Soil nematode abundance and functional group composition at a global scale

Root traits drive the recovery of soil nematodes during restoration of open mines in a tropical rainforest

Mining is a major threat to vegetation and soil in the tropical forests. Reforestation of degraded surface mines is critically dependent on the recovery of soil health, where the nematodes play an important role. However, the key determinants of community assembly of soil nematodes during mine-restoration remain unknown in the tropical rainforests. Here, the recovery of taxonomic diversity of nematode communities and their trophic groups during reforestation of an extremely degraded tropical open-mining area is studied. The factors that may impact their recovery, such as root traits (length, area and tissue density), soil properties (pH and soil organic matter content (SOM)), and taxonomic diversities of soil bacterial and fungal communities are investigated. Differences in these parameters were evaluated in the three soil types: (i) mined soil - the erstwhile soil that was removed during mining and stock-piled for 10 years at the foot of an extremely degraded open-mining area; (ii) reforested soil, sampled from a 10-year successful restoration, which used the mined soil for reforestation; and (iii) undisturbed soil, collected from an adjacent undisturbed/not-mined tropical rainforest. A total of 11, 34 and 29 nematode-genera were identified in mined-, undisturbed-, and reforested soils, respectively. The taxonomic diversities of the 5 nematode groups in the mined soil were 1.5-5.2 times lower than in the undisturbed soil, but were similar in the restored and undisturbed soils. Taxonomic diversities of phytophagous and predator nematodes were correlated to restored root traits; whereas of bacterivores, fungivores, and omnivores were correlated to pH, SOM, soil bacterial and fungal communities. Consequently, complete loss of roots during mining likely severely reduced the nematodes, but their recovery after reforestation led to the restoration of taxonomic diversity of nematode communities. The mix-planting fast-growing tree species may be appropriate for recovering soil health, including nematode diversity, during reforestation of open tropical mines.

An integrated fast-slow plant and nematode economics spectrum predicts soil organic carbon dynamics during natural restoration

Aboveground and belowground attributes of terrestrial ecosystems interact to shape carbon (C) cycling. However, plants and soil organisms are usually studied separately, leading to a knowledge gap regarding their coordinated contributions to ecosystem C cycling. We explored whether integrated consideration of plant and nematode traits better explained soil organic C (SOC) dynamics than plant or nematode traits considered separately. Our study system was a space-for-time natural restoration chronosequence following agricultural abandonment in a subtropical region, with pioneer, early, mid and climax stages. We identified an integrated fast-slow trait spectrum encompassing plants and nematodes, demonstrating coordinated shifts from fast strategies in the pioneer stage to slow strategies in the climax stage, corresponding to enhanced SOC dynamics. Joint consideration of plant and nematode traits explained more variation in SOC than by either group alone. Structural equation modeling revealed that the integrated fast-slow trait spectrum influenced SOC through its regulation of microbial traits, including microbial C use efficiency and microbial biomass. Our findings confirm the pivotal role of plant-nematode trait coordination in modulating ecosystem C cycling and highlight the value of incorporating belowground traits into biogeochemical cycling under global change scenarios.

Elevated O3 has stronger effects than CO2 on soil nematode abundances but jointly inhibits their diversity in paddy soils

Anthropogenic activities have resulted in rising atmospheric concentrations of carbon dioxide (CO2) and ozone (O3), exerting substantial direct and indirect impacts on soil biodiversity within agroecosystems. Despite the considerable attention given to the individual impacts of elevated CO2 and O3 levels, the combined effects on soil nematode communities have not been extensively explored. In this study, we investigated the interactive effects of elevated CO2 (+200 ppm, eCO2) and O3 (+40 ppb, eO3) levels on the abundance, diversity, and trophic composition of soil nematode communities associated with two rice cultivars (Nanjing 5055, NJ5055 and Wuyujing 3, WYJ3). Our findings revealed that soil nematodes had greater abundances under eO3, whereas eCO2 had no significant impacts. Conversely, both eCO2 and eO3, and their combination led to significant reductions in nematode generic richness, accompanied by a decline in the diversity particularly associated with the WYJ3 cultivar. Moreover, eCO2 and eO3 influenced nematode community composition and environmental factors, particularly for the WYJ3 cultivar. Both eCO2 and eO3 significantly increased soil nitrate levels. The changes in nematode community composition were related to soil nitrate levels, as well as nitrogen and carbon concentrations in rice plant roots. Furthermore, interactions between eCO2 and eO3 significantly impacted soil nematode abundance and trophic composition, revealing intricate consequences for soil nematode communities that transcend predictions based on single-factor experiments. This study unveils the potential impacts posed by eCO2 and eO3 on soil biodiversity mediated by rice cultivars, plant functional characteristics and soil feedback mechanisms, thereby underscoring the complex and interactive outcomes arising from concurrent drivers of climate change within the soil food web.

