sites in arid lands of western North America. Legend grayscale shows elevation of the terrain (meters).

Full size image

Clone libraries and phylogeny of amoA genes

Clones were obtained from PCR products of community DNA using the amoA primers (position 4–23 and 619–638) and protocol described by Francis et al. (2005). Primers designed to hybridize at the ends of the amoA gene are good options for general assays and have been successfully used for soils (Chen et al.2008; Mao et al.2011; Nicol and Prosser2011). One clone library was constructed for each desert region by pooling extracts from at least 10 individual sites. All PCR products were checked for quality against an EZ Load Precision Molecular Mass Ruler (Bio-Rad Laboratories, Hercules, CA, USA) on 1% agarose gels (with a TAE buffer base) by standard gel electrophoresis, followed by ethidium bromide staining and imaging using the Fluor-S MultiImager system (Bio-Rad Laboratories). Products were then purified for ligation using the QIAquick PCR Purification Kit (Qiagen Sample and Assay Technologies, Valencia, CA, USA) prior to constructing the libraries using the TOPO TA Cloning Kit (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s specifications. Cloning and transformation success were verified through PCR with 1 μl of clone-containing media as the template DNA. The clones obtained were then sequenced in the forward and reverse directions at a commercial laboratory.

Phylogenetic analyses were carried out on a single alignment file that included amoA gene sequences from our clone libraries (one representative sequence from each amoA phylotype that was recovered from the four deserts) as well as reference groups of AOA retrieved from GenBank and originating from previous studies (Venter et al.2004; Konneke et al.2005; Hallam et al.2006; Hatzenpichler et al.2008; de la Torre et al.2008; Walker et al.2010; Park et al.2010; Tourna et al.2011; Matsutani et al.2011; Jung et al.2011; Blainey et al.2011; Lehtovirta-Morley et al.2011; Santoro and Casciotti2011; French et al.2012; Mosier et al.2012). Additionally we included 3,619 high-quality sequences from the Dryad data repository (see sequence quality filtering by Fernandez-Guerra and Casamayor2012a). All sequences were combined and realigned using MAFFT (Katoh et al.2002) and analyzed with the phylogenetic tree building module of the MEGA 5 software package with the following parameters: neighbor-joining statistical method, Jukes-Cantor nucleotide substitution model, bootstrapping for 100 replicates, uniform rates, and complete deletion of gaps/missing data (Tamura et al.2011). Representative sequences of novel archaeal amoA genes from each of the deserts have been submitted to GenBank (NCBI accession numbers: Sonoran, EU439775; Great Basin, EU439776; Colorado Plateau, EU439777; Chihuahuan, EU439778).

Quantitative PCR of archaeal and bacterial amoA genes

For use in quantitative PCR (qPCR), we developed archaeal-specific amoA primers based on sequences obtained from our clone library work (those known to be present in our BSC samples) as well as those available in public databases. These primers, amoA310f (5′-TGGATACCBTCWGCAATG-3′) and amoA529r (5′-GCAACMGGACTATTGTAGAA-3′), were designed to yield PCR products of approximately 220 bp, of optimal length for qPCR. This primer set was then used for qPCR in 20 μl reactions that contained the following: 10 μl iTaq SYBR Green Master Mix (Bio-Rad Laboratories), 300 nM amoA310f/amoA529r, and 10 ng of environmental DNA. The reaction conditions had an initial denaturation step of 2.5 min at 95°C followed by 55 cycles of 15 s at 95°C and 1 min at 54°C, and a final dissociation step later used to check the fidelity of the qPCR results. For quantification, a standard curve (log-linear R2 > 0.97) was generated using a purified, linearized, and quantified archaeal amo A clone plasmid in a dilution series that spanned from 101 to 109 gene copies per reaction.

Bacterial amoA qPCR was carried out in 20 μl reactions using primers amoA-1f and amoA-2r (Rotthauwe et al.1997) at a final concentration of 500 nM, along with 10 μl iTaq SYBR Green Master Mix and 10 ng of environmental DNA. The reaction conditions were as follows: initial denaturation for 2.5 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 55°C, and a final dissociation step. A standard curve for quantification (log-linear R2 > 0.95) was generated using genomic DNA from Nitrosomonas europaea ATCC 19718 (Chain et al.2003) in a dilution series that spanned from 101 to 109 gene copies per reaction.

