Urbanization significantly impacts the connectivity of soil microbes involved in nitrogen dynamics at a watershed scale

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.

Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces

The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing-Tianjin-Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance-decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya)

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

Urban greenness and plant species are key factors in shaping air microbiomes and reducing airborne pathogens

Urban green space has been implicated in shaping airborne microbes, but there is an only rudimentary understanding of the key factors of urban green space affecting the composition and structures of airborne microbes. Here, we selected 40 urban sites based on stratified random sampling design and investigated the effects of multiple factors including landscapes, plant, soil, and anthropogenic factors on airborne microbial communities, especially bacterial and fungal pathogens. Bacterial and fungal communities in the control area with lower greenness were significantly (P < 0.05) different from those in other areas with a gradient of green space. The relative abundance of bacterial and fungal pathogens significantly (P < 0.05) decreased with increasing greenness. Other than soil thickness, soil type, slope position, and population density, plant species considerably contributed to the shift in the composition and abundance of potential bacterial and fungal pathogens. A significantly (P < 0.05) reduced abundance of bacterial and fungal pathogens was observed in areas with >30% masson pine. Together, these results provide insights into the importance of green space for providing health benefits for city dwellers by reducing pathogens in air, as well as providing support for the inclusion of plant species in the management of urban green space to reduce exposure risk of airborne pathogens.

Urbanisation differently affects decomposition rates of recalcitrant woody material and labile leaf litter

Litter decomposition is a fundamental ecosystem process and service that supplies nutrients to the soil. Although decomposition rate is influenced by litter quality, climatic conditions, the decomposer community and vegetation type in non-urban ecosystems, little is known about the degradation of different organic matter types in urban settings. We investigated the decomposition rates of recalcitrant (wood sticks for 4 years) and labile litter (green tea leaves in pyramid-shaped teabags for 3 years) in urban habitats that differed in level of management and disturbance. We found that recalcitrant woody material decomposed slower in urban habitat types (ca. 60–75% mass loss after 4 years in remnant spruce forests, park lawns, ruderal habitats) than in natural to semi-natural spruce forest soils (84% mass loss) outside the city. Labile tea litter, however, decomposed faster in typical open urban habitats (70% mass loss after 3 years in park lawns, ruderal habitats) than in forested habitats (60% mass loss in semi-natural and remnant spruce forests), with a remarkable dichotomy in decomposition rate between open and forested habitats. We suggest that the slower rate of wood decomposition in the city relates to its depauperate saprotrophic fungal community. The faster rate of labile litter decomposition in open habitats is difficult to explain, but is potentially a consequence of environmental factors that support the activity of bacteria over fungi in open habitats. We propose that the reintroduction of decaying woody material into the urban greenspace milieu could increase biodiversity and also improve the ability of urban soils to decompose an array of organic material entering the system. This reintroduction of decaying woody material could either occur by leaving cut logs – due to management – in urban remnant forests, which has been shown to be accepted as natural features by residents in Fennoscandian cities, and by placing logs in urban parks in ways that communicate their intentional use as part of urban landscape design and management.

Coupling Genomics and Hydraulic Information to Predict the Nitrogen Dynamics in a Channel Confluence

The simulation of nitrogen dynamics in urban channel confluences is essential for the evaluation and improvement of water quality. The omics-based modeling approaches that have been rapidly developed have been increasingly applied to characterize metabolisms of the microbial community and transformation of the associated materials. However, the transport of microorganisms and chemicals within and among different phases, which could be the rate-limiting step for the nitrogen dynamics, are always neglected or oversimplified in omics-based models. Therefore, this study proposes a novel simulation system coupling genomic and hydraulic information to simulate transport and transformation processes and provide predictions of nitrogen dynamics in a confluence. The proposed model was able to capture multiphase mass transport, microbial population dynamics, and nitrogen transformation and accurately predict gene abundances and nitrogen concentrations in both water and sediment; the mean relative errors were all lower than 40%. The model emphasized the importance of transport processes, which contributed more than 90% to gene abundances and chemical concentrations. Moreover, the simulation of reaction rates exhibited the specific nitrogen transformation processes in the confluence. The sulfide oxidation and the nitrate reduction and anaerobic ammonium oxidation, with the participation of the genes nap and hzo, respectively, were promoted as the main processes of nitrate and nitrite reduction.

Connections and Feedback: Aquatic, Plant, and Soil Microbiomes in Heterogeneous and Changing Environments

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.