Global changes and their environmental stressors have a significant impact on soil biodiversity-A meta-analysis

Identifying the main threats to soil biodiversity is crucial as soils harbor ∼60% of global biodiversity. Many previous meta-analyses investigating the impact of different global changes (GCs) on biodiversity have omitted soil fauna or are limited by the GCs studied. We conducted a broad-scale meta-analysis focused on soil fauna communities, analyzing 3,161 effect sizes from 624 publications studying climate change, land-use intensification, pollution, nutrient enrichment, invasive species and habitat fragmentation. Land-use intensification resulted in large reductions in soil fauna communities, especially for the larger-bodied groups. Unexpectedly, pollution caused the largest negative impact on soil biodiversity - particularly worrying due to continually increasing levels of pollution and poor mechanistic understanding of impacts relative to other GCs. Not all GCs and stressors were detrimental; organic-based nutrient enrichment often resulted in positive responses. Including soil biodiversity in large-scale analyses is vital to fully understand the impact of GCs across the different realms.

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.

Combining Masculinizing Resistance, Rotation, and Biocontrol to Achieve Durable Suppression of the Potato Pale Cyst Nematode: A Model

The pale cyst nematode, Globodera pallida, is a pest that poses a significant threat to potato crops worldwide. The most effective chemical nematicides are toxic to nontarget organisms and are now banned. Alternative control methods are therefore required. Crop rotation and biological control methods have limitations for effectively managing nematodes. The use of genetically resistant cultivars is a promising alternative, but nematode populations evolve, and virulent mutants can break resistance after just a few years. Masculinizing resistances, preventing avirulent nematodes from producing females, might be more durable than blocking resistances, preventing infection. Our demo-genetic model, tracking both nematode population densities and virulence allele frequencies, shows that virulence against masculinizing resistance may not be fixed in the pest population under realistic agricultural conditions. Avirulence may persist despite the uniform use of resistance. This is because avirulent male nematodes may transmit avirulent alleles to their progeny by mating with virulent females. Additionally, because avirulent nematodes do not produce females themselves, they weaken the reproductive rate of the nematode population, leading to a reduction in its density by at least 20%. This avirulence load can even lead to the collapse of the nematode population in theory. Overall, our model showed that combining masculinizing resistance, rotation, and biocontrol may achieve durable suppression of G. pallida in a reasonable time frame. Our work is supported by an online interactive interface allowing users (i.e., growers, plant health authorities, researchers) to test their own control combinations.

Robustness and variability in Caenorhabditis elegans dauer gene expression

Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an arrested, hypometabolic alternative to the third larval stage of the nematode. Dauers undergo dramatic tissue remodeling and extensive physiological, metabolic, behavioral, and gene expression changes compared to conspecifics that continue development and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. Therefore, dauer induction is an example of phenotypic plasticity. However, whether gene expression in dauer larvae induced to arrest development by different genetic or environmental triggers is invariant or varies depending on their route into dauer has not been examined. By using RNA-sequencing to characterize gene expression in different types of dauer larvae and computing the variance and concordance within Gene Ontologies (GO) and gene expression networks, we find that the expression patterns within most pathways are strongly correlated between dauer larvae, suggestive of transcriptional robustness. However, gene expression within specific defense pathways, pathways regulating some morphological traits, and several metabolic pathways differ between the dauer larvae. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in adaptation, allowing the dauers induced by different stimuli to survive in and exploit different niches.

Mapping safe drinking water use in low- and middle-income countries

Safe drinking water access is a human right, but data on safely managed drinking water services (SMDWS) is lacking for more than half of the global population. We estimate SMDWS use in 135 low- and middle-income countries (LMICs) at subnational levels with a geospatial modeling approach, combining existing household survey data with available global geospatial datasets. We estimate that only one in three people used SMDWS in LMICs in 2020 and identified fecal contamination as the primary limiting factor affecting almost half of the population of LMICs. Our results are relevant for raising awareness about the challenges and limitations of current global monitoring approaches and demonstrating how globally available geospatial data can be leveraged to fill data gaps and identify priority areas in LMICs.

Response of soil nematode community structure and metabolic footprint to nitrogen addition in alfalfa fields on the Loess Plateau

Nematodes serve as key indicators of soil health in ecological studies. Therefore, the current study examined the community structure and metabolic footprint of soil nematodes in alfalfa fields across varying levels of N supply in the semi-arid Loess Plateau. The findings offer theoretical guidance for the sustainable management of artificial alfalfa grasslands in this region. The research was based on alfalfa fields with different N application rates (0, 50, 100, 150 kg/ha2) as the research object, The shallow plate method was used to separate and extract soil nematodes, identify soil nematode groups, calculate ecological function index and metabolic footprint, and identify indicator species. A total of 6346 nematodes were isolated in this study, belonging to 27 genera and 19 families. Notably, the plant parasitic nematode Helicotylenchus was predominant. As N addition increased, the plant parasitic index (PPI) increased significantly. A N50 application significantly enhanced the soil nematode diversity index ( H ) and the free-living index (MI). The findings showcased a noticeable decrease in disturbance within the N50 soil nematode community. This resulted in a mature and stable community structure primarily attributed to the heightened abundance of omnivorous/predatory nematodes. Across various N levels, soil nematode communities underwent significant alterations in the soil food web structure through shifts in their metabolic footprint. Future strategies should focus on refining N management practices and integrating sustainable approaches like crop rotation and pest management. These efforts will contribute to guidelines ensuring artificial alfalfa grasslands lasting health and productivity.