Multiple measures were taken to ensure quality qPCR data. All reactions for both archaeal and bacterial amoA qPCR runs were carried out in triplicate to account for analytical variability. Triplicates were averaged prior to any data calculations reported in the results. Melting curves obtained in the denaturation step were visually inspected to verify the quality of each reaction and to insure the absence of primer-dimers. Reported results contain only determinations for which Ct values could be interpolated within our standard curves, and failed or suspect reactions (those with questionable melting curves) were excluded from the data set.

Data analyses

We downloaded environmental data from the Commission for Environmental Cooperation for elevation and climate (years 1950–2000; CEC,http://www.cec.org) and used ArcGIS version 10.1 to extract exact values (for environmental data) corresponding to coordinates from the sites used in this study (Additional file1). Canonical correspondence analysis (CCA; Ter Braak1986; Palmer1993) was used in the Palaeontological Statistics (PAST; Hammer et al.2001; Fu et al.2006) software package to explore associations between environmental factors [e.g., mean annual temperature (MAT) and mean annual precipitation (MAP)] and the dependent variables. The three dependent variables used were amoA gene abundances (archaeal, bacterial) and the archaeal to bacterial amoA ratio.

Statistical tests were carried out using SPSS (version 20.0 for Windows). Linear model assumptions were tested using Shapiro-Wilk and SPSS normal probability plots (for normality) and Levene’s test (for homoscedasticity), and data were transformed (natural log) when necessary. Bivariate Pearson correlation and linear regression analyses were performed to assess significance of relationships between amoA data and environmental factors throughout the four desert regions (Hocking1976). Significant differences of regression slopes across environmental gradients in replicated data for gene copy numbers were analyzed as a multiple linear regression (multiple dependent variables, one independent variable). Due to co-correlation of external factors (latitude positively correlated with elevation and MAP, and negatively with MAT), regressions were carried out separately for each independent variable to assess the potential effect of each variable without being able to interpret the combined effects of multiple variables (Smith et al.2009). The sets of dependent variables were archaeal amoA, bacterial amoA, ratio of archaeal to bacterial amoA, separately for the simple linear regression, and archaeal amoA vs. bacterial amoA in the multiple regression.

Results

Diversity and phylogeny of archaeal amoA genes of BSCs

To obtain a geographically integrated survey of the diversity in archaeal amoA genes, we analyzed clone libraries representing each of the four distinct desert systems across the western U.S. (Chihuahuan, Great Basin, Colorado Plateau, and Sonoran). Analysis of clone libraries, with more than 40 clones in each desert, revealed that monophyletic amoA gene populations corresponding to each desert region exist in arid land BSCs: only a single archaeal amoA phylotype was recovered from each desert (98.5–100% nucleotide similarity). Phylogeny (Figure 2) of the four representative sequences revealed that phylotypes from three of the deserts (Great Basin, Sonoran, and Colorado Plateau) were indistinguishable, grouping in a well-defined clade (>95% similarity, 76% bootstrap support), while a lone sequence type (representing the Chihuahuan Desert) was distinct (only 81% similarity to other amoA gene sequences obtained from BSCs). All four phylotypes, however, are part of the Group I.1b Nitrososphaera cluster as identified by Pester et al. (2012). The Chihuahuan Desert sequence grouped near sequences representing Nitrososphaera subcluster 2, closely related to the amoA gene of N. viennensis (Tourna et al.2011; the only pure thaumarchaeotal isolate from soil), while the other three desert phylotypes were most closely related to Nitrososphaera subclusters 6 and 11.

Figure 2
figure2

Phylogenetic tree of archaeal amoA gene sequences. Data were obtained from clone libraries of genomic community DNA isolated from biological soil crust samples in this study (indicated by an asterisk *), as well as reference sequences from GenBank for species of amoA-encoding archaea that have been characterized. Without clustering, these sequences were combined and realigned with 3,619 high-quality sequences from GenBank (Fernandez-Guerra and Casamayor 2012). Dashed lines connect the identified sequences to the position in the tree. Bracketed clustering groups are based on designations at multiple phylogenetic levels within the Thaumarchaeota as proposed by Pester et al. (2012).

