Dr. Beat Frey

Springtails (Collembola) and mites (Acari) are soil microarthropods, one of the most diverse animal groups in soils. They play a crucial role in organic matter cycling and are active throughout the food web as decomposers, bacterivores, fungivores, and carnivores. Only little is known about how these groups might respond to shifts in water availability, for example in the context of global change. Here, we investigated how soil microarthropods responded to long-term irrigation in a drought-prone Scots pine (Pinus sylvestris) forest in southern Switzerland. After more than a decade of doubling the annual rainfall, irrigation improved not only tree vitality but also soil quality, and with shifts in bacteria and fungi reflecting changes from oligotrophic to copiotrophic conditions. We assessed soil microarthropods with two approaches: (1) directly by soil DNA metabarcoding and (2) by morphological assessment after extraction of the animals with Macfadyen funnels. Another main aim of that study was to compare the results with the two approaches. The dominant Collembola genus in both assessment approaches was Parisotoma. The dominant Sarcoptiformes genus was Oppiella whereas Geolaelaps was the dominant Mesostigmata genus in both assessment approaches. Only the metabarcoding approach detected Trombidiformes genera, and only one genus, Microtydeus, had a classification confidence >80 %.
The abundance and alpha-diversity of Collembola and Acari did not change significantly as a result of the irrigation treatment, regardless of the assessment approaches applied. In contrast, microarthropod beta-diversity showed significantly shifts for Collembola and Acari, and for the Collembola order Entomobryomorpha and the Acari orders Sarcoptiformes, Mesostigmata, and Trombidiformes. A Procrustes analysis comparing the two assessment approaches indicated a significant effect of the irrigation treatment for the mite order Sarcoptiformes and a nearly significant effect for Collembola.
Using indicator species analysis a Parisotoma species was the only Collembola taxon in the metabarcoding assessment that was strongly associated with the irrigation treatment. With the morphological assessment, Parisotoma notabilis and Lepidocyrtus sp. were significantly associated with irrigation. For Acari, only the morphological approach let to Licnodamaeus pulcherrimus as a negative indicator taxon for irrigation. By using the morphospecies lists as a reference for validation and comparing it with the species list obtained through metabarcoding, we found that only a small percentage of Collembola and Acari morphospecies overlapped. The metabarcoding approach detected taxa that were not observed with the morphological assessment, such as Neelipleona, Symphypleona, or Trombidiformes. Due to the complexity of the taxa and the lack of comprehensive taxonomic identification and reference databases, identification at the species level is hardly possible. Further efforts to enrich the microarthropod reference database are urgently needed.

Earthworms and enchytraeids play an important role in biogeochemical cycles and are good indicators of soil fertility. However, assessing their assemblages is difficult, mainly because the methods to identify them require expert knowledge, which becomes a technical challenge when surveying large areas. Soil DNA metabarcoding is a promising method that enables the identification of individual species directly from a bulk composite sample in large field experiments. Here, we investigated in parallel both earthworm (family Lumbricidae) and enchytraeid (family Enchytraeidae) assemblages in three land-use types (arable land, grassland, forest) across 29 Swiss Soil Monitoring Network (NABO) sites, using high-throughput amplicon sequencing of marker genes. For both earthworms and enchytraeids, α-diversity was higher in grasslands than in arable land and forests, and it was significantly affected by soil physico-chemical, climate and biological properties, especially pH and climate properties. In addition, we found negative correlations between earthworms α-diversity and soil total carbon (TC) content and the soil carbon to nitrogen ratio. Using the DNA metabarcoding, we observed sequences of Aporrectodea nocturna in soils with low pH, while other Aporrectodea species occurred in soils with high pH. We identified Bimastos rubidus in soils with low pH but higher TC, total nitrogen, organic C, and low silt content, while the enchytraeids Cognettia sphagnetorum and Cernosvitoviella atrata occurred in forest soils with high water and organic matter contents. We identified some indicator taxa for the different land-use types, for grassland: Aporrectodea icterica, Lumbricus rubellus, Marionina communis, Fridericia bisetosa and Fridericia connata; arable land: Allolobophora chlorotica, Enchytraeus dichaetus, Achaeta iberica, Prodtodrilus antipae and Fridericia tuberosa; and for forest: Octolasion cyaneum, Octolasion lacteum and Cognettia chlorophila. Although these indicator taxa are unlikely to provide information about the effect of land-use change on soil biodiversity at large spatial scales, these species do drive assemblage differences between land-use types. Soil DNA metabarcoding could therefore assist land managers in monitoring soil biodiversity and quality.

