Relic DNA effects on the estimates of bacterial community composition and taxa dynamics in soil.

DNA-based analyses have become routine methods in soil microbial research, for their high throughput and resolution in characterizing microbial communities. Yet, concerns arise regarding the interference of relic DNA in estimates of viable bacterial community composition and individual taxa dynamics in soils that recovered from post-gamma irradiation. In this study, different soil samples with varying bacterial diversity but similar soil properties were randomly selected. We split each sample into two parts: one part was treated with propidium monoazide (PMA) before DNA extraction, PMA can bind to relic DNA and inhibit PCR amplification by chemical modification; DNA of the other part was extracted following the same process but without PMA pretreatment. Then, soil bacterial abundance was quantified by quantitative polymerase chain reaction, and bacterial community structure was examined by Illumina metabarcoding sequencing of 16S rRNA gene. The results showed that the higher bacterial richness and evenness were estimated when relic DNA was present. The variation trends of bacterial abundance, alpha diversity, and beta diversity remained the same, as reflected by the significant correlations between PMA-treated and -untreated samples (P < 0.05). Moreover, as the mean abundance increased, the reproducibility of detecting individual taxa dynamics between relic DNA present and absent treatments increased. These findings provide empirical evidence that a more even distribution of species abundance derived from relic DNA would result in the overestimation of richness in the total DNA pools and also have crucial implications for guiding proper application of high-throughput sequencing to estimate bacterial community diversity and taxonomic population dynamic. KEY POINTS: • Relic DNA effects on the bacterial community in sterilized soils were assessed. • More even species abundance distribution in relic DNA overestimates true richness. • The reproducibility of individual taxa dynamics increased with their abundance.

Carbonaceous Nanomaterials Have Higher Effects on Soybean Rhizosphere Prokaryotic Communities During the Reproductive Growth Phase than During Vegetative Growth.

Carbonaceous nanomaterials (CNMs) can affect agricultural soil prokaryotic communities, but how the effects vary with the crop growth stage is unknown. To investigate this, soybean plants were cultivated in soils amended with 0, 0.1, 100, or 1000 mg kg-1 of carbon black, multiwalled carbon nanotubes (MWCNTs), or graphene. Soil prokaryotic communities were analyzed by Illumina sequencing at day 0 and at the soybean vegetative and reproductive stages. The sequencing data were functionally annotated using the functional annotation of prokaryotic taxa (FAPROTAX) database. The prokaryotic communities were unaffected at day 0 and were altered at the plant vegetative stage only by 0.1 mg kg-1 MWCNTs. However, at the reproductive stage, when pods were filling, most treatments (except 1000 mg kg-1 MWCNTs) altered the prokaryotic community composition, including functional groups associated with C, N, and S cycling. The lower doses of CNMs, which were previously shown to be less agglomerated and thus more bioavailable in soil relative to the higher doses, were more effective toward both overall communities and individual functional groups. Taken together, prokaryotic communities in the soybean rhizosphere can be significantly phylogenetically and functionally altered in response to bioavailable CNMs, especially when soybean plants are actively directing resources to seed production.

Temporal Changes in the Function of Bacterial Assemblages Associated With Decomposing Earthworms.

Soil invertebrate corpse decomposition is an ecologically significant, yet poorly understood, process affecting nutrient biogeochemical cycling in terrestrial ecosystems. Here, we attempted to answer how the substrate chemistry and microbial community change during soil invertebrate (earthworm) decomposition and what roles microbes play in this process. Specifically, the dead earthworms (Amynthas corticis) were buried in two soils where the earthworms inhabited, or not, until more than 50% of the earthworm mass was lost. For both soils, earthworms decomposed faster during the early stage (between 0 and 3 days), as reflected by the higher rate of decomposition and increased accumulation of dissolved organic matter (DOM). This decomposition pattern was paralleled by bacterial community dynamics, where bacterial richness and diversity were significantly higher during early decomposition (p < 0.05) with the relative abundances of many genera decreasing as decomposition progressed. The succession of the bacterial community composition was significantly correlated with time-course changes in DOM composition (p < 0.05). Particularly, more functional groups (e.g., microbes associated with carbon, nitrogen, and sulfur cycling) were identified to be linked with the change of a specific DOM type during the early decomposition phase. By exploring the ecologically important process of soil invertebrate decomposition and its associated bacterial communities, this study provides evidence, e.g., a statistically significant positive correlation between bacterial community and DOM compositions, which supports the widely recognized yet less-tested microbial community structure-function relationship hypothesis in invertebrate decomposition.

Plant evenness modulates the effect of plant richness on soil bacterial diversity.

Understanding the relationships between aboveground and belowground biodiversity will help to expand our knowledge on how ecological communities and processes are interactively determined, and thus provide new perspectives for the conservation of biodiversity. Despite the theoretical analyses generally predicting a positive relationship between plant richness and soil microbial diversity, the results from empirical studies have been mixed, probably due to the effect of plant evenness. To investigate this relationship, we conducted field experiments in two geographically distinct sites (Linhai and Shenmu, >1400km apart), by simultaneously manipulating plant richness (2, 4, and 8 species) and evenness (homogeneous versus non-homogeneous). After one year, the bacterial response to plant richness with different plant evenness levels was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis. Our results showed that plant evenness modulated plant richness effects on bacterial community, as reflected by the more pronounced positive correlations between bacterial richness and plant richness in homogeneous plant community than in the non-homogeneous treatment. Additionally, plant community structure significantly affected bacterial communities only in the homogeneous treatment in Shenmu, but not in the non-homogeneous treatments. Our results demonstrate that plant evenness could regulate plant richness effects on bacterial alpha- and beta-diversity and thus provide valuable insights into the association between aboveground and belowground biodiversity.