Full size image

Abundance of archaeal and bacterial amoA genes of BSCs

Population densities of putative ammonia oxidizers were assayed through qPCR of amoA genes from the four arid regions. Archaeal amoA copy numbers average around 7 × 105 per gram of soil (332 copies per ng DNA) across all desert sites (Table 1), whereas their bacterial counterparts averaged only slightly (and nonsignificantly) below this value at 3 × 105 (154 copies per ng DNA). The sizes of the AOA populations in BSCs were more variable than those of AOB, with densities of archaeal amoA genes ranging over three orders of magnitude in individual sites within each desert (ca. five orders of magnitude across all deserts), and bacterial amoA genes ranging over only one to two orders of magnitude (ca. three orders of magnitude across all deserts). More notably, the average of the ratios for archaeal to bacterial amoA gene copy number for each desert (Table 2) were highest in the southernmost, warmer deserts (54.7 and 3.5 for Sonoran and Chihuahuan, respectively) as compared to the cold deserts of more northern latitudes (1.3 and 0.01 for Colorado Plateau and Great Basin, respectively).

Table 1 Population densities of ammonia-oxidizing microbes in biological soil crusts estimated by qPCR of amoA genes
Full size table
Table 2 Relative densities for ammonia-oxidizing microbial communities in biological soil crusts ( amoA or 16S genes)
Full size table

CCA revealed patterns between environmental factors and ammonia oxidizers across geographical provinces encompassed by the survey (trace p value < 0.01; Figure 3). Generally, the Sonoran Desert sites are associated with higher MAT, while those of the Great Basin and Colorado Plateau sites are more positively associated with elevation and MAP. Conditions associated with lower latitudes in our dataset (i.e., higher temperatures, lower elevation, lower precipitation) were negatively related to the size of the bacterial amoA population and positively related to both archaeal amoA and the ratio of archaeal to bacterial amoA.

Figure 3
figure3

Canonical correspondence analysis (CCA) across all study sites. The dependent variables (ammonia-oxidizing gene abundance and community data) ordinate along a gradient that is driven by vectors related to the independent variables (environmental factors). AOA/AOB, ratio of archaeal to bacterial amoA; MAT, mean annual temperature; MAP, mean annual precipitation; c, Chihuahuan Desert; p, Colorado Plateau; g, Great Basin; and s, Sonoran Desert.

Full size image

Correlation and regression approaches clearly confirmed distinct relationships between archaeal and bacterial amoA gene abundances of BSCs and specific environmental factors across the four deserts (Table 3). For example, archaeal amoA abundance was most strongly correlated with latitude (r = −0.53, p = 0.001). Bacterial amoA abundance, on the other hand, was most strongly correlated with elevation (r = 0.78, p < 0.001). Most revealing were the strong, significant correlations between the archaeal to bacterial amoA gene abundance ratio and a range of environmental factors: latitude, elevation, MAT, and MAP. These relationships translated into the general geographic trend of archaeal amoA gene abundance dominating over that of AOB in the warmer, more southern deserts, with AOB dominating in the more northern, colder deserts (Figure 4).

Figure 4
figure4

Relationship of archaeal to bacterial amoA ratio across all geographical locations. Ammonia-oxidizing community is correlated with (A) latitude and (B) mean annual temperature. Dotted line at y = 1 indicates division between archaeal vs. bacterial amoA dominance.

Full size image
Table 3 Results from correlation and multiple linear regression analyses for microbial communities in biological soil crusts
Full size table

Discussion

Our results show that archaeal amoA genes are conspicuously and widely represented in BSCs from several arid regions of North America, suggesting that archaea are potentially involved in the process of ammonia oxidation of these soil communities. In general, average AOA abundance in BSCs was 10- to 20-fold lower than in most other types of soils, with some overlap in range (He et al.2007; Leininger et al.2006), and less than 10-fold smaller as reported in few other environments (Chen et al.2008; Gleeson et al.2010; Zeglin et al.2011). Judged by the counts of amoA gene copies, AOA in fact outnumbered AOB when averaged over all sites.

