Urban land uses shape soil microbial abundance and diversity

Fungal diversity and key functional gene abundance in Iowa bioretention cells: implications for stormwater remediation potential

Stormwater bioretention cells are green stormwater infrastructure systems that can help mitigate flooding and remove contaminants. Plants and bacteria improve nutrient removal and degrade organic contaminants; however, the roles of fungi in bioretention cells are less known. Although mycorrhizal fungi aid in plant growth/improve nutrient uptake, there is a notable lack of research investigating fungal diversity in bioretention cells. Other types of fungi could benefit bioretention cells (e.g., white rot fungi degrade recalcitrant contaminants). This study addresses the knowledge gap of fungal function and diversity within stormwater bioretention cells. We collected multiple soil samples from 27 different bioretention cells in temperate-climate eastern Iowa USA, characterized soil physicochemical parameters, sequenced the internal transcribed spacer (ITS) amplicon to identify fungal taxa from extracted DNA, and measured functional gene abundances for two fungal laccases (Cu1, Cu1A) and a fungal nitrite reductase gene (nirKf). Fungal biodegradation functional genes were present in bioretention soils (mean copies per g: 7.4 × 105nirKf, 3.2 × 106Cu1, 4.0 × 108Cu1A), with abundance of fungal laccase and fungal nitrite reductase genes significantly positively correlated with soil pH and organic matter (Pearson's R: >0.39; rho < 0.05). PERMANOVA analysis determined soil characteristics were not significant explanatory variables for community composition (beta diversity). In contrast, planting specifications significantly impacted fungal diversity; the presence/absence of a few planting types and predominant vegetation type in the cell explained 89% of variation in fungal diversity. These findings further emphasize the importance of plants and media as key design parameters for bioretention cells, with implications for fungal bioremediation of captured stormwater contaminants.

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years. Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H'), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H' and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity. The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.

Unveiling the overlooked microbial niches thriving on building exteriors

Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.

Intercropping changed the soil microbial community composition but no significant effect on alpha diversity

Introduction

Enhancing the planning of the forest-agricultural composite model and increasing the efficiency with which forest land is utilized could benefit from a thorough understanding of the impacts of intercropping between forests and agriculture on soil physicochemical properties and microbial communities.

Methods

Populus cathayana × candansis cv. Xinlin No.1 and Glycine max intercrop soils, along with their corresponding monocrops, were used in this study's llumina high-throughput sequencing analysis to determine the composition and diversity of soil bacterial and fungal communities.

Results

The findings indicated that intercropping considerably raised the soil's total phosphorus content and significantly lowered the soil's carbon nitrogen ratio when compared to poplar single cropping. Furthermore, the total carbon and nitrogen content of soil was increased and the soil pH was decreased. The sequencing results showed that intercropping had no significant effect on soil alpha diversity. Intercropping could increase the composition of fungal community and decrease the composition of bacterial community in poplar soil. At the phylum level, intercropping significantly increased the relative abundance of four dominant phyla, i.e., Patescibacteria, Proteobacteria, Patescibacteria and Deinococcus-Thermus. And the relative abundances of only two dominant phyla were significantly increased. It was found that soil total phosphorus and available phosphorus content had the strongest correlation with soil bacterial community diversity, and soil pH had the strongest correlation with soil fungal community diversity.

Discussion

The results of this study were similar to those of previous studies. This study can serve as a theoretical foundation for the development of a poplar and black bean-based forest-agricultural complex management system in the future.

Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale

Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.