A case for the importance of following antibiotic resistant bacteria throughout the soil food web.

It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.

Genotype diversity enhances invasion resistance of native plants via soil biotic feedbacks.

Although native species diversity is frequently reported to enhance invasion resistance, within-species diversity of native plants can also moderate invasions. While the positive diversity-invasion resistance relationship is often attributed to competition, indirect effects mediated through plant-soil feedbacks can also influence the relationship. We manipulated the genotypic diversity of an endemic species, Scirpus mariqueter, and evaluated the effects of abiotic versus biotic feedbacks on the performance of a global invader, Spartina alterniflora. We found that invader performance on live soils decreased non-additively with genotypic diversity of the native plant that trained the soils, but this reversed when soils were sterilized to eliminate feedbacks through soil biota. The influence of soil biota on the feedback was primarily associated with increased levels of microbial biomass and fungal diversity in soils trained by multiple-genotype populations. Our findings highlight the importance of plant-soil feedbacks mediating the positive relationship between genotypic diversity and invasion resistance.

Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks.

Plants can suppress the growth of other plants by modifying soil properties. These negative plant-soil feedbacks are often species-specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown. Here, we investigated whether benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, allow maize plants to cope with plant-soil feedbacks. We find that three out of five tested crop species reduce maize (Zea mays L.) performance via negative plant-soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids restores the protective effect for benzoxazinoid-deficient mutants. Sterilization and reinoculation experiments suggest that benzoxazinoid-mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates context dependency. In conclusion, exuded plant secondary metabolites allow plants to cope with plant-soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative effects of soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations.

Temporal asynchrony of plant and soil biota determines ecosystem multifunctional stability.

The role of plant biodiversity in stabilizing ecosystem multifunctionality has been extensively studied; however, the impact of soil biota biodiversity on ecosystem multifunctional stability, particularly under multiple environmental changes, remains unexplored. By conducting an experiment with environmental changes (adding water and nitrogen to a long-term grazing experiment) and an experiment without environmental changes (an undisturbed site) in semi-arid grasslands, our research revealed that environmental changes-induced changes in temporal stability of both above- and belowground multifunctionality were mainly impacted by plant and soil biota asynchrony, rather than by species diversity. Furthermore, changes in temporal stability of above- and belowground multifunctionality, under both experiments with and without environmental changes, were mainly associated with plant and soil biota asynchrony, respectively, suggesting that the temporal asynchrony of plant and soil biota has independent and non-substitutable effects on multifunctional stability. Our findings emphasize the importance of considering both above- and belowground biodiversity or functions when evaluating the stabilizing effects of biodiversity on ecosystem functions.

No evidence that modification of soil microbiota by woody invader facilitates subsequent invasion by herbaceous species.

Many terrestrial ecosystems are co-invaded by multiple exotic species. The "invasional meltdown" hypothesis predicts that an initial invasive species will facilitate secondary invasions. In the plant kingdom, the potential underlying mechanisms of this hypothesis may be that modification of the soil properties by the initial invaders benefits for the subsequent exotic species invasion. In this study, we analyzed the composition of soil microbial communities and soil chemical properties from sites invaded by woody Rhus typhina, as well as uninvaded sites, to assess the impact of R. typhina invasion. Furthermore, we conducted a greenhouse experiment with multiple native-invasive pairs of herbaceous species to test whether R. typhina invasion facilitates subsequent exotic herb invasion. Our results showed that R. typhina invasion significantly altered the composition of soil fungal communities, especially pathogenic, endophytic, and arbuscular mycorrhizal fungi. However, this change in microbial composition led to neither direction nor magnitude changes in negative plant-soil feedback effects on both native and invasive species. This indicates that initial R. typhina invasion does not facilitate subsequent herb invasion, which does not support the "invasional meltdown" hypothesis. Additionally, R. typhina invasion significantly decreased soil total nitrogen and organic carbon contents, which may explain the significantly lower biomass of herbaceous roots grown in invaded soils compared with uninvaded soils. Alternately, although invasive herb growth was significantly more inhibited by soil microbiota compared with native herb growth, such inhibition cannot completely eliminate the risk of exotic herb invasion because of their innate growth advantages. Therefore, microbial biocontrol agents for plant invasion management should be combined with another approach to suppress the innate growth advantages of exotic species.

Restoration of soil multifunctional indicators requires more than thirty years in degraded shrubland of a semi-arid mountainous ecosystem.