The populations of amoA-bearing archaea are, however, of low diversity based on initial surveying in these systems using clone libraries, which mirrors the findings that archaeal diversity is also generally restricted in both bulk soils (Auguet et al.2010; Fernandez-Guerra and Casamayor2012) and in BSCs (Nagy et al.2005; Soule et al.2009). We note that most publicly available sequences that had high similarity (>97% at the nucleotide level) to those of BSCs from this study originated from terrestrial environments with source soils of relatively alkaline character (Leininger et al.2006; Shen et al.2008; Zhang et al.2009,2011; Liu et al.2010; Glaser et al.2010; Fan et al.2011). Because the number of samples analyzed is not exhaustive, we cannot assert with confidence that the two main amoA phylotypes found in BSCs in this study represent crust-specific lineages, although this remains a possibility to be explored further. Other studies have shown that certain AOA lineages have adapted to specific levels of pH (Gubry-Rangin et al.2010,2011). Arid lands are characteristically extreme environments exposed to intense UV radiation, limited availability of nutrients, alkaline soils, as well as distinct seasonal changes of long desiccation periods punctuated by pulsed precipitation events (Schlesinger1997; Safriel et al.2005), all of which may help carve separate niches for soil organisms (Wall and Virginia1999). AOA dynamics may be distinct and depend on the range of a certain environmental variable (e.g., temperature gradient in only alkaline soils) in different types of BSCs and other local conditions that affect crusts (Garcia-Pichel et al.2003; Pointing and Belnap2012). What seems clear is that crust-dwelling AOA are part of a broader consortium of archaea more related to the group I.1b Nitrososphaera cluster than to any other Thaumarchaeota group. All BSC amoA archaeal phylotypes were nested within a larger group that holds the sequence from the only pure culture isolate from soil capable of chemolithoautotrophic ammonia oxidation, Nitrososphaera viennensis (Tourna et al.2011).

Unexpected patterns of distribution emerged when AOA and AOB population size was related to geography. Variables that are associated with latitude become important predictors of amoA abundance. Since an AOA/AOB ratio of >10 (accounting for cell sizes, specific growth rates; Prosser and Nicol2012) suggests archaea outcompete bacteria in ammonia-oxidizing activities, such latitudinal factors likely structure communities and soil function across the dry lands surveyed here. Temperature was positively associated with AOA abundance and with the ratio of AOA/AOB, in support of other studies showing that AOA respond preferentially to elevated temperature in enrichment cultures (Kim et al.2012) and in soil microcosms (Tourna et al.2008), and correlate well with environmental temperature gradients (Bates et al.2011; Cao et al.2011), while some studies show negative or no response to temperature (Adair and Schwartz2008; Jung et al.2011). Together with our results, these findings suggest that temperature may be an important driver of niche separation for AOA, potentially leading to diverse ecosystem function responses that will depend on the magnitude of temperature change in the environment.

Based on previously reported qPCR determinations of 16S rRNA gene copy numbers for archaea from the same sample set (Soule et al.2009), AOA can account but for a small proportion of the extant total population of BSC archaea. Assuming the number of copies per cell for amo A (1 for archaea, 2.5 for bacteria) and 16S rRNA genes (1 for both archaea and bacteria) as can be inferred from known genome studies (Klappenbach et al.2001; Norton et al.2002; Hallam et al.2006; Blainey et al.2011), putative AOA represent only about ~5% of the archaeal populations present in BSCs across all deserts and as little as 0.03% on average for the Great Basin samples. Even when considering possible uncertainties in these estimates stemming from primer bias (Baker et al.2003; Agoguè et al.2008), our results are consistent with other soil environments globally (Lehtovirta et al.2009; Ochsenreiter et al.2003; Schleper and Nicol2010). This clearly implies that the bulk of archaeal populations in BSCs (particularly the few dominant crust phylotypes documented by Soule et al.2009) cannot be identified as AOA, leaving the functional role for the bulk of BSC archaea as undetermined. While archaea are potentially important for nitrification processes in arid lands, AOA must then be found among the rarer, possibly as yet to be detected, members of BSC microbial communities.