The Life-History Traits of Soil-Dwelling Nematode (Acrobeloides sp.) Exhibit More Resilience to Water Restriction Than Caenorhabditis elegans

In the context of climate warming, the intensity and frequency of drought occurrences are progressively increasing. However, current research on the impacts of drought on the life-history traits and physiological activities of animals rarely encompasses soil animals that play crucial roles within soil ecosystems. Therefore, this study focused on a soil nematode species (Acrobeloides sp.) and a model nematode (Caenorhabditis elegans) to investigate whether nematodes adjust the trade-off of their life-history traits to confront arid environments, utilizing a Petri dish experiment. Subsequently, we assessed the resilience of the two nematode species to moisture variations by comparing the extent of changes in various indicators (i.e., life-history traits, physiological traits, and oxidative stress) of nematodes before and after drought and rehydration. The results revealed that both nematode species are capable of adapting to arid environments by altering the trade-off between life-history traits. Specifically, they reduce reproductive investment and body mass while maintaining life span, thus responding to drought conditions. Follow-up rehydration experiments post-drought stress highlighted that the soil-dwelling nematode exhibits a superior recovery capacity in response to moisture fluctuations in comparison to the model nematode. To the best of our knowledge, this is the first investigation into life history of drought adaptation within soil-dwelling nematodes. Moreover, the findings hold significant implications for the exploration of drought adaptation and its mechanisms in soil-dwelling animals.

Energy flows through nematode food webs depending on the soil carbon and nitrogen contents after forest conversion

The swift proliferation of forests converted into monoculture plantations has profound impacts on soil nutrients, microbial communities, and many ecological processes and functions. Nematodes are soil microfauna that play a pivotal role in biogeochemical cycling and in soil food web, whereas the response of soil nematode communities and energy flows to forest conversion remains unknown. Here, we assessed the community composition and the energy flows of the nematode food webs as a function of soil chemistry after conversion from natural forests (Forest) to four plantations (8-year-old): Amygdalus persica (Peach), Myrica rubra (Berry), Camellia oleifera (Oil), and Cunninghamia lanceolata (Fir). After forest conversion, soil organic carbon (SOC) and total nitrogen (TN) contents decreased by 65 % and 55 %, respectively. Forest conversion strongly reduced the abundance (particularly large-bodied omnivorous-predatory nematodes), diversity, maturity, and stability of the soil nematode community. The shifts in composition and structure of nematode communities after forest conversion are reflected in changes in the abundance of predominant genera and trophic taxa, especially bacterivorous, fungivorous, and omnivorous-predatory nematodes. Acrobeloides notably increased, whereas Plectus, Prismatolaimus, Tylencholaimus, and Tripyla decreased. Accordingly, the abundances of r-strategy nematodes (cp value = 1-2) increased, but that of the K-strategists (cp value = 3-5) declined. Additionally, the energy flow across the soil nematode food web was reduced by 36 % and flow uniformity declined by 24 % after forest conversion. These changes in nematode diversity and abundance were triggered by diminishing soil C and N contents, thereby affecting the energy flows via the nematode food webs. Thus, forest conversion affects soil biotas and multi-functions from the perspective of nematode food web structure and energy flows, and underlines the interconnections between ecosystem and energy dynamics across multi-trophic levels, which is crucial for sustainable forest management.

Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

Stable body sizes in soil nematodes across altitudes: The role of intrageneric variation in community assembly

Animal body size exhibits rapid responses to environmental variations and displays considerable variability across ecological scales, significantly influencing ecological community assembly. However, our understanding of the extent of body size variation and its responses to environmental differences within soil fauna remains limited, impeding a comprehensive grasp of soil fauna's functional ecology. Here, we aim to investigate the magnitude of intrageneric body size variation and its implications for soil nematode community assembly along an altitudinal gradient. We examined soil nematode body size responses along an altitudinal gradient spanning from 3136 to 4128 m in an alpine mountain region of the eastern Tibetan Plateau. We assessed the contributions of intra- and intergeneric variations in body size, both within and among communities, using individual body size values. The implications of these variations for community assembly processes were determined through phenotypic variance ratios employing permutation tests. Our analyses did not reveal statistically significant correlations between altitude and the community-weighted mean body mass, regardless of considering intrageneric trait variation (IGTV). Approximately 15% of the variation in body size among communities and a substantial 72% of the variation in body size within communities can be attributed to IGTV. Altitude did not significantly affect IGTV within or among communities. Furthermore, our results underscored the dominant role of internal filtering within the community in governing nematode community assembly, with external filtering outside the community playing a limited role within our altitudinal range. Our findings emphasize the dominant role of body size variation within communities rather than among communities, attributable to strong internal filtering processes. These findings advance our understanding of body size variation in soil nematodes across ecological scales and highlight the pivotal role of intrageneric variation in shaping the functional ecology of soil fauna.

