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It has long been believed that soil microbial activity in tropical forest ecosystems is limited by phosphorus (P) rather than nitrogen (N) availability. In this study, we reviewed the methods used to determine the limiting nutrients and evaluated the validity of the widespread P‐limitation hypothesis in tropical forest soils. The most commonly used analysis method entails testing whether fertilization increased microbial biomass or soil respiration. Fertilization using microbial biomass as an indicator was not a satisfactory method because standing microbial biomass does not always signal microbial activity. An increase in soil respiration after fertilization was also an insufficient indicator because the negative response shown by organic matter decomposition to nutrient addition can also be driven by nutrient shortage (nutrient mining). Nutrient amendment can also shift microbial communities towards more copiotrophic organisms, which may exhibit lower microbial respiration rates. We suggest that P addition may accelerate soil organic matter decomposition compared with N, which is independent of the nutrient limitation of soil microbial activity. The negative response of organic matter decomposition to N addition through nutrient mining is driven by N shortage, which is less likely to occur with P. N addition inhibits microbial activity via chemical reactions, whereas P addition may stimulate activity through replacement by C bound to sorption sites in the soil, improving C availability. Thus, the P‐limitation hypothesis must be reconsidered because of the contrasting effects of exogenous N and P addition on soil microbial activity, which could lead to misdetection of P limitation on soil microbial activity in tropical forest ecosystems. We recommend caution in applying the statement that soil microbial activity in tropical forest ecosystems is limited by P until a novel method is established to accurately determine the nutrients limiting soil microbial activity at the ecosystem level. We proposed alternative ways to describe nutrient shortage for soil microbes. A plain language summary is available for this article. Plain Language Summary

With the continuous changes in climate patterns due to global warming, drought has become an important limiting factor in the development of terrestrial ecosystems. However, a comprehensive understanding of the impact of drought on soil microbial activity at a global scale is lacking. In this study, we aimed to examine the effects of drought on soil microbial biomass (carbon [MBC], nitrogen [MBN], and phosphorus [MBP]) and enzyme activity (β-1, 4-glucosidase [BG]; β-D-cellobiosidase [CBH]; β-1, 4-N-acetylglucosaminidase [NAG]; L-leucine aminopeptidase [LAP]; and acid phosphatase [AP]). Additionally, we conducted a meta-analysis to determine the degree to which these effects are regulated by vegetation type, drought intensity, drought duration, and mean annual temperature (MAT). Our results showed that drought significantly decreased the MBC, MBN, and MBP and the activity levels of BG and AP by 22.7%, 21.2%, 21.6%, 26.8%, and 16.1%, respectively. In terms of vegetation type, drought mainly affected the MBC and MBN in croplands and grasslands. Furthermore, the response ratio of BG, CBH, NAG, and LAP were negatively correlated with drought intensity, whereas MBN and MBP and the activity levels of BG and CBH were negatively correlated with drought duration. Additionally, the response ratio of BG and NAG were negatively correlated with MAT. In conclusion, drought significantly reduced soil microbial biomass and enzyme activity on a global scale. Our results highlight the strong impact of drought on soil microbial biomass and carbon- and phosphorus-acquiring enzyme activity.

A multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics, determines the phylogenetic composition of the microbial community and assesses its functional potential and activity along a thaw transition from intact permafrost to thermokast bog. Multi-omics survey of frozen-soil microbiomes The application of the various individual 'omics' tools to the study of microbial ecosystems has dramatically altered our view of their constituents and ecology over the past decade. Here Janet Jansson and colleagues develop an multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics to analyse microbial gene expression in frozen soils that form part of the Alaska Peatland Experiment. The results show that the community shifts along a natural thaw gradient from permafrost to seasonally thawed active layer to thermokarst bog and the authors find that there is a transition in the potential for several biogeochemical cycles with thaw, including those for denitrification, nitrate reduction, iron reduction and methane oxidation. Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere 1 . This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils 2 , 3 , 4 and a rapid shift in functional gene composition during short-term thaw experiments 3 . However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales 5 , 6 . Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

A wide range of prokaryotes produce and excrete bacteriocins (proteins with antimicrobial activity) to reduce competition from closely related strains. Application of bacteriocins is of great importance in food industries, while little research has been focused on the agricultural potential of bacteriocins. A number of bacteriocin producing bacteria are members of the phytomicrobiome, and some strains are plant growth promoting rhizobacteria (PGPR). Thuricin 17 is a single small peptide with a molecular weight of 3.162 kDa, a subclass IId bacteriocin produced by Bacillus thuringiensis NEB17, isolated from soybean nodules. It is either cidal or static to a wide range of prokaryotes. In this way, it removes key competition from the niche space of the producer organism. B. thuringiensis NEB17 was isolated from soybean root nodules, and thus is a member of the phytomicrobiome. Interestingly, thuricin 17 is not active against a wide range of rhizobial strains involved in symbiotic nitrogen fixation with legumes or against other PGPR. In addition, it stimulates plant growth, particularly in the presence of abiotic stresses. The stresses it assists with include key ones associated with climate change (drought, high temperature, and soil salinity). Hence, in the presence of stress, it increases the size of the overall niche space, within plant roots, for B. thuringiensis NEB17. Through its anti-microbial activity, it could also enhance plant growth via control of specific plant pathogens. None of the isolated bacteriocins have been examined as broadly as thuricin 17 on plant growth promotion. Thus, this review focuses on the effect of thuricin 17 as a microbe to plant signal that assists crop plants in managing stress and making agricultural systems more climate change resilient.