Conclusion

Microbial involvement in regulating the availability of usable forms of N and controlling productivity in pristine systems is critical for the ecosystem (Schimel and Bennett2004; van der Heijden et al.2008; Nannipieri and Eldor2009). BSCs of arid lands contain Thaumarchaeota that lose dominance to AOB with increasing latitude, from southern, warmer deserts to northern, colder climates. In some BSCs, AOB outnumber AOA by 100-fold, which to our knowledge is greater than any current report for soil environments where AOB dominate (e.g., Di et al.2009; Hallin et al.2009; Gleeson et al.2010), more closely resembling other types of ecosystems and conditions (estuary, Mosier and Francis2008; wastewater treatment bioreactor, Ye and Zhang2011). Niche differentiation plays a role amongst AOA and AOB communities in general (Gubry-Rangin et al.2011; Hatzenpichler2012), and the same may also be true for BSCs. The BSC system can be used in further research to elucidate novel aspects of ammonia oxidation and AOA, such as AOA capacity for mixotrophic growth and the potential for denitrifying ability (Bartossek et al.2010; Tourna et al.2011; Xu et al.2012). For example, phototrophic contributions in surface crusts create unique temporal and spatial gradients of pH, nitrogen, oxygen, and carbon availability (Garcia-Pichel and Belnap1996; Johnson et al.2007), which can be used to test AOA response at the microscale as well as across biogeographical regions. Overall, arid lands may provide further insight into environmental drivers of ammonia oxidation and community shifts of ammonia oxidizers, which has important implications for understanding nitrogen cycling at the global scale.

Abbreviations

BSC:

Biological soil crust

AOA:

Ammonia-oxidizing archaea

AOB:

Ammonia-oxidizing bacteria

MAT:

Mean annual temperature

MAP:

Mean annual precipitation.

References

  1. Adair KL, Schwartz E: Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA. Microb Ecol 2008, 56(3):420–426.

  2. Agogué H, Brink M, Dinasquet J, Herndl GJ: Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 2008, 456(7223):788–791.

  3. Auguet J, Barberan A, Casamayor EO: Global ecological patterns in uncultured Archaea. ISME J 2010, 4(2):182–190.

  4. Baker GC, Smith JJ, Cowan DA: Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003, 55(3):541–555.

  5. Bartossek R, Nicol GW, Lanzen A, Klenk H, Schleper C: Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiol 2010, 12(4):1075–1088.

  6. Bates ST, Garcia-Pichel F: A culture-independent study of free-living fungi in biological soil crusts of the Colorado Plateau: their diversity and relative contribution to microbial biomass. Environ Microbiol 2009, 11(1):56–67.

  7. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N: Examining the global distribution of dominant archaeal populations in soil. ISME J 2011, 5(5):908–917.

  8. Bates ST, Nash TH III, Garcia-Pichel F: Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States. Mycologia 2012, 104(2):353–361.

  9. Belnap J: Surface disturbances: their role in accelerating desertification. Environ Monit Assess 1995, 37(1–3):39–57.

  10. Belnap J, Lange OL: Biological soil crusts: structure, function, and management. Berlin, Germany: Springer Verlag; 2003.

  11. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR: Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS One 2011, 6(2):e16626.

  12. Campbell JH, Clark JS, Zak JC: PCR-DGGE Comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan Desert elevational gradient. Microb Ecol 2009, 57(2):261–266.

  13. Cao H, Li M, Hong Y, Gu J: Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment. Syst Appl Microbiol 2011, 34(7):513–523.

  14. Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M, Arp D: Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 2003, 185(9):2759–2773.

  15. Chen X, Zhu Y, Xia Y, Shen J, He J: Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ Microbiol 2008, 10(8):1978–1987.

  16. de la Torre JR, Walker CB, Ingalls AE, Koenneke M, Stahl DA: Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 2008, 10(3):810–818.

  17. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ: Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2009, 2: 621–624.

  18. Elbert W, Weber B, Burrows S, Steinkamp J, Büdel B, Andreae MO, Pöschl U: Contribution of cryptogamic covers to the global cycles of carbon and nitrogen. Nat Geosci 2012, 5(7):459–462.

  19. Evans RD, Johansen JR: Microbiotic crusts and ecosystem processes. Crit Rev Plant Sci 1999, 18(2):183–225.

  20. Fan F, Zhang F, Lu Y: Linking plant identity and interspecific competition to soil nitrogen cycling through ammonia oxidizer communities. Soil Biol Biochem 2011, 43(1):46–54.