Vegetation degradation in natural environments leads to considerable fluctuations in soil function indicators, particularly in the sensitive and delicate habitats of semi-arid regions. In this study, the dynamic of both litter and soil properties was examined in northern Iran, in sites with Crataegus melanocarpa and Berberis integerrima dominance. The chosen sites have been degraded in 1993 due to exploitation for fuel production. Litter and soil (0-10, 10-20 and 20-30 cm depths) samples were collected in sites that have been degraded [i.e., 10-years post-degradation (2003), 20-years post-degradation (2013), and 30-years post-degradation (2023)]. A site not to exposed to degradation (year 2023) was also included as a control. In total, 48 litter samples (4 study sites × 12 samples) and 144 soil samples (4 study sites × 3 depths × 12 samples) were collected. Our findings showed a significant reduction of approximately 60-70% in the chemical characteristics of the litter, such as phosphorus (P) and magnesium (Mg) after 10-years post-degradation (2003) compared to the control site. Soil fertility indicators were also reduced 2-6 times as a result of habitat degradation. Aligned with this, the biota population in the 10-year post-degradation site showed a decrease of 70-90% with respect to the control. Moreover, the densities of fungi and bacteria decreased by approximately 30%-70% and 45-80% respectively compared to the 30-year post-degraded site. The peak activation of soil enzymes including urease, acid phosphatase, arylsulfatase, and invertase was found in the site that was not subjected to degradation, being 3.5, 5.8, 6.7 and 6.7- times higher in comparison to the 10-year post-degradation site. Overall, the results showed that in the non-degraded ecosystems, the input of plant-based organic matter was accompanied by an increase in soil fertility, organism population and soil function. This pinpoints the importance of protecting plant species in these areas, while in degraded areas planting native species adapted to the region's climate and fertilization could significantly contribute to restoring these areas.

Consequences of Spiraea tomentosa invasion in Uropodina mite (Acari: Mesostigmata) communities in wet meadows.

Vegetation cover has been consistently reported to be a factor influencing soil biota. Massive spreading of invasive plants may transform native plant communities, changing the quality of habitats as a result of modification of soil properties, most often having a directional effect on soil microorganisms and soil fauna. One of the most numerous microarthropods in the litter and soil is Acari. It has been shown that invasive plants usually have a negative effect on mites. We hypothesized that invasive Spiraea tomentosa affects the structure of the Uropodina community and that the abundance and species richness of Uropodina are lower in stands monodominated by S. tomentosa than in wet meadows free of this alien species. The research was carried out in wet meadows, where permanent plots were established in an invaded and uninvaded area of each meadow, soil samples were collected, soil moisture was determined and the mites were extracted. We found that Uropodina mite communities differed in the abundance of individual species but that the abundance and richness of species in their communities were similar. S. tomentosa invasion led primarily to changes in the quality of Uropodina communities, due to an increase in the shares of species from forest and hygrophilous habitats. Our results suggest that alien plant invasion does not always induce directional changes in mite assemblages, and conclude that the impact of an alien species on Uropodina may cause significant changes in the abundance and richness of individual species without causing significant changes in the abundance and diversity of their community.

Aboveground herbivory can promote exotic plant invasion through intra- and interspecific aboveground-belowground interactions.

Aboveground herbivores and soil biota profoundly affect plant invasions. However, how they interactively affect plant invasions through plant-soil feedbacks (PSFs) remains unclear. To explore how herbivory by the introduced beetle Agasicles hygrophila affects Alternanthera philoxeroides invasions in China, we integrated multiyear field surveys and a 2-yr PSF experiment, in which we examined how herbivory affects PSFs on the performance of native and invasive plants and the introduced beetles. Despite increased herbivory from A. hygrophila, A. philoxeroides dominance over co-occurring congeneric native Alternanthera sessilis remained constant from 2014 to 2019. While occurring at lower abundances, A. sessilis experienced similar herbivore damage, suggesting apparent competitive effects. Our experiments revealed that herbivory on A. philoxeroides altered soil microbial communities, prolonged its negative PSF on A. sessilis, and decreased A. hygrophila larvae performance on the next-generation invasive plants. Consequently, A. hygrophila larvae performed better on leaves of natives than those of invasives when grown in soils conditioned by invasive plants defoliated by the introduced beetles. Our findings suggest that aboveground herbivory might promote rather than suppress A. philoxeroides invasion by enhancing its soil-mediated self-reinforcement, providing a novel mechanistic understanding of plant invasions. These findings highlight the need to incorporate an aboveground-belowground perspective during the assessment of potential biocontrol agents.

Oribatid mites in different Mediterranean crop rotations fertilized with animal droppings.