Global warming has led to permafrost thawing in mid-latitude alpine regions, resulting in greater availability of carbon (C) and nutrients in soils. However, how these changes will impact the functional genetic potential of permafrost soil microbiomes, and subsequently, how they will influence the microbially mediated feedback of mountain soils under climate change remains unknown. To help answer this question, we conducted a permafrost thawing experiment on the north-facing slope near the summit of Muot da Barba Peider (2979 m above sea level) in the Swiss Alps. Specifically, we transplanted permafrost soils from a depth of 160 cm to the active-layer topsoils (0–18 cm) and incubated the soils in situ for three years. Using shotgun metagenomics, we found that transplantation significantly altered the gene structure of the permafrost microbiome, with changes occurring in the short term (< one year) and remaining stable over time. Transplanted soils exhibited an enhanced functional genetic potential, particularly for genes related to "Information storage and processing", "Cellular processes and signaling" and "Metabolism" functions, which suggests increased cellular processes and metabolism. Carbohydrate-active enzymes involved in the degradation of both labile (such as starch) and recalcitrant (such as lignin) C substrates were enriched in transplanted soils, indicating an enhanced C-degradation potential. Nitrogen (N)-cycling genes related to the degradation and synthesis of N compounds, denitrification, assimilation and dissimilatory nitrate reduction were overrepresented in the transplanted soil, pointing to enhanced N assimilation and transformation potential. Our study elucidates how the permafrost microbiome may functionally respond to warming in the European Alps. This research complements observations from Tibetan and Arctic regions, improving our understanding of functional changes in thawing permafrost globally.

Background: Phosphorus (P) availability in soils regulates forest productivity. However, the drivers of soil P dynamics following forest management remain poorly understood, particularly in P-deficient forests in tropical and subtropical regions.
Method: Soil samples of 0–10 cm were collected from the plots after 9 years of thinning and understory removal (UR) in Pinus massoniana plantations in subtropical China. Soil physicochemical properties, microbial biomass and community composition, and Hedley P fractions were measured to assess the underlying mechanisms for the dynamics of soil P fractions.
Results: Compared to undisturbed plots, total soil inorganic P (Pi; + 24%) within the dominant species thinning (DST) plots showed a significant increase, which was associated with the accrual in resin-Pi (+ 30%), NaHCO₃-Pi (+ 21%), and C.CHl-Pi (+ 45%). These Pi fractions were primarily correlated with increased relative abundance of Ascomycota, Rozellomycota, and Proteobacteria. Conversely, post-management (thinning and UR) assessments revealed no significant changes in total P, total organic P (Po), and residual P. The observed decrease in total Po (– 9%) in DST plots was linked to reductions in NaHO-Po (– 7%) and C.CHl-Po (– 24%). Notably, these Po fractions were negatively affected by the relative abundance of Glomeromycota. Furthermore, variations in soil fungal and bacterial community structures accounted for 44.3% and 26.3% of the variances in soil Pi fractions, respectively, similarly explaining 20.4% and 33.3% for soil Po fractions, respectively.
Conclusions: These results indicate that P availability following forest management interventions within subtropical pine plantations is intricately connected to microbial community composition that enhances the transformation from Po into Pi forms.