  21. Fernandez-Guerra A, Casamayor EO: Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers. PLoS One 2012, 7(10):e47330.

  22. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 2005, 102(41):14683–14688.

  23. French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A: Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 2012, 78(16):5773–5780.

  24. Fu BJ, Zhang QJ, Chen LD, Zhao WW, Gulinck H, Liu GB, Yang QK, Zhu YG: Temporal change in land use and its relationship to slope degree and soil type in a small catchment on the Loess Plateau of China. Catena 2006, 65(1):41–48.

  25. Garcia-Pichel F, Belnap J: Microenvironments and microscale productivity of cyanobacterial desert crusts. J Phycol 1996, 32(5):774–782.

  26. Garcia-Pichel F, Lopez-Cortes A, Nubel U: Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado Plateau. Appl Environ Microbiol 2001, 67(4):1902–1910.

  27. Garcia-Pichel F, Johnson SL, Youngkin D, Belnap J: Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado Plateau. Microb Ecol 2003, 46(3):312–321.

  28. Garcia-Pichel F, Wojciechowski MF: The evolution of a capacity to build supra-cellular ropes enabled filamentous cyanobacteria to colonize highly erodible substrates. PLoS One 2009, 4(11):e7801.

  29. Glaser K, Hackl E, Inselsbacher E, Strauss J, Wanek W, Zechmeister-Boltenstern S, Sessitsch A: Dynamics of ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere following nitrate and ammonium fertilizer amendment. FEMS Microbiol Ecol 2010, 74(3):575–591.

  30. Gleeson DB, Mueller C, Banerjee S, Ma W, Siciliano SD, Murphy DV: Response of ammonia oxidizing archaea and bacteria to changing water filled pore space. Soil Biol Biochem 2010, 42(10):1888–1891.

  31. Gubry-Rangin C, Nicol GW, Prosser JI: Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 2010, 74(3):566–574.

  32. Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW: Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA 2011, 108(52):21206–21211.

  33. Gundlapally SR, Garcia-Pichel F: The community and phylogenetic diversity of biological soil crusts in the Colorado Plateau studied by molecular fingerprinting and intensive cultivation. Microb Ecol 2006, 52(2):345–357.

  34. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF: Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 2006, 4(4):E95.

  35. Hallin S, Jones CM, Schloter M, Philippot L: Relationship between N cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 2009, 3: 597–605.

  36. Hammer Ø, Harper DA, Ryan PD: PAST: paleontological statistics software package for education and data analysis. Palaeontol Electr 2001, 4: 1–9.

  37. Hatzenpichler R: Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 2012, 78(21):7501–7510.

  38. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M: A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 2008, 105(6):2134–2139.

  39. He J, Shen J, Zhang L, Zhu Y, Zheng Y, Xu M, Di H: Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 2007, 9(9):2364–2374.

  40. Hocking R: Analysis and selection of variables in linear-regression. Biometrics 1976, 32(1):1–49.

  41. Johnson SL, Budinoff CR, Belnap J, Garcia-Pichel F: Relevance of ammonium oxidation within biological soil crust communities. Environ Microbiol 2005, 7(1):1–12.

  42. Johnson SL, Neuer S, Garcia-Pichel F: Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands. Environ Microbiol 2007, 9(3):680–689.

  43. Jung J, Yeom J, Kim J, Han J, Lim HS, Park H, Hyun S, Park W: Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils. Res Microbiol 2011, 162(10):1018–1026.

  44. Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059–3066.

  45. Kim J, Jung M, Park S, Rijpstra WIC, Damste JSS, Madsen EL, Min D, Kim J, Kim G, Rhee S: Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 2012, 14(6):1528–1543.

  46. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM: rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 2001, 29(1):181–184.

  47. Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA: Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437(7058):543–546.

  48. Lehtovirta LE, Prosser JI, Nicol GW: Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol Ecol 2009, 70(3):367–376.

  49. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW: Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA 2011, 108(38):1–6.

  50. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C: Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442(7104):806–809.

  51. Liu Y, Zheng Y, Shen J, Zhang L, He J: Effects of mercury on the activity and community composition of soil ammonia oxidizers. Environ Sci Pollut Res 2010, 17(6):1237–1244.