Biopores are pores or voids in soil produced by roots, by earthworms, or by the occupation of earthworms in root pores, which are considered important microbial hotspots, especially in subsoil. We hypothesized that earthworms ( Lumbricus terrestris L.) exert stronger effects on microbial activities than decaying plant roots (of Cichorium intybus L.) in the subsoil because of the addition of pre-digested organic material. We tested this hypothesis by analyzing microbial biomass (C mic ), total organic C (C org ), and activities of eight enzymes (cellobiohydrolase, β-glucosidase, xylanase, acid phosphomonoesterase, leucine aminopeptidase, tyrosine aminopeptidase, chitotriosidase, and n -acetylglucosaminidase) down to 105-cm depth. The C mic increase was associated with a two- to threefold increase of C org content in biopores as compared to bulk soil. The highest percentage of C mic -to-C org (3.7 to 7.3 %) in the drilosphere demonstrated the enhancement of microbial efficiency for organic matter decomposition by earthworms. The availability of organic matter in biopores increased the activities of C- and N-targeting enzymes by 1.2–11.3 times, but reduced acid phosphomonoesterase activity by 10–40 % in biopores versus bulk soil. Introducing earthworms in root biopores caused 1.5–1.8 times higher microbial biomass and 1.2–1.9 times increased enzyme activities compared to the sole effect of earthworms. Soil depth showed a strong effect on the drilosphere, but only slight effects on the biochemical properties of root biopores and bulk soil. In conclusion, biopores are important microbial hotspots of C, N, and P transformations in subsoil. Earthworms exerted stronger effects on biochemical properties of biopores than decaying roots.

While numerous studies focus on the ecosystem effects of invasive mammals, few explore the causal mechanisms of such effects. Wild boar is one of the most widely introduced invasive mammal species in the world. By overturning extensive areas of vegetation and soil to feed on belowground resources, wild boar alter the soil food web and thus many microbial-mediated soil processes. Here, we take advantage of a long-term, 8-year, wild boar exclosure experiment across three plant community types in Patagonia, Argentina to explore how wild boar impact soil communities and their potential function. Previous work in this experimental system found that wild boar significantly impacted litter decomposition in the field, but it remained unclear if this effect was mediated through changes in abiotic or biotic soil properties. To explore both the abiotic and biotic drivers of decomposition, we measured soil moisture, soil temperature, soil bulk density, and soil respiration as well as soil micro-arthropod richness and abundance, earthworm abundance, and microbial biomass inside and outside of 10 exclosures in each of three plant community types. To assess potential microbial activity, we measured potential decomposition rates, substrate-induced respiration, and soil microbial enzyme activity. Rooting decreased soil moisture by 18% across plant communities, and soil respiration by 30% in Nothofagus and Austrocedrus forests. Additionally, rooting decreased soil micro-arthropod richness and abundance by ~ 80% in shrublands. However, rooting had no effect on soil potential microbial activity. Together, our results suggest that changes in both abiotic and biotic soil factors likely mediate observed wild boar impact on decomposition rates. Overall, we show that wild boar rooting alters soil functioning, but the pathway of impact varies by plant community, suggesting that wild boar impacts on native ecosystems can be difficult to predict.

Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0–5000 mg Cu kg−1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC50 ranging from 76 to 187 mg EDTA-extractable Cu kg−1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg−1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.

The agronomic use of compost and biochar as soil amendments may exhibit contrasting results in terms of soil fertility and plant nutrition. The effects of the biennial application of biochar, compost and a blend of compost:biochar (90:10; % dw:dw) on the agronomical performance of an organically managed and well established 25-year-old olive orchard was assessed 5 years after the initial application. The agronomical evaluation was based on the assessment of the soil physical, chemical, and biological characteristics, and the assessment of the soil fertility by both crop production and nutritional status of the orchard, and the bioassay with olive plantlets. Biochar mainly benefited the physical properties (bulk density, total porosity, aeration, water retention capacity) of soil, especially in the top 0–5 cm. Compost and its blend with biochar improved microbial activity, soil nutritional status (increasing the content of soluble organic C, N, and P) and favoured the formation of aggregates in soil. The bioassay conducted with young plantlets confirmed the enhanced soil fertility status in the three amended treatments, particularly in the case of biochar and its blend with compost. However, this effect was not significantly observed in the adult plants after 5 years of application, reflecting the slow response of adult olive trees to changes in fertilization. Based on these results, alongside the desirable long-residence time of biochar in soil and the ready availability of compost, the blend of biochar with compost assayed in this study is defined as a valid strategy for preparing high quality soil organic amendments.

Terrestrial ecosystems exhibit varied land uses as a result of both anthropogenic activities and natural processes. These variations in land use alter plant composition, soil characteristics, topography, and management practices, and hence lead to significant differences in soil microbial communities and their properties. This study evaluates the impact of distinct land use types (riparian, forest, pasture) on soil microbial biomass and microbial stoichiometric indices under uniform climatic and pedological conditions within a micro-basin in the Eastern Mediterranean region. The microbial biomass C (C mic ) in the riparian area was 2.5 and 4 times lower than in the meadow and forest areas, respectively. Additionally, the riparian zone’s microbial quotient ( q Mic) was 0.5 times higher than the forest and meadow areas. Microbial stoichiometric indices, particularly q Mic and metabolic quotient ( q CO 2 ), across all land uses, indicated that soils within this micro-basin were healthy and exhibited no signs of stress. The study further corroborated that land use exerts significant effects on soil microbial communities, with microbial biomass and activities largely influenced by soil organic matter. Notably, the C mic /N mic ratio remained within the range of 10–12 across all land uses, illustrating a fungal dominance in the microbial biomass. These findings underscore the role of land use patterns in altering soil properties, thereby influencing microbial biomass, microbial respiration, and stoichiometry in soils under similar environmental conditions.

Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation root exudation.