Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils

Abstract

New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.

Keywords: 16S RNA; environmental microbiology; metagenomics; microbial ecology; soil microbiology; urban ecology.

FIG 1

Accumulation curves indicating the number of phylotypes as a function of sequence coverage, with 95% confidence intervals. Phylotype accumulation given for each of the four soil types sampled (a) and for RNA versus DNA phylotypes across all samples (b). Eng, engineered; Non-eng, nonengineered.

FIG 2

Alpha diversity results for engineered and nonengineered soil communities for DNA (a), RNA (b), and all (c) phylotypes. Three alpha diversity measures are shown: phylogenetic diversity (top row), Chao1 phylotype richness (middle row), and evenness (bottom row). Individual samples are colored by soil type (a and b) and template (c). Significance of differences was tested using the Wilcoxon test; **, P < 0.005; *, P < 0.05. Park, park lawns; CTP, conventional tree pits.

FIG 3

Nonmetric multidimensional scaling (NMDS) ordination plots for DNA (a), RNA, colored by soil type (b), and all samples (c), colored by template. ANOSIM R values are 0.31 (a), 0.26 (b), and 0.39 (c), and clustering was significant in all cases with a P value of <0.001.

FIG 4

Relative abundance of DNA (a) and RNA (b) phylotypes in all four soil types, for all phyla with greater than 1% overall abundances. Phyla with significantly different phylotype abundances in engineered versus nonengineered sites are indicated for DNA (*) and RNA (†) (significance adjusted for false-discovery rate of P < 0.05). TP, tree pits.

FIG 5

Physical soil characteristics. (a) Differences in mean pH value and parts per million (ppm) of select nutrients and metals in engineered and nonengineered soils. **, two-tailed t test, P < 0.001; *, P < 0.05. (b) Significant Pearson correlations (P < 0.01) of pH with 16S Shannon diversity values based on DNA (gray) and RNA (blue).

FIG 6

Box plots of mean Shannon diversity values for engineered and nonengineered soil bacterial communities. Significance of differences was tested using the Wilcoxon test; **, P < 0.001; *, P < 0.05. Whiskers indicate standard errors.

FIG 7

Sample sites. (a) Engineered and nonengineered soil sites were sampled in the Bronx River sewershed, shaded pink in the inset map, in the Bronx, NY. Engineered sites included streetside (SS) swales (b) and right-of-way (ROW) swales (c). Nonengineered sites include park lawns and conventional tree pits. (The base map is from Google Maps.).