Bacterial diversity in agricultural soils during litter decomposition

Abstract

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.

FIG. 1.

DGGE DNA bands of single bacterial isolates and of mixtures added to autoclaved soil. The mixture was added undiluted and diluted 10-fold. Most isolates are reflected in the mixture.

FIG. 2.

DGGE DNA bands of P. fluorescens (P), Arthrobacter sp. (A), and Bacillus sp. (B) added to autoclaved soil in different ratios.

FIG. 3.

DNA extracted from rye grass and wheat straw on agarose gels. Lanes 1, 16, 17, and 32, 23-kbp marker; lanes 2, 15, 18, and 31, DNA Mass ladder (Life Technologies); lanes 3 to 12, five decomposition stages (days 0, 18, 58, 118, and 180, duplicate samples) for rye grass; lanes 13, 14, and 19 to 26, five decomposition stages (days 0, 18, 58, 118, and 180, duplicate samples) for wheat straw; lanes 27 to 30, rye grass (duplicate samples) from northern and southern Germany obtained on day 18.

FIG. 4.

DGGE patterns of 16S rRNA gene sequences during litter decomposition in soil in central Germany. Lanes 1, 6, 13, and 18, marker; lanes 2 to 12, five decomposition stages for wheat straw on days 0, 18, 58, 118, and 180 (W0, W18, W58, W118, and W180, respectively) (duplicate samples); lanes 14 to 17, rye grass on day 18 in soil in northern and southern Germany (R18n and R18s, respectively) (duplicate samples). The two replicates obtained on day 0 were derived from the second extract since DGGE for the first extract was not successful (see Fig. 6).

FIG. 5.

Qualitative PCA of 16S rRNA gene sequences during rye litter decomposition (A, X = 29.8%; Y = 25.2%; Z = 14.0%; Σ = 69.1%) and wheat litter decomposition (B, X = 36.2%; Y = 18.8%; Z = 15.5%; Σ = 70.5%). Symbols: •, day 0; ▴, day 18; ▾, day 58; ♦, day 118; ▪, day 180.

FIG. 6.

DGGE pattern of 16S rRNA gene sequences during litter decomposition in soil in central Germany. Lanes 1, 7, 14, and 17, marker; lane 2, negative control; lanes 3 to 13, five decomposition stages for rye grass on days 0, 18, 58, 118, and 180 (R0, R18, R58, R118, and R180, respectively) (duplicate samples); lanes 15 and 16, wheat straw on day 0 (W0).

FIG. 7.

Qualitative PCA of 16S rRNA gene sequences during decomposition of rye litter (open symbols) and wheat straw (solid symbols) on day 0 (○ and •), day 18 (▵ and ▴), day 58 (▿ and ▾), day 118 (⋄ and ♦), and day 180 (□ and ▪) (X = 19.3%; Y = 16.9%; Z = 14.2%; Σ = 50.4%).

FIG. 8.

Qualitative PCA of 16S rRNA gene sequences for rye litter after 18 days of decomposition in northern ▴, central ♦, and southern ▾ Germany (X = 29.8%; Y = 25.2%; Z = 14.0%; Σ = 69.1%).