Impact of moisture on microbial decomposition phenotypes and enzyme dynamics

Abstract

Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that (i) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, (ii) the identity of key chitin degraders varies with moisture level, and (iii) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.

Keywords: activity-based probes; carbon use efficiency; chitin; soil microbiome.

Figure 1

Soil biogeochemistry measurements reveal the impact of moisture and chitin amendment. (A) Cumulative soil respiration over the seven-day incubation with mean and standard deviation plotted for biological replicates (n = 5). (B) Salt extractable and microbial biomass carbon and nitrogen for each incubation condition. (C) Carbon use efficiency by proxy of the ratio between the respired carbon in CO₂ related to the microbial biomass carbon. Different lowercase letters indicate significance according to ANOVA and Tukey honest significant differences post hoc testing (P < .05).

Figure 2

Potential soil enzyme activities as impacted by moisture and chitin amendment after seven days. Lowercase letters indicate significance according to ANOVA and Tukey honest significant differences post hoc testing (P < .05). The scale varies among plots.

Figure 3

Kinetic curves of methylumbelliferyl linked substrate incubated samples. Each line is the average of three kinetic replicates per sample. (A) 4-Methylumbelliferyl β-D-N,N′,N′′-triacetylchitotriose (endochitinase) samples. (B) 4-Methylumbelliferyl N-acetyl-β-D-glucosaminide samples.

Figure 4

Changes in microbial diversity and composition from bulk soils across moisture and chitin treatments. Diversity measurements of 16S rRNA gene sequencing for bulk soil incubations compared from Day 0 to Day 7. (A) Averaged observed taxon count for each incubation treatment; error bars represent standard error. (B) Averaged Shannon index for each incubation treatment; error bars represent standard error. (C) Nonmetric multidimensional scaling of Bray–Curtis dissimilarity of community composition for relative abundance of the total incubated samples. (D) Sample composition at the beginning of the incubation. (E) Sample composition at the conclusion of the seven-day incubation. Ellipses represent 95% confidence intervals.

Figure 5

Varied abundance of chitinolytic genera in response to chitin treatment as determined by activity-based probe labeling. (A) Mean (± SE) relative abundance of taxa enriched using Chi3-ABP between moisture and chitin treatments. (B) Mean (± SE) relative abundance of taxa enriched using NAG-ABP between moisture treatments. Significance from DESeq2 analysis denoted by “^*” (P < .001, LFC > 2) only comparing chitin amendment within a moisture treatment. Error bars represent standard error.