Calcareous glacier forefields challenge prevailing ecological frameworks on microbial biodiversity and community assembly due to their unique bedrock. Early stages of soil development in these environments are notorious for their high turnover rates, demanding a high degree of replication for obtaining conclusive data. However, studies across different calcareous glaciers are still missing. Here, we robustly investigated both bacterial and fungal diversity, association networks, and assembly processes in four calcareous glacier forefields of the Alps, focusing on the earliest soil developmental stages (<25 years) early in the snow-free season. We found a diverse community of bacteria and fungi, potentially involved in P and N nutrient cycling. A core microbiome existing across all four locations suggests that certain microbes might be more successful colonizers of these ecosystems than others. Nearest taxon index revealed phylogenetically clustered microbial communities. These findings suggest that the distribution and colonization of some microbes were influenced by selective forces such as geography and climate during the early stages of soil development in calcareous glaciers. Interestingly, there were no common bacterial-fungal associations across the four locations, indicating that this habitat does not select for specific bacterial-fungal associations and that associations were driven by neutral processes. We discuss microbial communities and their interactions in these special calcareous glacier forefield habitats. Moreover, we present innovative approaches for studying microbial assembly that address both deterministic, intrinsic drivers, like specific microbial traits, and stochastic, extrinsic drivers, such as the opportunistic behavior of microbes.

Biological diversity in mountain ecosystems has been increasingly studied over the last decade. This is also the case for mountain soils, but no study to date has provided an overall synthesis of the current state of knowledge. Here we fill this gap with a first global analysis of published research on cryptogams, microorganisms, and fauna in mountain soils above the treeline, and a structured synthesis of current knowledge. Based on a corpus of almost 1400 publications and the expertise of 37 mountain soil scientists worldwide, we summarise what is known about the diversity and distribution patterns of each of these organismal groups, specifically along elevation, and provide an overview of available knowledge on the drivers explaining these patterns and their changes. In particular, we document an elevation-dependent decrease in faunal diversity above the treeline, while for cryptogams there is an initial increase above the treeline, followed by a decrease towards the nival belt. Thus, our data confirm the key role that elevation plays in shaping the biodiversity and distribution of these organisms in mountain soils. The response of prokaryote diversity to elevation, in turn, was more diverse, whereas fungal diversity appeared to be substantially influenced by plants. As far as available, we describe key characteristics, adaptations, and functions of mountain soil species, and despite a lack of ecological information about the uncultivated majority of prokaryotes, fungi, and protists, we illustrate the remarkable and unique diversity of life forms and life histories encountered in alpine mountain soils. By applying rule- as well as pattern-based literature-mining approaches and semi-quantitative analyses, we identified hotspots of mountain soil research in the European Alps and Central Asia and revealed significant gaps in taxonomic coverage, particularly among biocrusts, soil protists, and soil fauna. We further report thematic priorities for research on mountain soil biodiversity above the treeline and identify unanswered research questions. Building upon the outcomes of this synthesis, we conclude with a set of research opportunities for mountain soil biodiversity research worldwide. Soils in mountain ecosystems above the treeline fulfil critical functions and make essential contributions to life on land. Accordingly, seizing these opportunities and closing knowledge gaps appears crucial to enable science-based decision making in mountain regions and formulating laws and guidelines in support of mountain soil biodiversity conservation targets.

Aim: Conflicting distribution patterns of soil microbes along the elevation gradient in alpine ecosystems have been suggested based on observations from individual mountains. There remains a lack of biogeographical studies spanning multiple latitudes and climate zones, a scale appropriate to reveal general ecological patterns of soil microbial biomass (SMB) for alpine ecosystems. We conducted a large-scale sampling campaign along elevational gradients in seven mountains across mainland China and investigated the biogeographical patterns of soil microorganisms and quantified the influencing environmental factors.
Location: China.
Time Period: 2019.
Major Taxa Studied: Seed plant species and soil microorganisms.
Methods: We sampled aboveground plants and belowground soils along elevational gradients from closed forests located below the alpine treeline up to the upper elevational limit of vegetation in seven mountains. We analysed the distribution patterns of SMB and the ratio of fungi to bacteria (F/B) and quantified four types of environmental factors at local (i.e., plant functional traits, soil physicochemical properties, and topography) and regional (i.e., macroclimate) scales to determine the drivers of microbial biomass in alpine ecosystems. Results: We observed a hump-shaped pattern of SMB along the elevation gradients, with a maximum near the alpine treeline. The soil nutrient status and plant functional traits played the most decisive roles in shaping SMB. Local-scale environmental factors were more important than regional factors in determining SMB in alpine ecosystems.
Main Conclusions: Our study suggests that distribution patterns of SMB in alpine ecosystems are closely related to environmental heterogeneity rather than elevation alone. In the context of future temperature rises with global change, soil microbes can more easily track localised changes in microhabitats compared with top-down effects of macroclimate, indicating that effects of climate warming on soil microbes could possibly be buffered by local environmental factors in alpine ecosystems.