  52. Mao Y, Yannarell AC, Mackie RI: Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 2011, 6(9):e24750. 10.1371/journal.pone.0024750

  53. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA: Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 2009, 461(7266):976–979.

  54. Marusenko Y, Huber DP, Hall SJ: Fungi mediate nitrous oxide production but not ammonia oxidation in aridland soils of the southwestern US. Soil Biol Biochem 2013, 63: 24–36.

  55. Matsutani N, Nakagawa T, Nakamura K, Takahashi R, Yoshihara K, Tokuyama T: Enrichment of a novel marine ammonia-oxidizing archaeon obtained from sand of an eelgrass zone. Microb Environ 2011, 26(1):23–29.

  56. Mosier AC, Francis CA: Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 2008, 10: 3002–3016.

  57. Mosier AC, Lund MB, Francis CA: Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microb Ecol 2012, 64(4):955–963.

  58. Nagy ML, Perez A, Garcia-Pichel F: The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiol Ecol 2005, 54(2):233–245.

  59. Nannipieri P, Eldor P: The chemical and functional characterization of soil N and its biotic components. Soil Biol Biochem 2009, 41(12):2357–2369.

  60. Nicol GW, Prosser JI: Strategies to determine diversity, growth and activity of ammonia oxidising archaea in soil. Methods Enzymol 2011, 496: 3–34.

  61. Norton JM, Alzerreca JJ, Suwa Y, Klotz MG: Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 2002, 177(2):139–149.

  62. Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C: Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 2003, 5(9):787–797.

  63. Palmer MW: Putting things in even better order—the advantages of canonical correspondence-analysis. Ecology 1993, 74(8):2215–2230.

  64. Park B, Park S, Yoon D, Schouten S, Damste JSS, Rhee S: Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Microbiol 2010, 76(22):7575–7587.

  65. Pester M, Rattei T, Flechl S, Groengroeft A, Richter A, Overmann J, Reinhold-Hurek B, Loy A, Wagner M: amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 2012, 14(2):525–539.

  66. Pointing SB, Belnap J: Microbial colonization and controls in dryland systems. Nat Rev Microbiol 2012, 10(8):551–562.

  67. Prosser JI, Nicol GW: Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 2012, 20(11):523–531.

  68. Rotthauwe JH, Witzel KP, Liesack W: The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 1997, 63(12):4704–4712.

  69. Safriel U, Adeel Z, Niemeijer D, Puigdefabregas J, White R, Lal R, Winslow M, Ziedler J, Prince S, Archer E, King C: Dryland systems. In Ecosystems and human well-being. Edited by: Hassan R, Scholes RJ, Ash N. Washington DC: Findings of the Conditions and Trends Working Group of the Millennium Ecosystem Assessment. Island Press; 2005:623–662.

  70. Santoro AE, Casciotti KL: Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation. ISME J 2011, 5(11):1796–1808.

  71. Schimel JP, Bennett J: Nitrogen mineralization: challenges of a changing paradigm. Ecology 2004, 85(3):591–602.

  72. Schleper C, Nicol GW: Ammonia-oxidising archaea—physiology, ecology and evolution. Adv Microb Physiol 2010, 57(57):1–41.

  73. Schlesinger WH: Biogeochemistry: an analysis of global change. San Diego, USA: Academic; 1997.

  74. Shen J, Zhang L, Zhu Y, Zhang J, He J: Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 2008, 10(6):1601–1611.

  75. Smith AC, Koper N, Francis CM, Fahrig L: Confronting collinearity: comparing methods for disentangling the effects of habitat loss and fragmentation. Landscape Ecol 2009, 24(10):1271–1285.

  76. Soule T, Anderson IJ, Johnson SL, Bates ST, Garcia-Pichel F: Archaeal populations in biological soil crusts from arid lands in North America. Soil Biol Biochem 2009, 41(10):2069–2074.

  77. Stahl DA, de la Torre JR: Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 2012, 66: 83–101.

  78. Strauss SL, Day TA, Garcia-Pichel F: Nitrogen cycling in desert biological soil crusts across biogeographic regions in the Southwestern United States. Biogeochemistry 2012, 108(1–3):171–182.