Linking nematodes and ecosystem function: a trait-based framework

Trait-based approaches are being increasingly adopted to understand species' ecological strategies and how organisms influence ecosystem function. Trait-based research on soil organisms, however, remains poorly developed compared with that for plants. The abundant and diverse soil nematodes are prime candidates to advance trait-based approaches belowground, but a unified trait framework to describe nematode ecological strategies and assess their linkages with ecosystem function is lacking. We categorized nematode traits as morphological, physiological, life history, and community clusters, and proposed the nematode economics spectrum (NES) to better understand nematode ecological strategies and their association with ecosystem function. We argue that bridging the NES and the plant economics spectrum will facilitate a more holistic understanding of ecosystem carbon and nutrient cycling under global change.

Conceptualizing soil fauna effects on labile and stabilized soil organic matter

Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.

Global insect herbivory and its response to climate change

Herbivorous insects consume a large proportion of the energy flow in terrestrial ecosystems and play a major role in the dynamics of plant populations and communities. However, high-resolution, quantitative predictions of the global patterns of insect herbivory and their potential underlying drivers remain elusive. Here, we compiled and analyzed a dataset consisting of 9,682 records of the severity of insect herbivory from across natural communities worldwide to quantify its global patterns and environmental determinants. Global mapping revealed strong spatial variation in insect herbivory at the global scale, showing that insect herbivory did not significantly vary with latitude for herbaceous plants but increased with latitude for woody plants. We found that the cation-exchange capacity in soil was a main predictor of levels of herbivory on herbaceous plants, while climate largely determined herbivory on woody plants. We next used well-established scenarios for future climate change to forecast how spatial patterns of insect herbivory may be expected to change with climate change across the world. We project that herbivore pressure will intensify on herbaceous plants worldwide but would likely only increase in certain biomes (e.g., northern coniferous forests) for woody plants. Our assessment provides quantitative evidence of how environmental conditions shape the spatial pattern of insect herbivory, which enables a more accurate prediction of the vulnerabilities of plant communities and ecosystem functions in the Anthropocene.

Global Atlas of Methane Metabolism Marker Genes in Soil

Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

Reading tea leaves worldwide: Decoupled drivers of initial litter decomposition mass-loss rate and stabilization

The breakdown of plant material fuels soil functioning and biodiversity. Currently, process understanding of global decomposition patterns and the drivers of such patterns are hampered by the lack of coherent large-scale datasets. We buried 36,000 individual litterbags (tea bags) worldwide and found an overall negative correlation between initial mass-loss rates and stabilization factors of plant-derived carbon, using the Tea Bag Index (TBI). The stabilization factor quantifies the degree to which easy-to-degrade components accumulate during early-stage decomposition (e.g. by environmental limitations). However, agriculture and an interaction between moisture and temperature led to a decoupling between initial mass-loss rates and stabilization, notably in colder locations. Using TBI improved mass-loss estimates of natural litter compared to models that ignored stabilization. Ignoring the transformation of dead plant material to more recalcitrant substances during early-stage decomposition, and the environmental control of this transformation, could overestimate carbon losses during early decomposition in carbon cycle models.

Nematode Uptake Preference toward Different Nanoplastics through Avoidance Behavior Regulation

Expounding bioaccumulation pathways of nanoplastics in organisms is a prerequisite for assessing their ecological risks in the context of global plastic pollution. Invertebrate uptake preference toward nanoplastics is a key initial step of nanoplastic food chain transport that controls their global biosafety, while the biological regulatory mechanism remains unclear. Here, we reveal a preferential uptake mechanism involving active avoidance of nanoplastics by Caenorhabditis elegans and demonstrate the relationship between the uptake preference and nanoplastic characteristics. Nanoplastics with 100 nm in size or positive surface charges induce stronger avoidance due to higher toxicity, causing lower accumulation in nematodes, compared to the 500 nm-sized or negatively charged nanoplastics, respectively. Further evidence showed that nematodes did not actively ingest any types of nanoplastics, while different nanoplastics induced defense responses in a toxicity-dependent manner and distinctly stimulated the avoidance behavior of nematodes (ranged from 15.8 to 68.7%). Transcriptomics and validations using mutants confirmed that the insulin/IGF signaling (IIS) pathway is essential for the selective avoidance of nanoplastics. Specifically, the activation of DAF-16 promoted the IIS pathway-mediated defense against nanoplastics and stimulated the avoidance behavior, increasing the survival chances of nematodes. Considering the genetical universality of this defense response among invertebrates, such an uptake preference toward certain nanoplastics could lead to cascaded risks in the ecosystem.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence in C. elegans

Throughout history, humans have relied on plants as a source of medication, flavoring, and food. Plants synthesize large chemical libraries and release many of these compounds into the rhizosphere and atmosphere where they affect animal and microbe behavior. To survive, nematodes must have evolved the sensory capacity to distinguish plant-made small molecules (SMs) that are harmful and must be avoided from those that are beneficial and should be sought. This ability to classify chemical cues as a function of their value is fundamental to olfaction, and represents a capacity shared by many animals, including humans. Here, we present an efficient platform based on multi-well plates, liquid handling instrumentation, inexpensive optical scanners, and bespoke software that can efficiently determine the valence (attraction or repulsion) of single SMs in the model nematode, Caenorhabditis elegans. Using this integrated hardware-wetware-software platform, we screened 90 plant SMs and identified 37 that attracted or repelled wild-type animals, but had no effect on mutants defective in chemosensory transduction. Genetic dissection indicates that for at least 10 of these SMs, response valence emerges from the integration of opposing signals, arguing that olfactory valence is often determined by integrating chemosensory signals over multiple lines of information. This study establishes that C. elegans is an effective discovery engine for determining chemotaxis valence and for identifying natural products detected by the chemosensory nervous system.

