Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling

Abstract

Microbial ecologists have discovered novel rRNA genes (rDNA) in mesophilic soil habitats worldwide, including sequences that affiliate phylogenetically within the division Crenarchaeota (domain Archaea). To characterize the spatial distribution of crenarchaeal assemblages in mesophilic soil habitats, we profiled amplified crenarchaeal 16S rDNA sequences from diverse soil ecosystems by using PCR-single-strandedconformation polymorphism (PCR-SSCP) analysis. PCR-SSCP profiles provide a measure of relative microbial diversity in terms of richness (number of different phylotypes as estimated from the number of unique PCR-SSCP peaks) and evenness (abundance of each phylotype as estimated from the relative area under a peak). Crenarchaeal assemblages inhabiting prairie, forest, turf, and agricultural soils were characterized at six sampling locations in southern and central Wisconsin. Phylotype richness was found to be more stable than evenness among triplicate samples collected within 30 cm at each sampling location. Transformation of the PCR-SSCP data by principal-component analysis, followed by statistical testing (analysis of variance [P < 0.0001] and least-significant-difference analysis [␣ ‫؍‬ 0.5]), supported the conclusion that each location exhibited a unique profile. To further characterize the spatial distribution of crenarchaeal assemblages at one location, additional soil samples (a total of 30) were collected from agricultural field plots at the Hancock Agricultural Research Station. PCR-SSCP revealed a patchy spatial distribution of crenarchaeal assemblages within and between these plots. This mosaic of crenarchaeal assemblages was characterized by differences in phylotype evenness that could not be correlated with horizontal distance (15 to 30 m) or with depth (0 to 20 cm below the surface). Crenarchaeal 16S rDNA clone libraries were produced and screened for unique SSCP peaks. Clones representing the dominant phylotypes at each location were identified, sequenced, and found to group phylogenetically with sequences in crenarchaeal clade C1b.

Distantly sampled soils carry few species in common

“…The community structure, at the phylum level, is nonetheless highly site specific (for example, Dunbar et al, 1999;Hackl et al, 2004;Oline, 2006; Herrera et al, 2007;Labbe et al, 2007;Lamarche et al, 2007). In detailed studies community phyla structures also prove to be seasonally dynamic and highly heterogenous even in homogeneous landscapes (Axelrood et al, 2002;Franklin and Mills, 2003;Sliwinski and Goodman, 2004). A few studies have attempted to correlate community structure to ecological parameters (Sessitsch et al, 2001;Fierer and Jackson 2006;Fierer et al, 2007).…”

“…Soil community structures differ markedly between systems, and even across landscapes that appear macroscopically homogeneous. (for example, Axelrood et al, 2002;Franklin and Mills, 2003;Hackl et al, 2004;Sliwinski and Goodman, 2004;Oline, 2006;Herrera et al, 2007;Lamarche et al, 2007). Whole community studies and studies on the genotypes of individual taxa have revealed that, at high levels of taxonomic resolution, there is a degree of prokaryote endemism apparent across broad geographic scales (Fulthorpe et al, 1998;Cho and Tiedje, 2000;Wawrik et al, 2007).…”

Effect of Soil Type and Fertilizer Management on Archaeal Community in Upland Field Soils

“…In contrast, fungal communities are most closely associated with fertilizer treatment (38), i.e., changes in the soil nutrient status (18). There are a few reports on archaeal communities in agricultural soil ecosystems (8,23,29,36), but to date little is known about the effect of soil type and agricultural management practices on archaeal populations and community structure. In a long-term experimental field contained four different soil types, maintained under three different fertilizer management systems in Tsukuba, Japan, Suzuki et al (38) analyzed the effect of soil type and agricultural management practices, i.e., fertilizer type, on bacterial and fungal communities, but not on the archaeal community.…”

“…The group I lineage is composed of member of clades, I.1a, I.1b, I.1c and I.3. Clones aligning with group I.1b are the most widespread, having been detected from soils of agricultural fields (36), grasslands (24), woodlands (31), limestone (31), and deglaciated environments (25). Recent evidence suggests that members of the Group I.1a/b lineages are involved in nitrogen cycling, especially nitrification (33).…”

Filogenia molecular e cultivo de Archaea de solos de Cerrado sensu strictoc

“…Por esse motivo, as archaeas foram então por muito tempo associadas apenas a locais com ausência de oxigênio, altas temperaturas e extremos de pH ou salinidade, fazendo com que esses ambientes fossem alvos de muitos estudos relacionados a membros deste domínio (Darland et al, 1970;Balch et al, 1979;Fiala & Stetter, 1986;Mathrani et al, 1988;Barns et al, 1994;Blochl et al, 1997) Nos anos seguintes, muitos trabalhos relataram e seguem relatando a ampla distribuição das archaeas em diferentes ambientes terrestres e aquáticos mesófilos, assim como em ambientes extremos (Delong, 1998;Chaban et al, 2006). Archaeas já foram detectadas em diversos solos (Bintrim et al, 1997;Sliwinski & Goodman, 2004;Timonen & Bomberg, 2009), lagoas de água doce (Vissers et al, 2009), ecossistemas marinhos (Wuchter et al, 2006;Silveira et al, 2013), sedimentos (Glissman et al, 2003;Rodrigues et al, 2014), estações de tratamento de esgoto (Gray et al, 2002) e até em diversas partes do corpo humano (Eckburg et al, 2003;Horz & Conrads, 2010;, entre outros ambientes. Hoje em dia, considera-se que a distribuição de archaeas no ambiente seja equivalente à bacteriana.…”