  79. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731–2739.

  80. Ter Braak CJF: Canonical correspondence-analysis—a new eigenvector technique for multivariate direct gradient analysis. Ecology 1986, 67(5):1167–1179.

  81. Tourna M, Freitag TE, Nicol GW, Prosser JI: Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 2008, 10(5):1357–1364.

  82. Tourna M, Stieglmeier M, Spang A, Koenneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C: Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 2011, 108(20):8420–8425.

  83. van der Heijden MGA, Bardgett RD, van Straalen NM: The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 2008, 11(3):296–310.

  84. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO: Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66–74.

  85. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Gollabgir A, Hemp J, Huegler M, Karr EA, Koenneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA: Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 2010, 107(19):8818–8823.

  86. Wall DH, Virginia RA: Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 1999, 13(2):137–150.

  87. Xu M, Schnorr J, Keibler B, Simon HM: Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture. Appl Environ Microbiol 2012, 78(7):2137–2146.

  88. Ye L, Zhang T: Ammonia‒oxidizing bacteria dominates over ammonia‒oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading. Biotechnol Bioeng 2011, 108(11):2544–2552.

  89. Zeglin LH, Taylor AE, Myrold DD, Bottomley PJ: Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses. Environ Microbiol Rep 2011, 3(6):717–726.

  90. Zhang L, Wang M, Prosser JI, Zheng Y, He J: Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest. FEMS Microbiol Ecol 2009, 70(2):52–61.

  91. Zhang LM, Offre PR, He JZ, Verhamme DT, Nicol GW, Prosser JI: Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci USA 2010, 107(40):17240–17245.

  92. Zhang X, Liu W, Bai Y, Zhang G, Han X: Nitrogen deposition mediates the effects and importance of chance in changing biodiversity. Mol Ecol 2011, 20(2):429–438.

Download references

Acknowledgements

We thank Moria Nagy and G.S.N. Reddy for sharing their experiences with crust archaea. We are grateful to the staff of Sevilleta and Jornada LTER sites as well as the National Park Service (Canyonlands N.P. and Organ Pipe N.M.) for providing sampling permits, guidance, and hospitality. Finally, we thank Scott Bingham for assistance with qPCR and sequencing. This research was funded by an NSF grant from the Biodiversity Surveys and Inventories Program and by a USDA grant from the Soil Processes Program to FGP.

Author information

Affiliations

  1. School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, AZ, 85287-4501, USA

    • Yevgeniy Marusenko
    • , Ian Anderson
    •  & Ferran Garcia-Pichel

  2. Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA

    • Scott T Bates

  3. Bioscience Division, B-11, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

    • Shannon L Johnson

  4. Department of Biology, Indiana University-Purdue University, Fort Wayne, IN, USA

    • Tanya Soule

Authors

  1. Search for Yevgeniy Marusenko in:

  2. Search for Scott T Bates in:

  3. Search for Ian Anderson in:

  4. Search for Shannon L Johnson in:

  5. Search for Tanya Soule in:

  6. Search for Ferran Garcia-Pichel in:

Corresponding author

Correspondence to Ferran Garcia-Pichel.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

IA, SJ, SB, TS, and YM participated in lab bench and/or phylogenetic work. FGP and SB designed the experimental approach. YM, SB, TS and FGP contributed to the drafting of the manuscript. All authors contributed intellectually to the ideas and data interpretations in this work. All authors read and approved the final manuscript.

Electronic supplementary material

Additional file 1:Origin and type of biological soil crusts used in this study. File describes additional information about each site used in this study. Data include biogeographical province, site ID, and which sites were used for qPCR determinations (bacterial amoA, archaeal amoA, archaeal 16S rRNA), crust type, latitude, longitude, mean annual temperature, and mean annual precipitation. (DOCX 22 KB)

Authors’ original submitted files for images

Authors’ original file for figure 1

Authors’ original file for figure 2

Authors’ original file for figure 3

Authors’ original file for figure 4

Rights and permissions

Reprints and Permissions

About this article

Keywords

  • Biological soil crust
  • Desert
  • Arid
  • amoA
  • Ammonia oxidation
  • Nitrification
  • Nitrogen cycle
  • Thaumarchaeota