Soil animal communities demonstrate simplification without homogenization along an urban gradient

Urbanization profoundly impacts biodiversity and ecosystem function, exerting an immense ecological filter on the flora and fauna that inhabit it, oftentimes leading to simplistic and homogenous ecological communities. However, the response of soil animal communities to urbanization remains underexplored, and it is unknown whether their response to urbanization is like that of aboveground organisms. This study investigated the influence of urbanization on soil animal communities in 40 public parks along an urbanization gradient. We evaluated soil animal abundance, diversity, and community composition and related these measures to urban and soil characteristics at each park. The most urbanized parks exhibited reduced animal abundance, richness, and Shannon diversity. These changes were influenced by many variables underscoring the multifaceted influence of urbanization on ecological communities. Notably, contrary to our expectation, urbanization did not lead to community homogenization; instead, it acted stochastically, creating unique soil animal assemblages. This suggests that urban soil animal communities are concomitantly shaped by deterministic and stochastic ecological processes in urban areas. Our study highlights the intricate interplay between urbanization and soil animal ecology, challenging the notion of urban homogenization in belowground ecosystems and providing insight for managing and preserving belowground communities in urban areas.

Metal pollution drives earthworm biodiversity in urban lawns

Urban soils represent hotspots of metallic trace elements (MTEs) pollution. Despite the critical impact of soil organisms on soil ecosystem services, there is limited understanding regarding the effects of MTE levels in urban soils on these organisms. This is particularly surprising considering that earthworms, key organisms for soil ecosystems, are commonly used in MTE toxicity tests. This research investigates the impact of MTE pollution on earthworm communities in lawns within the city of Paris. In this study, we sampled a comprehensive array of earthworm communities, totalling 965 individuals from 13 distinct species belonging to Lumbricus, Aporrectodea, Allolobophora and Octolasion genera. These communities were collected from three different locations within 18 parks. At these sites, we assessed the concentrations of eight metals and metalloids in the soil (As, Cd, Cr, Cu, Zn, Ni, Pb and Hg), along with selenium concentrations and eight fundamental soil parameters, to examine the association between earthworm communities and soil attributes. Median MTE concentrations exceeded recommended statutory limit values by approximately 20 % (0.6 mg/kg Cd), 30 % (36.8 mg/kg Cu), 40 % (122.0 mg/kg Zn), and up to 90 % (0.6 mg/kg Hg and 99.7 mg.kg Pb). Nevertheless, these concentrations exhibited considerable variability both between and within parks, correlating with variations in earthworm community structures. Specifically, our results highlight that Cu concentrations in the soil explain about 6 % of the variation in the assemblage of earthworm species. Our findings underscore the importance of considering MTE pollution levels to enhance our comprehension of earthworm distribution in urban environments and its effects on the ecosystem services provided by urban lawns.

Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site

Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short- and medium-term effects on the diversity and the composition of soil microbial communities are well-documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long-term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.

Urbanization can accelerate climate change by increasing soil N2 O emission while reducing CH4 uptake

Urban land-use change has the potential to affect local to global biogeochemical carbon (C) and nitrogen (N) cycles and associated greenhouse gas (GHG) fluxes. We conducted a meta-analysis to (1) assess the effects of urbanization-induced land-use conversion on soil nitrous oxide (N₂ O) and methane (CH₄ ) fluxes, (2) quantify direct N₂ O emission factors (EF_d ) of fertilized urban soils used, for example, as lawns or forests, and (3) identify the key drivers leading to flux changes associated with urbanization. On average, urbanization increases soil N₂ O emissions by 153%, to 3.0 kg N ha^-1  year^-1 , while rates of soil CH₄ uptake are reduced by 50%, to 2.0 kg C ha^-1  year^-1 . The global mean annual N₂ O EF_d of fertilized lawns and urban forests is 1.4%, suggesting that urban soils can be regional hotspots of N₂ O emissions. On a global basis, conversion of land to urban greenspaces has increased soil N₂ O emission by 0.46 Tg N₂ O-N year^-1 and decreased soil CH₄ uptake by 0.58 Tg CH₄ -C year^-1 . Urbanization driven changes in soil N₂ O emission and CH₄ uptake are associated with changes in soil properties (bulk density, pH, total N content, and C/N ratio), increased temperature, and management practices, especially fertilizer use. Overall, our meta-analysis shows that urbanization increases soil N₂ O emissions and reduces the role of soils as a sink for atmospheric CH₄ . These effects can be mitigated by avoiding soil compaction, reducing fertilization of lawns, and by restoring native ecosystems in urban landscapes.

Spatial assortment of soil organisms supports the size-plasticity hypothesis

The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and, therefore, are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies for urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode, and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift, and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for example, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models.

Different rhizosphere soil microbes are recruited by tomatoes with different fruit color phenotypes

Background

To explore and utilize abundant soil microbes and their beneficial functions, the bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were analyzed using high-throughput sequencing technique.

Result

Our results indicated that different soil microbes in rhizospheres of tomatoes were exactly recruited by different color fruit tomatoes. For the reasons as not only soil bacterial community, but also soil fungal compositions were all different between red and yellow fruit tomatoes. For example, Nocardioides, norank_f_norank_o_Vicinamibacterales, norank_f_norank_o_norank_c_KD4-96, norank_f_Birii41, norank_f_norank_o_S085 and Bradyrhizobium were the specific dominant soil bacterial genera, and Lecythophora, Derxomyces and unclassified_f_Pyronemataceae were the dominant soil fungal genera in the rhizospheres of red tomato varieties. By contrast, unclassified_f__Micromonsporaceae, Acidipila, Roseisolibacter, Gaiella and norank_f_Xanthobacteraceae were the unique dominant soil bacterial genera in the rhizospheres of yellow tomato varieties. And unclassified_o__Onygenales, Trichocladium, unclassified_c__Sordariomycetes, Pseudogymnoascus, Acremonium, Oidiodendron, Phialemonium, Penicillium, Phialosimplex were the unique dominant soil fungal genera in rhizospheres of yellow tomato varieties. Moreover, a higher abundance of specific soil bacterial and fungal genera in the rhizosphere was found in rhizospheres of the yellow than those of the red tomato varieties.

Conclusion

Soil bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were found significantly different which growing in the same environment under the identical managements. It suggested that different soil microbes in rhizospheres exactly were recruited by different phenotypes tomato varieties related to fruit color formation.