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

With their various feeding types, soil nematodes play a crucial role in the soil food web. Here, we investigated if and how soil nematodes responded to a long-term irrigation in a drought-prone Scots pine (Pinus sylvestris) forest in southern Switzerland, applied to study whether greater soil water availability would improve tree health and reduce tree mortality. After 14 years of irrigation, tree vitality and soil development had improved significantly. However, morphological observations of the soil nematodes revealed a decrease in their total number in the irrigated plots. Overall, the irrigated plots had a lower nematode richness compared with the dry control plots, but the Shannon index did not differ between the two treatments. In addition, the nematode community shifted significantly as a result of the irrigation. Soil physical parameters, such as sand and silt contents and bulk density, were significantly positively correlated with the nematode community in the irrigation treatment. According to a DNA marker sequence analysis, a total of 43 genera of nematodes were assigned. Predatory nematodes were significantly less abundant in the irrigated plots than in the dry control plots, as the average number decreased to 74 in the irrigated plots compared to 3579 in the dry control plots, while non-predators were not significantly affected. A differential abundance analysis revealed that the genera Tripyla and Anatonchus were the predators that declined the most. Overall, marker sequence analysis of forest soil nematodes appears to be a suitable tool for assessing changes in nematode communities and taxa. The disappearance of predatory nematodes under irrigation, however, can perhaps only be explained if other predatory animal groups, such as predatory mites or millipedes, are also analyzed at the same time.

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.

Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio^® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.

Grazing plays a significant role in shaping both aboveground vegetation and belowground microbial communities in arid and semi-arid grasslands, which in turn affects ecosystem functions and sustainability. Therefore, it was essential to implement effective grazing management practices to preserve ecological balance and support sustainable development in these delicate environments. To optimize the traditional continuous grazing policy, we conducted a 10-year seasonal grazing experiment with five treatments in a typical grassland in northern China: no grazing (NG), continuous summer grazing (CG), and three seasonal grazing treatments (G57 in May and July, G68 in June and August, and G79 in July and September). Our study found that although grazing reduced plant community biomass, G68 treatment maintained high plant height and community diversity (P < 0.05). Grazing did not affect soil bacterial and archaeal alpha diversity, but CG treatment reduced soil fungal diversity (P < 0.05). CG reduced the archaeal network's vertices (which represent microbial taxa, OTUs) and connections (ecological interactions between taxa), but seasonal grazing increased its complexity. Furthermore, grazing did not change bacterial networks but enhanced cross-domain interactions (relationships between different biological groups) of plant-soil fungi and plant-soil archaea. Overall, we used the Mantel test to find that soil microbial diversity was positively correlated with soil physicochemical properties rather than plant community characteristics after grazing. These findings are beneficial for the optimization of sustainable grassland management policies and the protection of plant and soil biodiversity.

Background: Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.

Results: Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.

Conclusions: Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities.

