Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile

Abstract

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

FIG. 1.

Proportions of major bacterial groups within clone libraries (384 random clones sequenced) obtained from soil aggregates from the A, B, unsaturated C (C-u), and saturated C (C-s) horizons. The table lists the diversity indices for the bacterial sequences recovered from the four horizons. Estimates of phylotype richness were calculated according to the abundance-based coverage estimate (ACE) and the bias-corrected Chao1 estimator. The Shannon-Weiner diversity index, which takes into account species richness and evenness, was also calculated. The evenness of the population is estimated by the inverse of the Simpson's index (1/D), which is sensitive to the level of phylotype dominance. The percentage of coverage was calculated using Good's coverage equation.

FIG. 2.

Neighbor-joining phylogenetic tree of Acidobacteria-affiliated 16S rRNA sequences for the A, B, unsaturated C (C-u), and saturated C (C-s) horizons. As identified by Zimmerman et al. (94), intersubdivision tree topologies differ depending on the tree-building methods (e.g., neighbor joining, maximum parsimony, or maximum likelihood) utilized, yet relationships within subdivisions are consistently stable regardless of the algorithm utilized. Here we utilize the distance-based neighbor-joining method, which results in a different ordering of the previously assigned subdivision numbers while maintaining a stable branching order within each subdivision. Bootstrap values (n = 1,000) of greater than 50% are indicated at nodes. Escherichia coli is the outgroup.

FIG. 3.

Rarefaction curves indicating archaeal 16S rRNA and amoA richness within clone libraries derived from the B, unsaturated C (C-u), and saturated C (C-s) horizons. The dashed line represents 1:1, indicative of infinite diversity. The table lists the archaeal 16S rRNA and amoA sequence diversity indices as described for Fig. 1. OTUs were defined as groups of sequences sharing 97% (16S rRNA) and 95% (amoA) nucleotide sequence identity.

FIG. 4.

Neighbor-joining phylogenetic trees of archaeal 16S rRNA (left) and amoA (right) clone sequences for the B, unsaturated C (C-u), and saturated C (C-s) horizons. Bootstrap values (n = 1,000) of greater than 50% are indicated at nodes. The tree is based on 690 (16S rRNA) and 575 (amoA) masked nucleotide positions. Both the archaeal 16S rRNA and amoA gene trees are rooted with the amoA-containing ammonia-oxidizing bacterium Nitrosomonas europaea.

FIG. 5.

Neighbor-joining phylogenetic tree of 16S rRNA clone sequences obtained from the Fe(III)-reducing enrichments and of the closely affiliated saturated C horizon bacterial clones (BacC-s; gray shading). The A (pink), B (red), unsaturated C (C-u) (green), and saturated C (C-s) (blue) horizons were enriched with ferrihydrite as the electron acceptor and lactate (Lac), acetate (Ac), or ethanol (Et) as the electron donor. The tree is based on 1,060 masked nucleotide positions and Geothrix fermentans is the outgroup. Bootstrap values (n = 1,000) of greater than 50% are indicated at nodes.

FIG. 6.

Proportion of bacterial phyla enriched under Fe(III)-reducing conditions as a function of soil horizon. Dominant species are indicated in the representative bar graph for each horizon.

FIG. 7.

Phylogenetic tree reflecting the relationship of sulfate-reducing bacteria within the saturated C horizon (C-s) based on an ∼500-bp region of dsrAB gene fragment. The tree was constructed by neighbor joining based on Jukes-Cantor-corrected DNA distances. Bootstrap values (n = 1,000) of greater than 50% are indicated at nodes. Tree topologies and clade designations were stable and consistently recovered by analysis of the DSR α subunit, β subunit, or partial α and β subunit genes. Thermodesulfovibrio islandicus of the Nitrospira phylum is the outgroup.