Unsustainable soil management is one of the drivers of soil degradation, but impact assessment requires the development of indicators. Oribatids might be considered as early indicators of disturbances due to the stability of their community. The aim of this study was to investigate the feasibility of oribatids as bioindicators of sustainable agricultural practices. Under a dry Mediterranean climate, three fertilization experiments - two under a two-crop rotation system and one under maize monoculture and established 12 years earlier - were sampled 3× for oribatid identification during the last annual cropping cycle. The hypothesis was that different nutrient and crop managements affect the number of oribatid species and individuals present, and these parameters could be used as indicators of soil degradation. In total, 18 oribatid species were identified, and 1974 adult individuals were recovered. Maximum abundance was found prior to sowing. Pig slurry (PS) vs. control, and dairy cattle manure (CM) vs. mineral fertilization increased oribatid abundance. This increase was evident when the average applied rates with PS were ca. 2 Mg of organic matter (OM) ha- 1 yr- 1, or higher than ca. 4 Mg OM ha- 1 yr- 1 for CM. When the preceding crop was wheat and PS or CM were used, Oribatula (Zygoribatula) excavata (which reproduces sexually) predominated. In maize monoculture fertilized with CM, Tectocepheus sarekensis and Acrotritia ardua americana (which can reproduce through parthenogenesis) prevailed vs. Oribatula, which indicated a heavily disturbed soil. Under this specific Mediterranean environment, the predominance of certain parthenogenic oribatid species and the number of individuals provide advanced warning on soil degradation.

Responses of soil fauna communities to the individual and combined effects of multiple global change factors.

Soil fauna plays a key role in regulating biogeochemical cycles, but how multiple global change factors (GCFs) may affect faunal communities remains poorly studied. We conducted a meta-analysis using 1154 observations to evaluate the individual and combined effects of elevated CO2 , nitrogen (N) addition, warming, increased rainfall and drought on soil fauna density and diversity. Here we show that, overall, individual and combined effects of GCFs had negligible effects on soil fauna density and diversity, except that density was negatively affected by drought (-27.4%) and positively affected by increased rainfall individually (+24.9%) and in combination with N addition (+67.3%) or warming (+70.4%). GCF effects varied among taxonomic groups both in magnitude and direction. Variables such as latitude, elevation and experimental setting significantly impacted both individual and combined effects. Our results suggest that soil fauna density is affected by changed rainfall regimes, while diversity is resistant against individual and combined effects of multiple GCFs.

Is the climate change mitigation effect of enhanced silicate weathering governed by biological processes?

A number of negative emission technologies (NETs) have been proposed to actively remove CO2 from the atmosphere, with enhanced silicate weathering (ESW) as a relatively new NET with considerable climate change mitigation potential. Models calibrated to ESW rates in lab experiments estimate the global potential for inorganic carbon sequestration by ESW at about 0.5-5 Gt CO2  year-1 , suggesting ESW could be an important component of the future NETs mix. In real soils, however, weathering rates may differ strongly from lab conditions. Research on natural weathering has shown that biota such as plants, microbes, and macro-invertebrates can strongly affect weathering rates, but biotic effects were excluded from most ESW lab assessments. Moreover, ESW may alter soil organic carbon sequestration and greenhouse gas emissions by influencing physicochemical and biological processes, which holds the potential to perpetuate even larger negative emissions. Here, we argue that it is likely that the climate change mitigation effect of ESW will be governed by biological processes, emphasizing the need to put these processes on the agenda of this emerging research field.

Land-use legacies predispose the response of trees to drought in restored forests.

Transformative change is required to achieve conservation of the globe's natural resources. Ambitious forest restoration can help achieve this change. Restoration success depends on trees persisting through multiple stressors, with drought standing out as one of utmost importance. However, research tends to focus on tree inciting factors of tree decline, like drought, whilst ignoring the fundamental importance of context, potentially leading to the wasted restoration effort. Indeed, the propensity of trees to succumb to, or resist, drought depends on whether they are predisposed to fail or succeed. Here, I argue that this predisposition crucially depends on the nature and characteristics of the former land use at the restoration site and propose a research agenda that will help enable the successful upscaling of forest restoration ambitions by revealing the land-use history-determined conditions under which tree species are likely to succeed in an era of environmental challenges.

Soil fauna drives vertical redistribution of soil organic carbon in a long-term irrigated dry pine forest.