Over recent decades, there has been a noticeable change in vegetation diversity accompanied by increased plant productivity in tundra systems of the High-Arctic, leading to elevated carbon and nutrient inputs into the soil. This shift can alter microbial community composition and activity in these ecosystems. In this study, we aimed to identify genes transcribed by active microorganisms and compare their expression in unamended and amended soils with labile carbon and/or nitrogen compounds. We also assessed gene expression differences in tundra soils with varying edaphic characteristics (upslope vs. downslope sites). We amended soils with either glycine or cellulose or left them unamended (i.e., control) for 7 days of incubation, and we isolated and sequenced RNA using Illumina technology. Whereas we observed only a weak transcriptional response after cellulose addition, the glycine addition significantly influenced transcriptional patterns, with upregulation of carbon- and nitrogen-cycling genes. Notably, microbial taxa from the Pseudomonadaceae and Micrococcaceae families showed the most pronounced response to glycine, indicating a shift of the communities towards copiotrophic organisms. This response was consistent across the two soil types, suggesting a common impact on microbial community activity. These findings suggest that an increase in carbon and nitrogen inputs could substantially affect microbial functioning in High-Arctic tundra soils, with potential implications for ecosystem dynamics under global warming.

Soil microorganisms are pivotal in global biogeochemical cycles, significantly influencing energy flow and climate regulation. The Deyeuxia angustifolia wetland in the Sanjiang Plain, northeastern China, represents a key ecological area, yet the impact of organic nitrogen (Urea) addition on its soil microbial community remains largely unexplored. This study delves into the assembly patterns and processes of soil microbial communities following seven years of urea addition in this wetland, utilizing high-throughput sequencing technology. Our findings reveal that urea addition leads to a decrease in soil pH and an increase in various soil nutrients, including dissolved organic carbon, total nitrogen, organic carbon, dissolved organic nitrogen, nitrate, and ammonia nitrogen. While urea addition significantly alters soil bacterial and fungal β-diversity, it does not affect their α-diversities. Comparative analysis across nitrogen treatments shows significant shifts in 24 bacterial and 21 fungal taxa. The abundance of a few bacterial genera (Bradyrhizobium and Haliangium) decreases with increasing N addition; while the abundance of a few fungal genera (Penicillium and Coniochaeta) increases with the increasing N addition. Random forest models revealed that rare genera (e.g., Syntrophorhabdus, Terrimonas, Galerina, and Mariannaea) also play an important role during organic nitrogen addition. Co-occurrence network analysis indicates a weakening interaction between bacteria and fungi with increased urea addition, accompanied by shifts in dominant bacterial and fungal phyla. Mantel test revealed a correlation between bacterial community diversity, network topology properties and various soil physico-chemical properties, while only network topology properties were correlated with soil physicochemical properties in the fungal community. Structural equation modeling (SEM) suggested that organic nitrogen addition affect soil bacterial and fungal structure by influencing plant diversity, plant biomass, and environmental factors. Community assembly analysis reveals a stochastic dominance in bacterial communities and a deterministic dominance in fungal communities under urea addition. Overall, this study enhances our understanding of soil microbial community responses to organic nitrogen addition in wetland ecosystems, offering insights for their sustainable management.

It is widely known that antibiotics can affect the structure and function of soil microbial communities, but the specific degree of impact and controlled factors on different indicators remain inconclusive. We conducted a multiple hierarchical mixed effects meta-analysis on 2564 observations that were extracted from 60 publications, to comprehensively assess the impact of antibiotics on soil microbiota. The results showed that antibiotics had significant negative effects on soil microbial biomass, α-diversity and soil enzyme activity. Under neutral initial soil, when soil was derived from agricultural land or had a fine-textured, the negative impacts of antibiotics on soil microbial community were exacerbated. Both single and mixed additions of antibiotics had significant inhibitory effects on soil microbial enzyme activities. The Random Forest model predicted the following key moderators involved in the effects of antibiotics on the soil microbiome, and antibiotics type, soil texture were key moderators on the severity of soil microbial biomass changes. Soil texture, temperature and single or combined application constitute of antibiotics were the main drivers of effects on soil enzyme activities. The reported results can be helpful to assess the ecological risk of antibiotics in a soil environment and provides a scientific basis for the rational of antibiotics use in the soil environment.

