Mining the Drilosphere: Bacterial Communities and Denitrifier Abundance in a No-Till Wheat Cropping System

Effects of cadmium and pyrene on earthworm-associated bacterial communities: Unveiling new perspectives for soil pollution management

Earthworms are considered to be excellent bioindicators of soil pollution. In recent years, there has been increasing interest in examining the effects of soil pollution on earthworm-associated microbiomes, with a particular focus on the gut microbiomes. However, relatively little effort has been invested in comprehensively investigating other microbiomes associated with earthworms and their responses to soil pollution. To fill this gap, we systematically studied the effects of Cd, pyrene, and combined pollution on the bacterial community in different vermicompartments, i.e., burrow wall, gut, and cast, in both epigeic Eisenia fetida and anecic Metaphire guillelmi, using a 2D-terraria incubator and high-throughput sequencing techniques. The results showed that bacterial alpha diversity followed the order of burrow wall > cast > gut, and this did not vary with soil pollution or earthworm ecotypes. Moreover, the dominant phyla in the vermicompartments were similar across different pollution treatments. Principal coordinate analysis (PCoA) revealed that the bacterial communities in different vermicompartments and ecotypes of earthworm were separated from each other, whereas they were grouped together in polluted treatments and unpolluted conditions. These results imply that even in polluted soil, vermicompartment and earthworm ecotypes remain the most significant factors affecting earthworm-associated microbiomes. However, the impacts of soil pollution on the bacterial composition in each vermicompartment were still evident. A comprehensive analysis revealed that the gut bacterial communities are more sensitive to soil contamination than casts and burrow wall in different ecotypes. Additionally, linear discriminant analysis of effect size (LefSe) identified several bacteria in Gemmatimonadota, the Firmicutes phylum in the burrow walls, and Patescibacteria (phyla) in the gut as potential biomarkers for pyrene contamination in soil. This research provides a comprehensive understanding of the effects of soil pollution on earthworm-associated microbiomes, thereby enhancing our understanding of earthworm ecotoxicology and soil pollution management.

Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil

Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.

Impact of Physicochemical Parameters on the Diversity and Distribution of Microbial Communities Associated with Three South African Peatlands

Peatlands are complex wetland-like ecosystems that harbor diverse microbial communities. In this study, the microbial communities (fungal and actinobacterial) associated with an unimpacted peatland (Vankervelsvlei; VV), an impacted peatland (Goukou River system; GK), and a developing peatland (Nuwejaars River system; NR) were determined through ITS and 16S rRNA metataxonomic analyses. Unidentified Acidimicrobiales dominated in GK and NR, unidentified Intrasporangiaceae and Solirubobacterales in NR, and Corynebacterium, Propionibacterium, and Streptomyces species in VV. The fungal phyla, Ascomycota and Basidiomycota, dominated all three sites, and harbored unique fungal taxa belonging to a wide range of fungal guilds. Physicochemical properties of the peat collected from the three sites were analyzed in association with microbial community structures in order to determine which parameters acted as the main drivers for microbial diversity. BEST analysis (linking microbial diversity patterns to environmental variables) showed that nitrogen (N), aluminum (Al), phosphorus (P), and potassium (K) were the most significant physicochemical drivers of actinobacterial community structure, while iron (Fe) and humification were the environmental parameters that affected the fungal communities the most. In conclusion, this study has provided some insight into the fungal and actinobacterial communities associated with three South African peatlands and the main environmental drivers that influence these communities.

Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

The spatial heterogeneity of soil’s microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray–Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Sources and subsurface transport of dissolved reactive phosphorus in a semiarid, no-till catchment with complex topography

The subsurface transport of dissolved reactive phosphorus (DRP) from artificially drained agricultural fields can impair water quality, especially in no-till fields. The distribution of soil P in the wheat (Triticum aestivum L.)-dominated Palouse region in the inland U.S. Pacific Northwest varies greatly due to its steep and complex topography, and a legacy (∼130 yr) of excessive soil erosion and deposition processes. The primary goal of this research was to better understand the magnitude and temporal dynamics of DRP export from an artificial drain line and the variability of subsurface DRP leaching within a long-term, no-till field. Dissolved reactive P in drain line effluent was monitored across three water years. Large intact soil cores were extracted at contrasting field locations (toe and top slope positions) to measure DRP leachate concentration and relative P sorption. Drain line DRP concentration was predominantly >0.05 mg L^-1 and often exceeded 0.1 mg L^-1 during winter and early spring. Mean leachate DRP levels were significantly higher in toe slope cores than in top slope cores (0.11 and 0.02 mg L^-1 , respectively). Saturated hydraulic conductivity varied widely across cores and was not correlated with leachate DRP concentration. All soil cores exhibited high P sorption potential, even under conditions of preferential flow. These findings suggest that much of the DRP transport in these landscapes is derived from P hotspots located in toe slope positions. Application of soil P fertilizer amounts in variable rates that account for spatial variability in P transport may minimize P enrichment and subsequent leaching in these locations.