Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains

Abstract

The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of beta-PROTEOBACTERIA: As a whole, alpha-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the alpha-, beta-, and gamma-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and beta-proteobacterial isolates were most abundant during winter, while the alpha- and gamma-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.

FIG. 1.

Maximum, minimum, and average daily air temperatures for the Saddle climate monitoring station on Niwot Ridge for the period in 1999 during which the primary samples for this study were collected.

FIG. 2.

Results of phylogenetic tree permutation (PTP) analysis, performed with PAUP software using 50,000 random permutations of the original data. The histogram shows the frequencies of tree lengths generated randomly, assuming the null hypothesis that the communities do not differ phylogenetically. The arrow shows the tree length (77 steps) of the original unpermuted data, corresponding to a P value of 0.005.

FIG. 3.

Frequency of major bacterial groups in 16S rRNA clone libraries for soil collected in winter, spring, and summer. Error bars are standard errors for three spatial replicates. acido, Acidobacterium; actino, Actinobacteria; alpha, beta, gamma, and delta, α, β, γ, and δ subgroups of Proteobacteria, respectively; Verruco, Verrucomicrobium; other, other miscellaneous bacterial divisions.

FIG. 4.

Maximum-likelihood phylogenetic tree of selected 16S rRNA clones that represent the full bacterial diversity of the libraries. Winter clones begin with W, spring clones with P, and summer clones with S. Other sequences are from GenBank.

FIG. 5.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the Acidobacterium division. Winter clones begin with W, spring clones with P, and summer clones with S. Other sequences are from GenBank. Sequences occurring more than once are indicated with an asterisk (Table 2).

FIG. 6.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the α subgroup (A) and the β, γ, and δ subgroups (B) of the Proteobacteria division. Winter clones begin with W, spring clones with P, and summer clones with S. Cultured bacterial isolates from the alpine begin with DL. Other sequences are from GenBank. Sequences occurring more than once are indicated with an asterisk (Table 2).

FIG. 6.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the α subgroup (A) and the β, γ, and δ subgroups (B) of the Proteobacteria division. Winter clones begin with W, spring clones with P, and summer clones with S. Cultured bacterial isolates from the alpine begin with DL. Other sequences are from GenBank. Sequences occurring more than once are indicated with an asterisk (Table 2).

FIG. 7.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the Verrucomicrobium division. Winter clones begin with W, spring clones with P, and summer clones with S. Other sequences are from GenBank. Sequences occurring more than once are indicated with an asterisk (Table 2).

FIG. 8.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the CFB division. Winter clones begin with W, spring clones with P, and summer clones with S. Cultured bacterial isolates from the alpine soil begin with DL. Other sequences are from GenBank.

FIG. 9.

Maximum-likelihood phylogenetic tree of 16S rRNA clones within the Actinobacteria division. Winter clones begin with W, spring clones with P, and summer clones with S. Cultured bacterial isolates from the alpine soil begin with DL. Other sequences are from GenBank.

FIG. 10.

Seasonal abundance of selected bacterial isolates based on dot blotting experiments. Values are hybridization signals standardized with known quantities of genomic DNA. The P value is given where the hybridization signal changed significantly over time, based on linear regression analysis. Fluor., fluorescent; Actino, Actinobacteria.