Nitrogen cycling in terrestrial ecosystems is critical for biodiversity, vegetation productivity and biogeochemical cycling. However, little is known about the response of functional nitrogen cycle genes to global change factors in soils under different land uses. Here, we conducted a multiple hierarchical mixed effects meta-analyses of global change factors (GCFs) including warming (W+), mean altered precipitation (MAP+/−), elevated carbon dioxide concentrations (eCO₂), and nitrogen addition (N+), using 2706 observations extracted from 200 peer-reviewed publications. The results showed that GCFs had significant and different effects on soil microbial communities under different types of land use. Under different land use types, such as Wetland, Tundra, Grassland, Forest, Desert and Agriculture, the richness and diversity of soil microbial communities will change accordingly due to differences in vegetation cover, soil management practices and environmental conditions. Notably, soil bacterial diversity is positively correlated with richness, but soil fungal diversity is negatively correlated with richness, when differences are driven by GCFs. For functional genes involved in nitrification, eCO₂ in agricultural soils and the interaction of N+ with other GCFs in grassland soils stimulate an increase in the abundance of the AOA-amoA gene. In agricultural soil, MAP+ increases the abundance of nifH. W+ in agricultural soils and N+ in grassland soils decreased the abundance of nifH. The abundance of the genes nirS and nirK, involved in denitrification, was mainly negatively affected by W+ and positively affected by eCO₂ in agricultural soil, but negatively affected by N+ in grassland soil. This meta-analysis was important for subsequent research related to global climate change. Considering data limitations, it is recommended to conduct multiple long-term integrated observational experiments to establish a scientific basis for addressing global changes in this context.

Microplastics (MPs) pollution is recognized as a global emerging threat with serious potential impacts on ecosystems. Our meta-analysis was conducted based on 117 carefully selected publications, from which 2160 datasets were extracted. These publications described experiments in which MPs were added to soil (in laboratory or greenhouse experiments or in the field) after which the soil microbial community was analyzed and compared to a control group. From these publications, we extracted 1315 observations on soil bacterial alpha diversity and richness indices and 845 datasets on gene abundance of bacterial genes related to the soil nitrogen cycle. These data were analyzed using a multiple hierarchical mixed effects meta-analysis. The mean effect of microplastic exposure was a significant decrease of soil bacterial community diversity and richness. We explored these responses for different regulators, namely MPs addition rates, particle size and plastic type, soil texture and land use, and study type. Of the bacterial processes involved in the soil nitrogen cycle, MPs addition significantly promoted assimilation of ammonium, nitrogen fixation and urea decomposition, but significantly inhibited nitrification. These results suggest that MPs contamination may have considerable impacts on soil bacterial community structure and function as well as on the soil nitrogen cycle.

China has experienced a notorious increase in nitrogen (N) deposition as a result of anthropogenic activities, particularly in temperate areas. While aboveground biodiversity has been extensively studied, the impact of long-term N deposition on the diversity, composition, and function of the soil microbiome remains largely unexplored. In this study, we evaluated alterations in the diversity, composition, and function of soil bacterial and fungal communities in response to varying levels of N deposition (LN = low N addition, 40 kg N ha⁻¹ yr⁻¹; HN = high N addition, 80 kg N ha⁻¹ yr⁻¹) using Illumina MiSeq sequencing technology in a temperate natural wetland. N deposition had no discernible impact on bacterial α diversity, whereas fungal α diversity exhibited a significant decrease in response to high N addition only. Additionally, N deposition led to a notable increase in the relative abundance of the bacterial phylum Patescibacteria but a decrease in Latescibacteria. The relative abundance of Epsilonbacteraeota was highest in the unamended plots and lowest in the low N addition plots. Furthermore, N addition significantly increased the relative abundance of Ascomycota while decreasing that of Mortierellomycota, with no significant effect observed on Basidiomycota. Structural equation modeling (SEM) indicated that soil organic carbon (SOC), and total and available N were the two primary drivers shaping bacterial and fungal communities. Our study demonstrated that bacterial communities were less responsive to N addition compared to fungal communities, emphasizing the significance of simultaneously evaluating the soil microbiome in response to global changes.