Contrasting Euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns

Highlights

• We report a pyrosequencing survey of Euryarchaeota in various ecosystems.

• Upland soils and paddy soils harbor distinct assemblages of Euryarchaeota.

• Upland Euryarchaeota exhibit pH- and H₂O%-impacted biogeographical patterns.

• Paddy Euryarchaeota exhibit pH- and NH₄⁺-N-impacted biogeographical patterns.

• Our results emphasize the dominant role of pH in shaping terrestrial Euryarchaeota.

Abstract

Euryarchaeota, as an important and ubiquitous Archaea phylum, contributes substantially to global energy cycling. However, there is a considerable lack of knowledge regarding their biogeographic patterns in terrestrial ecosystems. Here barcoded pyrosequencing was employed to compare the relative abundance, diversity and community composition of Euryarchaeota in 92 soil samples, collected from a variety of ecosystem types. A total of 96,534 euryarchaeal sequences were classified from pyrosequencing of the archaeal 16S rRNA gene, comprising 22.5% of the total archaeal sequences detected. Paddy soils harbored contrasting Euryarchaeota communities from upland soils (including cropland, grassland, forest, and tea orchard soil), at all taxonomic resolutions from phylum to genus level. Within upland soils, the relative abundance of Euryarchaeota in Archaea, and Euryarchaeota operational taxonomic unit (OTU) richness are significantly influenced by soil pH and H₂O%. Similar observations held true for the beta diversity patterns, with soil pH and H₂O% best explaining the variance of the pairwise Bray–Curtis dissimilarity. By comparison, within paddy soils, the Euryarchaeota abundance in Archaea, and the alpha and beta diversity patterns, could be best predicted along the gradients of soil pH and NH₄⁺-N. These findings were further corroborated by the evident pH-, H₂O%- or NH₄⁺-N-associated distributions of several major Euryarchaeota orders. Taken together, our results emphasized the significant importance of soil pH as the prevailing environmental factor in shaping the terrestrial Euryarchaeota.

Introduction

Despite widespread occurrence and physiological diversity in terrestrial ecosystems, Euryarchaeota remain a largely less-explored Archaea phylum, which contain psychrophiles, thermophiles, mesophiles, halophiles and alkaliphiles, mostly with unresolved metabolic properties (Pesaro and Widmer, 2002; Poplawski et al., 2007). Euryarchaeota have been known to involve in greenhouse gas production, with methane as the end-product of the anaerobic respiration, and this biological process accounted for about 74% of the emitted atmospheric methane on Earth (Liu and Whitman, 2008). In addition to methanogenesis, Euryarchaeota were also found to be capable of oxidizing methane (Michaelis et al., 2002), fixing nitrogen (Raymond et al., 2004), reducing nitrate (Cabello et al., 2004), and metabolizing sulfur and iron (Edwards et al., 2000). Phylogenetic analyses of over 8,000 deposited archaeal rRNA gene sequences suggest that Euryarchaeota are the most diverse Archaea phylum, containing about 33 distinct phylogenetic groups (Schleper et al., 2005). However, currently available knowledge for the ecophysiological characteristics of Euryarchaeota primarily generated from the purely cultured strains and about 30 complete genome sequences deposited in databases, with most of them being distantly related to the mesophilic lineages, so there is still an incomplete understanding of the whole Euryarchaeota community (Barberan et al., 2011).

In addition to these culture-dependent studies, growing numbers of environmental ribosomal gene investigations have greatly expanded our view of Euryarchaeota with diverse and abundant uncultured lineages (Schleper et al., 2005). Euryarchaeota were frequently described and recovered in marine environments (DeLong, 1992), freshwater habitats (Auguet et al., 2010), hypersaline sediments (Hollister et al., 2010), paddy soils (Liesack et al., 2000), bovine rumen (Whitford et al., 2001), termite guts (Purdy, 2007), and anaerobic bioreactors (McHugh et al., 2003). Therefore, most of Euryarchaeota lineages were usually considered as strict anaerobes, and only sporadically reported in the well-aerated parts of forest, grassland and agricultural soil environments (Pesaro and Widmer, 2002; Poplawski et al., 2007). Compared with the intensively researched paddy soils, studies on Euryarchaeota in upland soil ecosystems are relatively less common, thus their potential function and community diversity were largely underestimated. For instance, the methanogens, being considered as strictly obligate anaerobic Euryarchaeota, were recently shown to diversify and successfully colonize in many types of aerated upland soils sampled globally (Angel et al., 2012). The methane production was activated when these upland soils were incubated under anoxic microcosms as slurry (Angel et al., 2012). In some other aerated surface upland soils, Euryarchaeota were reported with a high abundance, suggesting that certain Euryarchaeota groups were not strictly dependent on anoxic environments and might be tolerant to aerated conditions (Pesaro and Widmer, 2002; Bomberg and Timonen, 2007). But due to the methodological limitations employed in these studies, for example, Terminal Restriction Fragment Length Polymorphism (T-RFLP) and clone libraries which lacked phylogenetic or taxonomic resolution, our knowledge of these widely distributed Euryarchaeota in terrestrial environments still remains scarce.

With the advent of the barcoded pyrosequencing technology, we could now be able to survey the complex unculturable communities in a greater sequencing depth (Roesch et al., 2007). The superior advantages of next-generation sequencing have been exploited to elucidate the environmental distributions of soil-dwelling microbes across large-scale biogeographical regions (Jones et al., 2009; Lauber et al., 2009; Rousk et al., 2010). Some comprehensive surveys of terrestrial Archaea have provided valuable insights into the biogeographic patterns of the total Archaea community (Bates et al., 2011; Cao et al., 2012) or functional archaeal lineages (Gubry-Rangin et al., 2012; Pester et al., 2012), and showed great importance of environmental factors in structuring archaeal ecological niches. However, no studies have been carried out to directly compare the large-scale distribution patterns of Euryarchaeota across various terrestrial ecosystems. It remains not fully understood that whether aerated upland soils encompass contrasting or similar Euryarchaeota communities to anoxic terrestrial ecosystems (e.g. paddy soils), or whether these ecosystems exhibit similar soil variable-impacted distribution patterns.

The present study was designed to obtain a broad overview of the ecological characteristics of Euryarchaeota in 92 soil samples, collected from a wide variety of terrestrial ecosystems, including cropland, grassland, forest, tea orchard, and paddy soils. We used 454 barcoded pyrosequencing to generate archaeal 16S rRNA gene sequences, and compared the relative abundance, diversity, and taxonomic composition of the classified soil Euryarchaeota across different terrestrial biomes. We also tried to determine the influences of various edaphic factors on the biogeographic patterns of soil Euryarchaeota.