Effects of climate on the distribution and conservation of commonly observed European earthworms

Belowground biodiversity distribution does not necessarily reflect aboveground biodiversity patterns, but maps of soil biodiversity remain scarce because of limited data availability. Earthworms belong to the most thoroughly studied soil organisms and-in their role as ecosystem engineers-have a significant impact on ecosystem functioning. We used species distribution modeling (SDMs) and available data sets to map the spatial distribution of commonly observed (i.e., frequently recorded) earthworm species (Annelida, Oligochaeta) across Europe under current and future climate conditions. First, we predicted potential species distributions with commonly used models (i.e., MaxEnt and Biomod) and estimated total species richness (i.e., number of species in a 5 × 5 km grid cell). Second, we determined how much the different types of protected areas covered predicted earthworm richness and species ranges (i.e., distributions) by estimating the respective proportion of the range area. Earthworm species richness was high in central western Europe and low in northeastern Europe. This pattern was mainly associated with annual mean temperature and precipitation seasonality, but the importance of predictor variables to species occurrences varied among species. The geographical ranges of the majority of the earthworm species were predicted to shift to eastern Europe and partly decrease under future climate scenarios. Predicted current and future ranges were only poorly covered by protected areas, such as national parks. More than 80% of future earthworm ranges were on average not protected at all (mean [SD] = 82.6% [0.04]). Overall, our results emphasize the urgency of considering especially vulnerable earthworm species, as well as other soil organisms, in the design of nature conservation measures.

Grazing alters the soil nematode communities in grasslands: A meta-analysis

Grazing causes great disturbances in grassland ecosystems and may change the abundance, diversity, and ecological function of soil biota. Because of their important role in nutrient cycling and as good environmental indicators, nematodes are very representative soil organisms. However, the mechanisms by which grazing intensity, livestock type, duration, and environmental factors (e.g., climate and edaphic factors) affect soil nematodes remain poorly understood. In this study, we collected 1964 paired observations all over the world from 53 studies to clarify the grazing response patterns of soil nematodes and their potential mechanisms. Overall, grazing significantly decreased the abundance of bacterial-feeding (BF) nematodes (-16.54%) and omnivorous-predatory (OP) nematodes (-36.81%), and decreased nematode community diversity indices (Shannon-Weiner index: -4.33%, evenness index: -9.22%, species richness: -5.35%), but had no effect on ecological indices under a global regional scale. The response of soil nematodes to grazing varied by grazing intensity, animals, and duration. Heavy grazing decreased OP nematode abundance, but had no effect on the abundance of other trophic groups, or on diversity or ecological indices. Grazing by small animals had stronger effects than that by large animals and mixed-size animals on BF, fungal-feeding (FF), plant-feeding (PF) and OP nematodes, the Shannon-Wiener index, and the species richness index. The abundance of FF and OP nematodes influenced significantly under short-term grazing. The evenness index decreased significantly under long-term grazing (>10 years). Climate and edaphic factors impacted the effects of grazing on nematode abundance, diversity, and ecological indices. When resources (i.e., rain, heat, and soil nutrients) were abundant, the negative effects of grazing on nematodes were reduced; under sufficiently abundant resources, grazing even had positive effects on soil nematode communities. Thus, the influence of grazing on soil nematode communities is resource-dependent. Our study provides decision makers with grazing strategies based on the resource abundance. Resource-poor areas should have less grazing, while resource-rich areas should have more grazing to conserve soil biodiversity and maintain soil health.

Biogeographic patterns and drivers of soil viromes

Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.

Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions

Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.

Virus-induced changes in root volatiles attract soil nematode vectors to infected plants

Plant-derived volatiles mediate interactions among plants, pathogenic viruses, and viral vectors. These volatile-dependent mechanisms have not been previously demonstrated belowground, despite their likely significant role in soil ecology and agricultural pest impacts. We investigated how the plant virus, tobacco rattle virus (TRV), attracts soil nematode vectors to infected plants. We infected Nicotiana benthamiana with TRV and compared root growth relative to that of uninfected plants. We tested whether TRV-infected N. benthamiana was more attractive to nematodes 7 d post infection and identified a compound critical to attraction. We also infected N. benthamiana with mutated TRV strains to identify virus genes involved in vector nematode attraction. Virus titre and associated impacts on root morphology were greatest 7 d post infection. Tobacco rattle virus infection enhanced 2-ethyl-1-hexanol production. Nematode chemotaxis and 2-ethyl-1-hexanol production correlated strongly with viral load. Uninfected plants were more attractive to nematodes after the addition of 2-ethyl-1-hexanol than were untreated plants. Mutation of TRV RNA2-encoded genes reduced the production of 2-ethyl-1-hexanol and nematode attraction. For the first time, this demonstrates that virus-driven alterations in root volatile emissions lead to increased chemotaxis of the virus's nematode vector, a finding with implications for sustainable management of both nematodes and viral pathogens in agricultural systems.