Summer droughts strongly affect soil organic carbon (SOC) cycling, but net effects on SOC storage are unclear as drought affects both C inputs and outputs from soils. Here, we explored the overlooked role of soil fauna on SOC storage in forests, hypothesizing that soil faunal activity is particularly drought-sensitive, thereby reducing litter incorporation into the mineral soil and, eventually, long-term SOC storage. In a drought-prone pine forest (Switzerland), we performed a large-scale irrigation experiment for 17 years and assessed its impact on vertical SOC distribution and composition. We also examined litter mass loss of dominant tree species using different mesh-size litterbags and determined soil fauna abundance and community composition. The 17-year-long irrigation resulted in a C loss in the organic layers (-1.0 kg C m-2 ) and a comparable C gain in the mineral soil (+0.8 kg C m-2 ) and thus did not affect total SOC stocks. Irrigation increased the mass loss of Quercus pubescens and Viburnum lantana leaf litter, with greater effect sizes when meso- and macrofauna were included (+215%) than when excluded (+44%). The enhanced faunal-mediated litter mass loss was paralleled by a many-fold increase in the abundance of meso- and macrofauna during irrigation. Moreover, Acari and Collembola community composition shifted, with a higher presence of drought-sensitive species in irrigated soils. In comparison, microbial SOC mineralization was less sensitive to soil moisture. Our results suggest that the vertical redistribution of SOC with irrigation was mainly driven by faunal-mediated litter incorporation, together with increased root C inputs. Our study shows that soil fauna is highly sensitive to natural drought, which leads to a reduced C transfer from organic layers to the mineral soil. In the longer term, this potentially affects SOC storage and, therefore, soil fauna plays a key but so far largely overlooked role in shaping SOC responses to drought.

Application of plant-soil feedbacks in the selection of crop rotation sequences.

Plant-soil feedback (PSF) can be a major driver of plant performance in communities, and this concept can be used in selecting crop rotation sequences to maximize agricultural yields. Potential benefits of using PSF in this context include nutrient use optimization, pathogen reduction, and enhancement of mutualisms between crops and microbes. Yet the contributions of these combined mechanisms are poorly understood. Here we investigated the relative contributions of these mechanisms using five major crops commonly cultivated in rotation (alfalfa, canola, maize, soybean, and wheat) under controlled conditions. We trained soil by growing each of the five crops in a "training phase," and then reciprocally planted the five crops in the trained soils in a "feedback phase." To tease out soil biota from nutrient effects, we established three treatments: "control" (trained unsterilized soil used in the feedback phases), "biota" (sterilized soil in the feedback phase inoculated with soil biota from the control treatment after the training phase), and "nutrient" (sterilized soils in both phases). Plant-soil feedback for each crop was calculated by comparing the total biomass of each crop grown in soils trained by each of the four other crops (i.e., in rotation) against total biomass in self-trained soil (i.e., monocropping). We found that PSF values varied among crop combinations in all the treatments, but such variation was the greatest in the nutrient treatment. Overall, soil biota feedback tended to be lower, whereas nutrient feedback tended to be greater compared to the unsterilized control soil, suggesting that effects of antagonistic biota outweighed those of beneficial microbes in the biota treatment, and that plants optimized nutrient uptake when the soil microbiome was absent in the nutrient treatment. Furthermore, soils in the nutrient treatment trained by the legume crops (alfalfa and soybean) tended to provide the greatest positive feedback, emphasizing the important legacy of N2 fixers in crop rotation. Taken together, our data demonstrate how nutrients and soil biota can be integral to PSFs among crops, and that assessing PSFs under controlled conditions can serve as a basis to determine the most productive crop rotation sequences prior to field testing.

Phytoremediation of 137Cs: factors and consequences in the environment.

Radionuclide contamination is a concerning threat due to unexpected nuclear disasters and authorized discharge of radioactive elements, both in the past and in present times. Use of atomic power for energy generation is associated with unresolved issues concerning storage of residues and contaminants. For example, the nuclear accidents in Chernobyl 1986 and Fukushima 2011 resulted in considerable deposition of cesium (Cs) in soil, along with other radionuclides. Among Cs radioactive variants, the anthropogenic radioisotope 137Cs (t½ = 30.16 years) is of serious environmental concern, owing to its rapid incorporation into biological systems and emission of ß and γ radiation during the decaying process. To remediate contaminated areas, mostly conventional techniques are applied that are not eco-friendly. Hence, an alternative green technology, i.e., phytoremediation, should in future be considered and implemented. This sustainable technology generates limited secondary waste and its objectives are to utilize hyper-accumulating plants to extract, stabilize, degrade, and filter the radionuclides. The review highlights plant mechanisms for up-taking radionuclides and influences of different environmental factors involved in the process, while considering its long-term effects.

Synergy of the Tropical Earthworm Pontoscolex corethrurus and Oil Palm Bagasse in the Removal of Heavy Crude Oil.