Simple, inexpensive, and rapid approach to detect changes in the structure of soil free-living nematodes

A general limitation of ecological investigations based on nematodes is related to the difficult and time-consuming taxonomic identification of species. Therefore, nematologists are investing many efforts to develop alternative approaches as proxies applicable in biomonitoring assessment. Recently, an alternative method that combines morpho-functional traits was proposed for detecting assemblage changes of marine nematodes. In view of the promising results, it was tested the same approach to document taxonomic structure changes of soil free-living and plant parasitic nematodes. Specifically, this attempt was carried out using three data sets that include studies from various European regions and different types of ecosystems: forests, grasslands and maize crops. Multivariate statistical analysis revealed that the simple combination of the four traits (i.e., buccal cavity cuticularization occurrence, amphideal fovea size and shape, morphology of the cuticle and pharynx) in a single code number perfectly mirrors the taxonomic structure trends of the nematode assemblage at genus level. Therefore, we predict that similar results can be also obtained by directly encoding nematode specimens with the selected traits and we point to new important advances if this procedure can be coupled with advanced machine learning.

Trophic interactions in soil micro-food webs drive ecosystem multifunctionality along tree species richness

Rapid biodiversity losses under global climate change threaten forest ecosystem functions. However, our understanding of the patterns and drivers of multiple ecosystem functions across biodiversity gradients remains equivocal. To address this important knowledge gap, we measured simultaneous responses of multiple ecosystem functions (nutrient cycling, soil carbon stocks, organic matter decomposition, plant productivity) to a tree species richness gradient of 1, 4, 8, 16, and 32 species in a young subtropical forest. We found that tree species richness had negligible effects on nutrient cycling, organic matter decomposition, and plant productivity, but soil carbon stocks and ecosystem multifunctionality significantly increased with tree species richness. Linear mixed-effect models showed that soil organisms, particularly arbuscular mycorrhizal fungi (AMF) and soil nematodes, elicited the greatest relative effects on ecosystem multifunctionality. Structural equation models revealed indirect effects of tree species richness on ecosystem multifunctionality mediated by trophic interactions in soil micro-food webs. Specifically, we found a significant negative effect of gram-positive bacteria on soil nematode abundance (a top-down effect), and a significant positive effect of AMF biomass on soil nematode abundance (a bottom-up effect). Overall, our study emphasizes the significance of a multitrophic perspective in elucidating biodiversity-multifunctionality relationships and highlights the conservation of functioning soil micro-food webs to maintain multiple ecosystem functions.

Dynamics of soil biota and nutrients at varied depths in a Tamarix ramosissima-dominated natural desert ecosystem: Implications for nutrient cycling and desertification management

The underground community of soil organisms, known as soil biota, plays a critical role in terrestrial ecosystems. Different ecosystems exhibit varied responses of soil organisms to soil physical and chemical properties (SPCPs). However, our understanding of how soil biota react to different soil depths in naturally established population of salinity tolerant Tamarix ramosissima in desert ecosystems, remains limited. To address this, we employed High-Throughput Illumina HiSeq Sequencing to examine the population dynamics of soil bacteria, fungi, archaea, protists, and metazoa at six different soil depths (0-100 cm) in the naturally occurring T. ramosissima dominant zone within the Taklimakan desert of China. Our observations reveal that the alpha diversity of bacteria, fungi, metazoa, and protists displayed a linear decrease with the increase of soil depth, whereas archaea exhibited an inverse pattern. The beta diversity of soil biota, particularly metazoa, bacteria, and protists, demonstrated noteworthy associations with soil depths through Non-Metric Dimensional Scaling analysis. Among the most abundant classes of soil organisms, we observed Actinobacteria, Sordariomycetes, Halobacteria, Spirotrichea, and Nematoda for bacteria, fungi, archaea, protists, and metazoa, respectively. Additionally, we identified associations between the vertical distribution of dominant biotic communities and SPCPs. Bacterial changes were mainly influenced by total potassium, available phosphorus (AP), and soil water content (SWC), while fungi were impacted by nitrate (NO3-) and available potassium (AK). Archaea showed correlations with total carbon (TC) and AK thus suggesting their role in methanogenesis and methane oxidation, protists with AP and SWC, and metazoa with AP and pH. These correlations underscore potential connections to nutrient cycling and the production and consumption of greenhouse gases (GhGs). This insight establishes a solid foundation for devising strategies to mitigate nutrient cycling and GHG emissions in desert soils, thereby playing a pivotal role in the advancement of comprehensive approaches to sustainable desert ecosystem management.