The tropical endogeic earthworm Pontoscolex corethrurus, a non-standard species used in ecotoxicity, has been found in crude oil-contaminated habitats. We estimated the removal of total hydrocarbons from heavy crude "Maya" oil on an artificially contaminated soil with a median lethal concentration of P. corethrurus and an addition of oil palm bagasse. P. corethrurus had a high survival rate, and the addition of oil palm bagasse led to a greater growth and an increase in abundance of bacteria and fungi. The activity of P. corethrurus and the nutritional quality of oil palm bagasse had a significant impact on the removal of a larger amount of petroleum hydrocarbons from contaminated soil. We concluded that the endogeic earthworm P. corethrurus and oil palm bagasse acted synergistically to achieve a more effective removal of total petroleum hydrocarbons from soil. These results show the potential for using P. corethrurus to remove, either directly or indirectly, crude oil from soil.

Forest fire induces short-term shifts in soil food webs with consequences for carbon cycling.

We tested for fire-induced (5-6 years post-fire) changes in the structure and functioning of the soil food web along a 3000-km north-south transect across European Russia, spanning all major forest types in the northern hemisphere outside the tropics. The total biomass of the detrital food web, including microbes and invertebrates, was not affected by fire. However, fire reduced the biomass of microfauna and mites, but had no impact on mesofauna or macrofauna. Fire also reduced rates of carbon (C) mobilisation by soil biota. Our results demonstrate that fire-induced shifts in soil food webs have significant short-term effects on forest soil C cycling, but that these effects vary across forest types and geographic locations.

Soil Microbes Generate Stronger Fitness Differences than Stabilization among California Annual Plants.

AbstractSoil microorganisms influence a variety of processes in plant communities. Many theoretical and empirical studies have shown that dynamic feedbacks between plants and soil microbes can stabilize plant coexistence by generating negative frequency-dependent plant population dynamics. However, inferring the net effects of soil microbes on plant coexistence requires also quantifying the degree to which they provide one species an average fitness advantage, an effect that has received little empirical attention. We conducted a greenhouse study to quantify microbially mediated stabilization and fitness differences among 15 pairs of annual plants that co-occur in southern California grasslands. We found that although soil microbes frequently generate negative frequency-dependent dynamics that stabilize plant interactions, they simultaneously generate large average fitness differences between species. The net result is that if the plant species are otherwise competitively equivalent, the impact of plant-soil feedbacks is to often favor species exclusion over coexistence, a result that becomes evident only by quantifying the microbially mediated fitness difference. Our work highlights that comparing the stabilizing effects of plant-soil feedbacks to the fitness difference they generate is essential for understanding the influence of soil microbes on plant diversity.

Mechanisms underpinning nonadditivity of global change factor effects in the plant-soil system.

Plant-soil systems are key for understanding the effects of factors of global change. Recent work has highlighted the general importance of considering the simultaneous incidence of some factors or stressors. To help mechanistically dissect the possible interactions of such factors, we here propose three broad groups of mechanisms that may generally lead to nonadditivity of responses within a plant-soil system: direct factor interactions (that is one factor directly changing another), within-plant information processing and crosstalk, and effects of factors on groups of soil biota interacting with plants. Interactions are also possible within and across these groups. Factor interactions are very likely to be present in experiments, especially when dealing with an increasing number of factors. Identifying the nature of such interactions will be essential for understanding and predicting global change impacts on plants and soil.

Soil sample pooling generates no consistent inference bias: a meta-analysis of 71 plant-soil feedback experiments.

There is current debate on how soil sample pooling affects the measurement of plant-soil feedbacks. Several studies have suggested that pooling soil samples among experimental units reduces variance and can bias estimates of plant-soil feedbacks. However, it is unclear whether pooling has resulted in systematic mismeasurement of plant-soil feedbacks in the literature. Using data from 71 experiments, we tested whether pairwise plant-soil feedback direction, magnitude and variance differed among soil pooling treatments. We also tested whether pooling has altered our understanding of abiotic and biotic drivers that influence pairwise plant-soil feedbacks. Pooling of soil samples among experimental units was used in 42% of examined experiments. Contrary to predictions, pooling did not affect mean pairwise plant-soil feedback effect size or within-experiment variance. Accounting for soil sample pooling also did not significantly alter our understanding of the drivers of pairwise plant-soil feedbacks. We conclude that there is no evidence that soil sample pooling systematically biases estimates of plant-soil feedback direction, magnitude, variance or drivers across many studies. Given the debate of whether to pool soil samples, researchers should be aware of potential criticisms and carefully consider how experimental design and soil pooling methods influence interpretation of experiments.