Livestock grazing modifies soil nematode body size structure in mosaic grassland habitats

Body size is closely related to the trophic level and abundance of soil fauna, particularly nematodes. Therefore, size-based analyses are increasingly prominent in unveiling soil food web structure and its responses to anthropogenic disturbances, such as livestock grazing. Yet, little is known about the effects of different livestock on the body size structure of soil nematodes, especially in grasslands characterized by local habitat heterogeneity. A four-year field grazing experiment from 2017 to 2020 was conducted in a meadow steppe characterized by typical mosaics of degraded hypersaline patches and undegraded hyposaline patches to assess the impacts of cattle and sheep grazing on the body size structure of soil nematodes within and across trophic groups. Without grazing, the hypersaline patches harbored higher abundance of large-bodied nematodes in the community compared to the hyposaline patches. Livestock grazing decreased large-bodied nematodes within and across trophic groups mainly by reducing soil microbial biomass in the hypersaline patches, with sheep grazing resulting in more substantial reductions compared to cattle grazing. The reduction in large-bodied nematode individuals correspondingly resulted in decreases in nematode community-weighted mean (CWM) body size, nematode biomass, and size spectra slopes. However, both cattle and sheep grazing had minimal impacts on the CWM body size and size spectra of total nematodes in the hyposaline patches. Our findings suggest that livestock grazing, especially sheep grazing, has the potential to simplify soil food webs by reducing large-bodied nematodes in degraded habitats, which may aggravate soil degradation by weakening the bioturbation activities of soil fauna. In light of the widespread land use of grasslands by herbivores of various species and the ongoing global grassland degradation of mosaic patches, the recognition of the trends revealed by our findings is critical for developing appropriate strategies for grassland grazing management.

Fertilizer management for global ammonia emission reduction

Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems1-5. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy4,5. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr-1, lower than previous estimates that did not fully consider fertilizer management practices6-9. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr-1) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.

Response of soil micro-food web to nutrient limitation along a subtropical forest restoration

Forest ecosystem productivity and function is strongly influenced by the interaction between soil organisms and their resource use that can be impeded by an imbalance of ecological stoichiometry. Soil microorganisms are known to have an important role in biogeochemical cycling which is strongly influenced by ecological stoichiometry. However, there is limited understanding of how soil micro-food web respond to stoichiometric imbalances during forest restoration. Here, we investigated the effect of forest restoration on soil physio-chemical properties and the structure and function of soil micro-food web along a chronosequence of transformation stages: (i) early stage monoculture plantation of Chinese fir (Cunninghamia lanceolata) comprised of three age classes (5, 10 and 20 years); (ii) mid-stage conifer-broadleaved mixed forest; and (iii) late-stage mixed species broadleaved forest in south China. Results showed that forest restoration from C. lanceolata monocultures to mixed species broadleaved forest significantly increased soil organic carbon and total nitrogen. Soil bacteria, fungi, protists and nematodes abundance increased and the co-occurrence networks of soil biota became more complex and stable along the restoration chronosequence. In contrast, soil nitrogen and phosphorus limitations, particularly phosphorus limitation, increased along the chronosequence. In addition, soil exoenzyme activity suggested that the microbial investment in resource acquisition shifted from C- to nutrient-acquiring enzymes from the earlier to the later restoration stages. Availability of soil resources (e.g., dissolved organic carbon, ammonium, and available phosphate) appeared to have an important role in regulating soil food web composition, structure and stability during forest restoration. We conclude that nutrient limitation, particularly phosphorus limitation, likely has an important role in determining the stability of soil food webs during forest restoration. These findings contribute to our understanding of the relationships between soil nutrient limitation and soil micro-food web, and have implications for carbon sequestration through forest restoration and management in southern China.

Global biogeography and ecological implications of cobamide-producing prokaryotes

Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

Nematodes: an overlooked tiny engineer of plant health

Nematodes are a crucial component of rhizosphere biodiversity, affecting plant health as the most abundant and functionally diverse soil animals. Plant-parasitic nematodes are generally considered harmful, which may overlook their potential benefits to plants when coexisting with free-living nematodes in soil. We provide new insights into nematodes as vital plant partners. Plant root damage by plant-parasitic nematodes creates opportunities for pathogens and beneficial microbiota to colonize the rhizosphere. Free-living nematodes coordinate microbiota to suppress plant diseases, but they are susceptible to mortality from plant pathogens, potentially favoring pathogen release in the root zone. We conclude that the nematode's role in regulating plant pathogens represents a missing link, constraining our ability to predict and control soil-borne diseases in healthy plants.

Leguminous crop restores the carbon flow attenuation from nitrogen loading within soil nematode food web in a Camellia oleifera plantation

Excessive nitrogen (N) loading poses a substantial risk to soil biodiversity and disrupts carbon (C) flows within the soil food web. Intercropping with legumes is often considered a sustainable way to maintain soil N availability and mitigate the associated detrimental effects. However, it remains unclear whether and how legume crops restore energetic attenuation caused by N loading within the soil food web. Here, we conducted a two-year field experiment using randomized block design in a subtropic Camellia oleifera plantation with high wet N deposition. We examined the effects of applying N fertilizers at normal or half levels (168 or 84 kg N ha-1yr-1) and intercropping legumes (Arachis hypogaea or Cassia tora) on the soil nematode food web. We observed that N fertilization suppressed the majority of nematode trophic groups, weakened the stability of food web structure, and diminished the C flows across the bacterial and fungal energy channels. Conversely, intercropping with legumes (particularly with C. tora) bolstered the densities of bacterivore and fungivore nematodes. This enhancement facilitated interactions within the soil micro-food web, and subsequently augmented the C flows within their respective channels. Model predictions suggested that the detrimental effects of N fertilizers on the nematode food web are primarily linked to decreased soil pH resulting from soil N accumulation. Notably, higher soil organic C was found to mitigate these effects. Furthermore, N-enriched legume substrates played a beneficial role in stimulating soil microbial activities and facilitating C flows through bottom-up control. Our findings emphasize the positive impacts of legume crops on mitigating soil biodiversity loss and restoring energetic attenuation within soil food web under N-saturated soil conditions. These findings provide valuable insights for agroforestry management practices aimed at sustaining soil health and ecosystem resilience.

The origin of bi-dimensionality in plant root traits

Plant roots show extraordinary diversity in form and function in heterogeneous environments. Mounting evidence has shown global bi-dimensionality in root traits, the root economics spectrum (RES), and an orthogonal dimension describing mycorrhizal collaboration; however, the origin of the bi-dimensionality remains unresolved. Here, we propose that bi-dimensionality arises from the cylindrical geometry of roots, allometry between root cortex and stele, and independence between root cell wall thickness and cell number. Root geometry and mycorrhizal collaboration may both underlie the bi-dimensionality. Further, we emphasize why plant roots should be cylindrical rather than flat. Finally, we highlight the need to integrate organ-, cellular-, and molecular-level processes driving the bi-dimensionality in plant roots to fully understand plant diversity and functions.

Comparative Genomics of Sex, Chromosomes, and Sex Chromosomes in Caenorhabditis elegans and Other Nematodes

The nematode phylum has evolved a remarkable diversity of reproductive modes, including the repeated emergence of asexuality and hermaphroditism across divergent clades. The species-richness and small genome size of nematodes make them ideal systems for investigating the genome-wide causes and consequences of such major transitions. The availability of functional annotations for most Caenorhabditis elegans genes further allows the linking of patterns of gene content evolution with biological processes. Such gene-centric studies were recently complemented by investigations of chromosome evolution that made use of the first chromosome-scale genome assemblies outside the Caenorhabditis genus. This review highlights recent comparative genomic studies of reproductive mode evolution addressing the hybrid origin of asexuality and the parallel gene loss following the emergence of hermaphroditism. It further summarizes ongoing efforts to characterize ancient linkage blocks called Nigon elements, which form central units of chromosome evolution. Fusions between Nigon elements have been demonstrated to impact recombination and speciation. Finally, multiple recent fusions between autosomal and the sex-linked Nigon element reveal insights into the dynamic evolution of sex chromosomes across various timescales.

Global patterns and drivers of plant-soil microbe interactions

Plant-soil feedback (PSF) is an important mechanism determining plant community dynamics and structure. Understanding the geographic patterns and drivers of PSF is essential for understanding the mechanisms underlying geographic plant diversity patterns. We compiled a large dataset containing 5969 observations of PSF from 202 studies to demonstrate the global patterns and drivers of PSF for woody and non-woody species. Overall, PSF was negative on average and was influenced by plant attributes and environmental settings. Woody species PSFs did not vary with latitude, but non-woody PSFs were more negative at higher latitudes. PSF was consistently more positive with increasing aridity for both woody and non-woody species, likely due to increased mutualistic microbes relative to soil-borne pathogens. These findings were consistent between field and greenhouse experiments, suggesting that PSF variation can be driven by soil legacies from climates. Our findings call for caution to use PSF as an explanation of the latitudinal diversity gradient and highlight that aridity can influence plant community dynamics and structure across broad scales through mediating plant-soil microbe interactions.

Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer

Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.

Integrated global assessment of the natural forest carbon potential

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2-5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellite-derived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151-363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

Co-option of an Astacin Metalloprotease Is Associated with an Evolutionarily Novel Feeding Morphology in a Predatory Nematode

Animals consume a wide variety of food sources to adapt to different environments. However, the genetic mechanisms underlying the acquisition of evolutionarily novel feeding morphology remain largely unknown. While the nematode Caenorhabditis elegans feeds on bacteria, the satellite species Pristionchus pacificus exhibits predatory feeding behavior toward other nematodes, which is an evolutionarily novel feeding habit. Here, we found that the astacin metalloprotease Ppa-NAS-6 is required for the predatory killing by P. pacificus. Ppa-nas-6 mutants were defective in predation-associated characteristics, specifically the tooth morphogenesis and tooth movement during predation. Comparison of expression patterns and rescue experiments of nas-6 in P. pacificus and C. elegans suggested that alteration of the spatial expression patterns of NAS-6 may be vital for acquiring predation-related traits. Reporter analysis of the Ppa-nas-6 promoter in C. elegans revealed that the alteration in expression patterns was caused by evolutionary changes in cis- and trans-regulatory elements. This study suggests that the co-option of a metalloprotease is involved in an evolutionarily novel feeding morphology.

Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem

The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.

Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus

Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.

The global biogeography of tree leaf form and habit

Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4 Gt), 54% (335.7 Gt), 22% (136.2 Gt) and 3% (18.7 Gt), respectively. We further project that, depending on future emissions pathways, 17-34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling.

Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Microbiome predators in changing soils

Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators.