Microbial biomass measured as total lipid phosphate in soils of different organic content

Field-aged rice hull biochar stimulated the methylation of mercury and altered the microbial community in a paddy soil under controlled redox condition changes

Mercury (Hg) contaminated paddy soils are hot spots for methylmercury (MeHg) which can enter the food chain via rice plants causing high risks for human health. Biochar can immobilize Hg and reduce plant uptake of MeHg. However, the effects of biochar on the microbial community and Hg (de)methylation under dynamic redox conditions in paddy soils are unclear. Therefore, we determined the microbial community in an Hg contaminated paddy soil non-treated and treated with rice hull biochar under controlled redox conditions (< 0 mV to 600 mV) using a biogeochemical microcosm system. Hg methylation exceeded demethylation in the biochar-treated soil. The aromatic hydrocarbon degraders Phenylobacterium and Novosphingobium provided electron donors stimulating Hg methylation. MeHg demethylation exceeded methylation in the non-treated soil and was associated with lower available organic matter. Actinobacteria were involved in MeHg demethylation and interlinked with nitrifying bacteria and nitrogen-fixing genus Hyphomicrobium. Microbial assemblages seem more important than single species in Hg transformation. For future directions, the demethylation potential of Hyphomicrobium assemblages and other nitrogen-fixing bacteria should be elucidated. Additionally, different organic matter inputs on paddy soils under constant and dynamic redox conditions could unravel the relationship between Hg (de)methylation, microbial carbon utilization and nitrogen cycling.

Microbial strategies for phosphorus acquisition in rice paddies under contrasting water regimes: Multiple source tracing by 32P and 33P

Microbial acquisition and utilization of organic and mineral phosphorus (P) sources in paddy soils are strongly dependent on redox environment and remain the key to understand P turnover and allocation for cell compound synthesis. Using double 32/33P labeling, we traced the P from three sources in a P-limited paddy soil: ferric iron-bound phosphate (Fe-P), wheat straw P (Straw-P), and soil P (Soil-P) in microbial biomass P (MBP) and phospholipids (Phospholipid-P) of individual microbial groups depending on water regimes: (i) continuous flooding or (ii) alternate wetting and drying. 32/33P labeling combined with phospholipid fatty acid analysis allowed to trace P utilization by functional microbial groups. Microbial P nutrition was mainly covered by Soil-P, whereas microorganisms preferred to take up P from mineralized Straw-P than from Fe-P dissolution. The main Straw-P mobilizing agents were Actinobacteria under alternating wetting and drying and other Gram-positive bacteria under continuous flooding. Actinobacteria and arbuscular mycorrhiza increased P incorporation into cell membranes by 1.4-5.8 times under alternate wetting and drying compared to continuous flooding. The Fe-P contribution to MBP was 4-5 times larger in bulk than in rooted soil because (i) rice roots outcompeted microorganisms for P uptake from Fe-P and (ii) rhizodeposits stimulated microbial activity, e.g. phosphomonoesterase production and Straw-P mineralization. Higher phosphomonoesterase activities during slow soil drying compensated for the decreased reductive dissolution of Fe-P. Concluding, microbial P acquisition strategies depend on (i) Soil-P, especially organic P, availability, (ii) the activity of phosphomonoesterases produced by microorganisms and roots, and (iii) P sources - all of which depend on the redox conditions. Maximizing legacy P utilization in the soil as a function of the water regime is one potential way to reduce competition between roots and microbes for P in rice cultivation.

A slow-fast trait continuum at the whole community level in relation to land-use intensification

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.

Setting new standards: Multiphasic analysis of microplastic mineralization by fungi

Plastic materials provide numerous benefits. However, properties such as durability and resistance to degradation that make plastic attractive for variable applications likewise foster accumulation in the environment. Fragmentation of plastics leads to the formation of potentially hazardous microplastic, of which a considerable amount derives from polystyrene. Here, we investigated the biodegradation of polystyrene by the tropical sooty mold fungus Capnodium coffeae in different experimental setups. Growth of C. coffeae was stimulated significantly when cultured in presence of plastic polymers rather than in its absence. Stable isotope tracing using 13C-enriched polystyrene particles combined with cavity ring-down spectroscopy showed that the fungus mineralized polystyrene traces. However, phospholipid fatty acid stable isotope probing indicated only marginal assimilation of polystyrene-13C by C. coffeae in liquid cultures. NMR spectroscopic analysis of residual styrene contents prior to and after incubation revealed negligible changes in concentration. Thus, this study suggests a plastiphilic life style of C. coffeae despite minor usage of plastic as a carbon source and the general capability of sooty mold fungi to stimulate polystyrene mineralization, and proposes new standards to identify and unambiguously demonstrate plastic degrading capabilities of microbes.

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

Electric field as extracellular enzyme activator promotes conversion of lignocellulose to humic acid in composting process

To promote efficient conversion of lignocellulose to humus (HS) during composting, a novel bio-electrochemical technology was applied and explored the effect and mechanism of electrification on carbon conversion during different composting periods. The results showed that supplementary electric field played different roles during composting. In the early stage, organic matter mineralization was significantly accelerated under electric field application, that was embodied in a 29.8% increase of CO2 emission due to the enhanced metabolic activity of microorganisms. However, the electric field functioned as an extracellular enzyme activator during the later stage since the abundance of functional microorganisms related to lignocellulose degradation was increased by 1.5-2.8 fold that effectively promoted the conversion of lignocellulose to HS. The humic acid content of the compost products increased by 23.0-32.9% compared with control. This study elucidated how electric fields affect carbon conversion during composting, which provides a novel strategy for returning agricultural wastes to soil.

Hydroxy fatty acids in the surface Earth system

Lipids are ubiquitous and highly abundant in a wide range of organisms and have been found in various types of environmental media. These molecules play a crucial role as organic tracers by providing a chemical perspective on viewing the material world, as well as offering a wealth of information on metabolic activities. Among the diverse lipid compounds, hydroxy fatty acids (HFAs) with one to multiple hydroxyl groups attached to the carbon chain stand out as important biomarkers for different sources of organic matter. HFAs are widespread in nature and are involved in biotransformation and oxidation processes in living organisms. The unique chemical and physical properties attributed to the hydroxyl group make HFAs ideal biomarkers in biomedicine and environmental toxicology, as well as organic geochemistry. The molecular distribution patterns of HFAs can be unique and diagnostic for a given class of organisms, including animals, plants, and microorganisms. Thus, HFAs can act as a valuable proxy for understanding the ecological relationships between different organisms and their environment. Furthermore, HFAs have numerous industrial applications due to their higher reactivity, viscosity, and solvent miscibility. This review paper integrates the latest research on the sources and chemical analyses of HFAs, as well as their applications in industrial/medicinal production and as biomarkers in environmental studies. This review article also provides insights into the biogeochemical cycles of HFAs in the surface Earth system, highlighting the importance of these compounds in understanding the complex interactions between living organisms and the environment.

Artificial light at night (ALAN) causes shifts in soil communities and functions

Artificial light at night (ALAN) is increasing worldwide, but its effects on the soil system have not yet been investigated. We tested the influence of experimental manipulation of ALAN on two taxa of soil communities (microorganisms and soil nematodes) and three aspects of soil functioning (soil basal respiration, soil microbial biomass and carbon use efficiency) over four and a half months in a highly controlled Ecotron facility. We show that during peak plant biomass, increasing ALAN reduced plant biomass and was also associated with decreased soil water content. This further reduced soil respiration under high ALAN at peak plant biomass, but microbial communities maintained stable biomass across different levels of ALAN and times, demonstrating higher microbial carbon use efficiency under high ALAN. While ALAN did not affect microbial community structure, the abundance of plant-feeding nematodes increased and there was homogenization of nematode communities under higher levels of ALAN, indicating that soil communities may be more vulnerable to additional disturbances at high ALAN. In summary, the effects of ALAN reach into the soil system by altering soil communities and ecosystem functions, and these effects are mediated by changes in plant productivity and soil water content at peak plant biomass. This article is part of the theme issue 'Light pollution in complex ecological systems'.

Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.

Ecosystem consequences of invertebrate decline

Human activities cause substantial changes in biodiversity.1,2 Despite ongoing concern about the implications of invertebrate decline,3,4,5,6,7 few empirical studies have examined the ecosystem consequences of invertebrate biomass loss. Here, we test the responses of six ecosystem services informed by 30 above- and belowground ecosystem variables to three levels of aboveground (i.e., vegetation associated) invertebrate community biomass (100%, 36%, and 0% of ambient biomass) in experimental grassland mesocosms in a controlled Ecotron facility. In line with recent reports on invertebrate biomass loss over the last decade, our 36% biomass treatment also represented a decrease in invertebrate abundance (-70%) and richness (-44%). Moreover, we simulated the pronounced change in invertebrate biomass and turnover in community composition across the season. We found that the loss of invertebrate biomass decreases ecosystem multifunctionality, including two critical ecosystem services, aboveground pest control and belowground decomposition, while harvested plant biomass increases, likely because less energy was channeled up the food chain. Moreover, communities and ecosystem functions become decoupled with a lower biomass of invertebrates. Our study shows that invertebrate loss threatens the integrity of grasslands by decoupling ecosystem processes and decreasing ecosystem-service supply.

Water limitation intensity shifts carbon allocation dynamics in Scots pine mesocosms

Background and aims

Tree species worldwide suffer from extended periods of water limitation. These conditions not only affect the growth and vitality of trees but also feed back on the cycling of carbon (C) at the plant-soil interface. However, the impact of progressing water loss from soils on the transfer of assimilated C belowground remains unresolved.

Methods

Using mesocosms, we assessed how increasing levels of water deficit affect the growth of Pinus sylvestris saplings and performed a 13C-CO2 pulse labelling experiment to trace the pathway of assimilated C into needles, fine roots, soil pore CO2, and phospholipid fatty acids of soil microbial groups.

Results

With increasing water limitation, trees partitioned more biomass belowground at the expense of aboveground growth. Moderate levels of water limitation barely affected the uptake of 13C label and the transit time of C from needles to the soil pore CO2. Comparatively, more severe water limitation increased the fraction of 13C label that trees allocated to fine roots and soil fungi while a lower fraction of 13CO2 was readily respired from the soil.

Conclusions

When soil water becomes largely unavailable, C cycling within trees becomes slower, and a fraction of C allocated belowground may accumulate in fine roots or be transferred to the soil and associated microorganisms without being metabolically used.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11104-023-06093-5.

Microbial assemblies with distinct trophic strategies drive changes in soil microbial carbon use efficiency along vegetation primary succession in a glacier retreat area of the southeastern Tibetan Plateau

Soil microbial carbon use efficiency (CUE) is a vital physiological parameter in assessing carbon turnover. Yet, how the microbial assemblies with distinct trophic strategies regulate the soil microbial CUE remains elusive. Based on the oligotrophic-copiotrophic framework, we explored the role of microbial taxa with different trophic strategies in mediating microbial CUE (determined by a ¹³C-labeled approach) along the vegetation primary succession in Hailuogou glacier retreat area of the southeastern Tibetan Plateau. Results showed that soil microbial CUE ranged from 0.54 to 0.72 (averaging 0.62 ± 0.01 across all samples) and increased staggeringly along the vegetation succession. Microbial assemblies with distinct trophic strategies were crucial regulators of soil microbial CUE. Specifically, microbial CUE increased with microbial oligotroph: copiotroph ratios, oligotroph-dominated stage had a higher microbial CUE than copiotroph-dominated ones. The prevalence of oligotrophic members would be the underlying microbial mechanism for the high microbial CUE. Given that oligotrophs predominate in more recalcitrant carbon soils and their higher microbial CUE, we speculate that oligotrophs are likely to potentially enhance carbon sequestration in soils. In addition, the responses of the microbial CUE to fungal oligotroph: copiotroph ratios were higher than bacterial ones. Fungal taxa may play a dominant role in shaping microbial CUE relative to bacterial members. Overall, our results constructed close associations between microbial trophic strategies and CUE and provide direct evidence regarding how microbial trophic strategies regulate microbial CUE. This study is a significant step forward for elucidating the physiological mechanisms regulating microbial CUE and has significant implications for understanding microbial-mediated carbon cycling processes.

Coriander (Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning

The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.

Microbial drivers of plant richness and productivity in a grassland restoration experiment along a gradient of land-use intensity

Plant-soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land-use intensity (LUI) on PSFs. We conducted a disturbance and seed addition experiment in 10 grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities. Greater plant biomass at high LUI was related to a decrease in the fungal to bacterial ratios, indicating highly productive grasslands to be dominated by bacteria. Lower enzyme activity per microbial biomass at high plant species richness indicated a slower carbon (C) cycling. The relative abundance of fungal saprotrophs decreased, while pathogens increased with LUI and disturbance. Both fungal guilds were negatively associated with plant richness, indicating the mechanisms underlying PSFs depended on LUI. We show that LUI and disturbance affect fungal functional composition, which may feedback on plant species richness by impeding the establishment of pathogen-sensitive species. Therefore, we highlight the need to integrate LUI including its effects on PSFs when planning for practices that aim to optimize plant diversity and productivity.

Long-term organic fertilizer additions elevate soil extracellular enzyme activities and tobacco quality in a tobacco-maize rotation

Organic fertilizer is effective in improving soil quality, and promoting crop growth. Combined organic and inorganic fertilization has been proved as a more favorable way to tobacco yield and quality. However, the mechanisms underlying tobacco yield and quality under combinations of different organic and inorganic fertilizer remain unclear. We conducted a 12-year tobacco (Nicotiana tabacum L.)-maize crop rotation field experiment in Yanhe experimental station, China to examine the yields and qualities of tobacco, soil nutrients, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycles in response to different fertilization treatments. Five fertilization treatments (no fertilization; 75 kg N fertilizer ha^-1; 450 kg oil cake ha^-1 + 75 kg N fertilizer ha^-1; 15,000 kg pig dung ha^-1 + 60 kg N fertilizer ha^-1; 3,000 kg straw ha^-1 + 75 kg N fertilizer ha^-1) were applied to tobacco while maize was fertilized with inorganic compound fertilizers. After 12 years of tobacco-maize rotation, the results showed that organic fertilizer additions elevate tobacco yield and quality, and the soil extracellular enzymes activities. Gram-negative bacteria, actinomycetes, and total soil microbial biomass were increased by organic fertilizer additions, both plant-based (oil cake and straw) and animal-based (pig dung) organics. The levels of soil organic matter, total organic carbon, total phosphorus and available phosphorus are higher in pig dung addition treatment than oil cake and straw additions. By variance analysis with respect to fertilization treatments, organic sources differentially affected the activities of diverse soil enzymes. The redundancy analysis gave that yield and quality of tobacco leaves (upper, middle, and lower leaves) positively related to soil extracellular enzyme activities. Based on analysis of yield and quality of tobacco leaves with extracellular enzyme activities and soil nutrients, it is suggested animal-based organic fertilizer, thus pig dung, should be used in combining with chemical fertilizers to improve the quality of tobacco and soil nutrients.

Soil organic carbon decomposition responding to warming under nitrogen addition across Chinese vegetable soils

Chemical fertilization in excess and warming disrupt the soil microbes and alter resource stoichiometry, particularly in intensive vegetable soils, while the effects of these variables on the temperature sensitivity of soil organic carbon (SOC) decomposition (Q₁₀) and SOC stability remain elusive. Thus, we collected six long-term vegetable soils along a climatic gradient to examine the microbial mechanisms and resource stoichiometry effects on fluctuations in Q₁₀ and SOC stability induced by warming and fertilization from vegetable soils. Our results showed that the SOC decomposition was dominated by microbes and regulated by stoichiometry. Compared to cold sites, higher Q₁₀ of SOC decomposition was observed in warm sites, accompanied by lower enzyme activities, microbial CUE, and C:N ratio. In this context, warming reduced SOC stability as evidenced by up to 31.8% greater Q₁₀ (1.45) at warm sites than at cold sites (1.10) owing to less richness of microbial communities and lower microbial CUE. The relatively lower pH and labile organic C value restricted the development of microbial richness, and decreased C- and N-related enzyme activities and a lower C:N ratio resulted in microbial CUE reduction. Additionally, N fertilization altered the C:N imbalance and enhanced SOC stability in vegetable soils, exhibiting an increase of Q₁₀ values, particularly of great importance in warm sites. Collectively, our findings emphasize the importance of the microbial mechanism and resource stoichiometry in predicting variations in Q₁₀ and fluctuations in SOC stability, and provide theoretical advice on improving management policies in the context of warming and fertilization from vegetable soils.

Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability

Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH₄NO₃ solution; 0 [N0], 20 [N1], and 40 [N2] g N m^-2 year^-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH₄⁺-N and NO₃^--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.

Assessing Microbial Monitoring Methods for Challenging Environmental Strains and Cultures

This paper focuses on the comparison of microbial biomass increase (cell culture growth) using field-relevant testing methods and moving away from colony counts. Challenges exist in exploring the antimicrobial growth of fastidious strains, poorly culturable bacteria and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacterial growth that can be efficient surrogates for classical optical density or colony-forming unit measurements. Here, six species grown in pure culture were monitored using optical density, ATP assays, DNA concentrations and 16S rRNA qPCR. Each of these methods have different advantages and disadvantages concerning the measurement of growth and activity in complex field samples. The species used as model systems for monitoring were: Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. All four techniques were found to successfully measure and detect cell biomass/activity differences, though the shape and accuracy of each technique varied between species. DNA concentrations were found to correlate the best with the other three assays (ATP, DNA concentrations and 16S rRNA-targeted qPCR) and provide the advantages of rapid extraction, consistency between replicates and the potential for downstream analysis. DNA concentrations were determined to be the best universal monitoring method for complex environmental samples.

Absence of a home-field advantage within a short-rotation arable cropping system

Aims

The home-field advantage (HFA) hypothesis predicts faster decomposition of plant residues in home soil compared to soils with different plants (away), and has been demonstrated in forest and grassland ecosystems. It remains unclear if this legacy effect applies to crop residue decomposition in arable crop rotations. Such knowledge could improve our understanding of decomposition dynamics in arable soils and may allow optimisation of crop residue amendments in arable systems by cleverly combining crop-residue rotations with crop rotations to increase the amount of residue-derived C persisting in soil.

Methods

We tested the HFA hypothesis in a reciprocal transplant experiment with mesh bags containing wheat and oilseed rape residues in soils at three stages of a short-rotation cropping system. Subsets of mesh bags were retrieved monthly for six months to determine residue decomposition rates, concomitantly measuring soil available N, microbial community structure (phospholipid fatty acid analysis), and microbial activity (Tea Bag Index protocol) to assess how plants may influence litter decomposition rates via alterations to soil biochemical properties and microbial communities.

Results

The residues decomposed at similar rates at all rotational stages. Thorough data investigation using several statistical approaches revealed no HFA within the crop rotation. Soil microbial community structures were similar at all rotational stages.

Conclusions

We attribute the absence of an HFA to the shortness of the rotation and soil disturbance involved in intensive agricultural practices. It is therefore unlikely that appreciable benefits could be obtained in short conventionally managed arable rotations by introducing a crop-residue rotation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11104-022-05419-z.

Interactions between biochar, arbuscular mycorrhizal fungi and photosynthetic processes in potato (Solanum tuberosum L.)

Pyrolyzed biomass, generating biochar for use as soil amendment, is recognized as a promising strategy for carbon sequestration. Current understanding of the interactions between biochar, arbuscular mycorrhizal (AM), and plant photosynthesis, in terms of biochemical processes and CO₂ uptake, is fragmentary. The aim of this study was to investigate the effects on photosynthesis in potato including maximum rate of carboxylation by Rubisco (V_cmax), maximum rate of electron transport rate for RuBP-regeneration (J_max), mesophyll conductance (g_m) and other plant traits. Four types of biochar (wheat or miscanthus straw pellets pyrolyzed at temperatures of either 550 °C or 700 °C) were amended into low phosphorus soil. Potato plants were inoculated with the AM fungus Rhizophagus irregularis (M+) or not (M-). The results showed that four types of biochar generally decreased nitrogen and phosphorus content of potato, especially the biochars pyrolyzed at high temperature. This negative effect of biochar on nutrient content was alleviated by AM. It was found that V_cmax was limited by low plant nitrogen content as well as leaf area and phosphorus content. Plant phosphorus content also limited J_max, which was mutually constrained by V_cmax of leaves. Low g_m was an additional limiting factor for photosynthesis. The g_m was positively correlated to nitrogen content, which influenced the leaf anatomical structure by alteration of leaf mass per area. In conclusion, the influence of interactions between quality of biochar and AM symbiosis on photosynthesis of potato seems to relate to effects on plant nutrient content and leaf structures. Accordingly, a model for the dependence of V_cmax on nitrogen and phosphorus content and their interactive effect exhibited a high correlation coefficient. As potato plants form AM symbiosis under natural field conditions, the extent and interaction with the quality of amended biochar can be a determining factor for plant nutrient content, growth and yield.

Deep-rooted perennial crops differ in capacity to stabilize C inputs in deep soil layers

Comprehensive climate change mitigation necessitates soil carbon (C) storage in cultivated terrestrial ecosystems. Deep-rooted perennial crops may help to turn agricultural soils into efficient C sinks, especially in deeper soil layers. Here, we compared C allocation and potential stabilization to 150 cm depth from two functionally distinct deep-rooted perennials, i.e., lucerne (Medicago sativa L.) and intermediate wheatgrass (kernza; Thinopyrum intermedium), representing legume and non-legume crops, respectively. Belowground C input and stabilization was decoupled from nitrogen (N) fertilizer rate in kernza (100 and 200 kg mineral N ha⁻¹), with no direct link between increasing mineral N fertilization, rhizodeposited C, and microbial C stabilization. Further, both crops displayed a high ability to bring C to deeper soil layers and remarkably, the N₂-fixing lucerne showed greater potential to induce microbial C stabilization than the non-legume kernza. Lucerne stimulated greater microbial biomass and abundance of N cycling genes in rhizosphere soil, likely linked to greater amino acid rhizodeposition, hence underlining the importance of coupled C and N for microbial C stabilization efficiency. Inclusion of legumes in perennial cropping systems is not only key for improved productivity at low fertilizer N inputs, but also appears critical for enhancing soil C stabilization, in particular in N limited deep subsoils.

Inoculum Sources Modulate Mycorrhizal Inoculation Effect on Tamarix articulata Development and Its Associated Rhizosphere Microbiota

(1) Background: Soil degradation is an increasingly important problem in many parts of the world, particularly in arid and semiarid areas. Arbuscular mycorrhizal fungi (AMF) isolated from arid soils are recognized to be better adapted to these edaphoclimatic conditions than exogenous ones. Nevertheless, little is known about the importance of AMF inoculum sources on Tamarix articulata development in natural saline soils. Therefore, the current study aims at investigating the efficiency of two AMF-mixed inoculums on T. articulata growth, with consideration of its rhizosphere microbiota. (2) Methods: indigenous inoculum made of strains originating from saline soils and a commercial one were used to inoculate T. articulata in four saline soils with different salinity levels under microcosm conditions with evaluation of rhizosphere microbial biomasses. (3) Results: Our findings showed that indigenous inoculum outperforms the commercial one by 80% for the mycorrhizal rate and 40% for plant biomasses, which are correlated with increasing shoot phosphorus content. Soil microbial biomasses increased significantly with indigenous mycorrhizal inoculum in the most saline soil with 46% for AMF, 25% for saprotrophic fungi and 15% for bacterial biomasses. (4) Conclusion: Present results open the way towards the preferential use of mycorrhizal inoculum, based on native AMF, to perform revegetation and to restore the saline soil microbiota.

Suppression of Arbuscular Mycorrhizal Fungi Aggravates the Negative Interactive Effects of Warming and Nitrogen Addition on Soil Bacterial and Fungal Diversity and Community Composition

We examined the impacts of warming, nitrogen (N) addition, and suppression of arbuscular mycorrhizal fungi (AMF) on soil bacterial and fungal richness and community composition in a field experiment. AMF root colonization and the concentration of an AMF-specific phospholipid fatty acid (PLFA) were significantly reduced after the application of the fungicide benomyl as a soil drench. Warming and N addition had no independent effects but interactively decreased soil fungal richness, while warming, N addition, and AMF suppression together reduced soil bacterial richness. Soil bacterial and fungal species diversity was lower with AMF suppression, indicating that AMF suppression has a negative effect on microbial diversity. Warming and N addition decreased the net loss of plant species and the plant species richness, respectively. AMF suppression reduced plant species richness and the net gain of plant species but enhanced the net loss of plant species. Structural equation modeling (SEM) demonstrated that the soil bacterial community responded to the increased soil temperature (ST) induced by warming and the increased soil available N (AN) induced by N addition through changes in AMF colonization and plant species richness; ST directly affected the bacterial community, but AN affected both the soil bacterial and fungal communities via AMF colonization. In addition, higher mycorrhizal colonization increased the plant species richness by increasing the net gains in plant species under warming and N addition. IMPORTANCE AMF can influence the composition and diversity of plant communities. Previous studies have shown that climate warming and N deposition reduce the effectiveness of AMF. However, how AMF affect soil bacterial and fungal communities under these global change drivers is still poorly understood. A 4-year field study revealed that AMF suppression decreased bacterial and fungal diversity irrespective of warming or N addition, while AMF suppression interacted with warming or N addition to reduce bacterial and fungal richness. In addition, bacterial and fungal community compositions were determined by mycorrhizal colonization, which was regulated by soil AN and ST. These results suggest that AMF suppression can aggravate the severe losses to native soil microbial diversity and functioning caused by global changes; thus, AMF play a vital role in maintaining belowground ecosystem stability in the future.

Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.

Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning

Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.

Production of Organic Acids by Arbuscular Mycorrhizal Fungi and Their Contribution in the Mobilization of Phosphorus Bound to Iron Oxides

Most plants living in tropical acid soils depend on the arbuscular mycorrhizal (AM) symbiosis for mobilizing low-accessible phosphorus (P), due to its strong bonding by iron (Fe) oxides. The roots release low-molecular-weight organic acids (LMWOAs) as a mechanism to increase soil P availability by ligand exchange or dissolution. However, little is known on the LMWOA production by AM fungi (AMF), since most studies conducted on AM plants do not discriminate on the LMWOA origin. This study aimed to determine whether AMF release significant amounts of LMWOAs to liberate P bound to Fe oxides, which is otherwise unavailable for the plant. Solanum lycopersicum L. plants mycorrhized with Rhizophagus irregularis were placed in a bicompartmental mesocosm, with P sources only accessible by AMF. Fingerprinting of LMWOAs in compartments containing free and goethite-bound orthophosphate (OP or GOE-OP) and phytic acid (PA or GOE-PA) was done. To assess P mobilization via AM symbiosis, P content, photosynthesis, and the degree of mycorrhization were determined in the plant; whereas, AM hyphae abundance was determined using lipid biomarkers. The results showing a higher shoot P content, along with a lower N:P ratio and a higher photosynthetic capacity, may be indicative of a higher photosynthetic P-use efficiency, when AM plants mobilized P from less-accessible sources. The presence of mono-, di-, and tricarboxylic LMWOAs in compartments containing OP or GOE-OP and phytic acid (PA or GOE-PA) points toward the occurrence of reductive dissolution and ligand exchange/dissolution reactions. Furthermore, hyphae grown in goethite loaded with OP and PA exhibited an increased content of unsaturated lipids, pointing to an increased membrane fluidity in order to maintain optimal hyphal functionality and facilitate the incorporation of P. Our results underpin the centrality of AM symbiosis in soil biogeochemical processes, by highlighting the ability of the AMF and accompanying microbiota in releasing significant amounts of LMWOAs to mobilize P bound to Fe oxides.

Land-use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects

Soil microbial community functions are essential indicators of ecosystem multifunctionality in managed land-use systems. Going forward, the development of adaptation strategies and predictive models under future climate scenarios will require a better understanding of how both land-use and climate disturbances influence soil microbial functions over time. Between March and November 2018, we assessed the effects of climate change on the magnitude and temporal stability of soil basal respiration, soil microbial biomass and soil functional diversity across a range of land-use types and intensities in a large-scale field experiment. Soils were sampled from five common land-use types including conventional and organic croplands, intensive and extensive meadows, and extensive pastures, under ambient and projected future climate conditions (reduced summer precipitation and increased temperature) at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Land-use and climate treatment interaction effects were significant in September, a month when precipitation levels slightly rebounded following a period of drought in central Germany: compared to ambient climate, in future climate treatments, basal respiration declined in pastures and increased in intensive meadows, functional diversity declined in pastures and croplands, and respiration-to-biomass ratio increased in intensive and extensive meadows. Low rainfall between May and August likely strengthened soil microbial responses toward the future climate treatment in September. Although microbial biomass showed declining levels in extensive meadows and pastures under future climate treatments, overall, microbial function magnitudes were higher in these land-use types compared to croplands, indicating that improved management practices could sustain high microbial ecosystem functioning in future climates. In contrast to our hypothesis that more disturbed land-use systems would have destabilized microbial functions, intensive meadows and organic croplands showed stabilized soil microbial biomass compared to all other land-use types, suggesting that temporal stability, in addition to magnitude-based measurements, may be useful for revealing context-dependent effects on soil ecosystem functioning.

Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data

Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.

Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magna carcasses and 13C-labelled maize leaves (Zea mays) were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2 analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C-N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.

Ester Linked Fatty Acid (ELFA) method should be used with caution for interpretating soil microbial communities and their relationships with environmental variables in forest soils

As an alternative for phospholipid fatty acid (PLFA) analysis, a simpler ester linked fatty acid (ELFA) analysis has been developed to characterize soil microbial communities. However, few studies have compared the two methods in forest soils where the contribution of nonmicrobial sources may be larger than that of microbial sources. Moreover, it remains unclear whether the two methods yield similar relationships of microbial biomass and composition with environmental variables. Here, we compared PLFA and ELFA methods with respect to microbial biomass and composition and their relationships with environmental variables in six oriental oak (Quercus variabilis) forest sites along a 1500-km latitudinal gradient in East China. We found that both methods had a low sample-to-sample variability and successfully separated overall community composition of sites. However, total, bacterial, and fungal biomass, the fungal-to-bacterial ratio, and the gram-positive to gram-negative bacteria ratio were not significantly or strongly correlated between the two methods. The relationships of these microbial properties with environmental variables (pH, precipitation, and clay) greatly differed between the two methods. Our study indicates that despite its simplicity, the ELFA method may not be as feasible as the PLFA method for investigating microbial biomass and composition and for identifying their dominant environmental drivers, at least in forest soils.

Response of carbon and microbial properties to risk elements pollution in arctic soils

A 180-day incubation study was conducted to evaluate the effects of risk elements (REs) on organic carbon use and microbial activities in organic soils in the Arctic during the summer snowmelt period. Soils were artificially spiked with Cd, Pb, Cr, Ni, Cu, As, and a combination of these REs according to the levels measured in Arctic soils from REs-polluted industrial sites. During the incubation period, microbial activities and microbial biomass carbon (MBC) formation were inhibited, and microbial quotient (qCO2) values were relatively high in the spiked soils indicating that more energy was used by microbes for maintenance under REs stress. Meanwhile, microbial metabolism was significantly restrained. Microbial Specific phospholipid fatty acids (PLFAs) were reduced in RE spiked soils relative to the control, especially in the As- and multi-RE-spiked soils. The abundance of both fungi and bacteria was reduced in response to RE amendments by 14-24% and 1-55%, respectively. PLFA biomarkers indicated a shift in soil microbial community structure and activities influenced by REs, consequently having a negative effect on soil organic carbon degradation. This study addresses the knowledge gap regarding the alternation of biochemical reactions in Arctic soils under anthropogenic REs with relevant contamination levels.

Suppression of arbuscular mycorrhizal fungi decreases the temporal stability of community productivity under elevated temperature and nitrogen addition in a temperate meadow

Global change alters how terrestrial ecosystems function and makes them less stable over time. Global change can also suppress the development and effectiveness of arbuscular mycorrhizal fungi (AMF). This is concerning, as AMF have been shown to alleviate the negative influence of global changes on plant growth and maintain species coexistence. However, how AMF and global change interact and influence community temporal stability remains poorly understood. Here, we conducted a 4-year field experiment and used structural equation modeling (SEM) to explore the influence of elevated temperature, nitrogen (N) addition and AMF suppression on community temporal stability (quantified as the ratio of the mean community productivity to its standard deviation) in a temperate meadow in northern China. We found that elevated temperature and AMF suppression independently decreased the community temporal stability but that N addition had no impact. Community temporal stability was mainly driven by elevated temperature, N addition and AMF suppression that modulated the dominant species stability; to a lesser extent by the elevated temperature and AMF suppression that modulated AMF richness associated with community asynchrony; and finally by the N addition and AMF suppression that modulated mycorrhizal colonization. In addition, although N addition, AMF suppression and elevated temperature plus AMF suppression reduced plant species richness, there was no evidence that changes in community temporal stability were linked to changes in plant richness. SEM further showed that elevated temperature, N addition and AMF suppression regulated community temporal stability by influencing both the temporal mean and variation in community productivity. Our results suggest that global environmental changes may have appreciable consequences for the stability of temperate meadows while also highlighting the role of belowground AMF status in the responses of plant community temporal stability to global change.

Iron-reducing bacteria decompose lignin by electron transfer from soil organic matter

Iron-reducing bacteria (IRB) are crucial for electron transfer in anaerobic soil microsites. The utilization of the energy gathered by this mechanism by decomposers of organic matter is a challenging and fascinating issue. We hypothesized that bacteria reducing Fe(III) (oxyhydr)oxides to soluble Fe(II) obtain electrons from reduced soil organic matter (SOM_r) involving lignin oxidation. Iron-reducing bacteria were isolated from topsoils of various climates (humid temperate, cold temperate, subpolar), vegetation types (mostly grasslands and forests), and derived from various parent materials treatments assigned as Granitic, Volcanic-allophanic, Fluvio-glacial, Basaltic-Antarctic and Metamorphic. After the screening of IRB by phospholipid fatty acid (PLFA) analysis and PCR identification (full-length 16S rDNA), the IRB were inoculated to 20 samples (five soils and 4 replicates) and a broad range of parallel processes were traced. Geobacter metallireducens and Geobacter lovleyi were the main Geobacteraceae-strains present in all soils and strongly increased the activity of ligninolytic enzymes: lignin peroxidase and manganese peroxidase. Carbon dioxide (CO₂) released from IRB-inoculated soils was 140% higher than that produced by Fenton reactions (induced by H₂O₂ and Fe(II) addition) but 40% lower than in non-sterile soils. CO₂ release was closely correlated with the produced Fe (II) and H₂O₂ consumption. The highest CO₂ was released from Basaltic-Antarctic soils with the highest Fe content and was closely correlated with lignin depolymerization (detection by fluorescence images). All IRB oxidized the lignin contained in the SOM within a wide pH range and in soils from all parent materials. We present a conceptual model showing electron shuttling from SOM containing lignin (as a C and energy source) to IRB to produce energy and promote Fe(III) (oxyhydr)oxides reduction was proposed and discussed.

Do Invasive Earthworms Affect the Functional Traits of Native Plants?

As ecosystem engineers, invasive earthworms are one of the main drivers of plant community changes in North American forests previously devoid of earthworms. One explanation for these community changes is the effects of earthworms on the reproduction, recruitment, and development of plant species. However, few studies have investigated functional trait responses of native plants to earthworm invasion to explain the mechanisms underlying community changes. In a mesocosm (Ecotron) experiment, we set up a plant community composed of two herb and two grass species commonly found in northern North American forests under two earthworm treatments (presence vs. absence). We measured earthworm effects on above- and belowground plant biomass and functional traits after 3 months of experiment. Our results showed that earthworm presence did not significantly affect plant community biomass and cover. Furthermore, only four out of the fifteen above- and belowground traits measured were affected by earthworm presence. While some traits, such as the production of ramets, the carbon and nitrogen content of leaves, responded similarly between and within functional groups in the presence or absence of earthworms, we observed opposite responses for other traits, such as height, specific leaf area, and root length within some functional groups in the presence of earthworms. Plant trait responses were thus species-specific, although the two grass species showed a more pronounced response to earthworm presence with changes in their leaf traits than herb species. Overall, earthworms affected some functional traits related to resource uptake abilities of plants and thus could change plant competition outcomes over time, which could be an explanation of plant community changes observed in invaded ecosystems.

Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.

Methylation procedures affect PLFA results more than selected extraction parameters

Microorganisms are key players in organic matter and nutrient cycles of terrestrial ecosystems. The analysis of microbial membrane lipids, phospholipid fatty acids (PLFAs) has strongly improved our understanding of how microbial processes contribute to these cycles. The analysis has proven to yield robust results, but adaptations of analytical parameters to laboratory needs might lead to pitfalls and impede comparability of PLFA results between different studies. Here, we show how a set of four analytical parameters (freeze-drying vs. field moist, amount of sample extracted, age of solvent mixture, and methylation methods) influence the quantitative and qualitative results of PLFA analysis. Freeze-drying vs. field moist samples and the amount of sample extracted had only minor effects on PLFA concentrations and recovery of the microbial community structure. Nevertheless, these parameters are important to consider, especially if treatment effects in an experiment are expected to be low. The use of a four weeks old extraction solution resulted in 12% lower PLFA concentrations as well as significant differences in the relative abundance of functional microbial groups. This suggests that extraction solution should be prepared on the day of extraction or that the different components of the extraction solution should be added sequentially to the sample. Most importantly, the choice of the methylation method led to differences in both, PLFA concentrations (35%) and the relative abundance of functional microbial groups, making comparisons between studies difficult. Our study provides a valuable ranking of parameters that need to be considered during PLFA method implementation in a laboratory and also highlights the fact that comparability of studies using different methylation methods might be limited.

Root trait-microbial relationships across tundra plant species

Fine roots, and their functional traits, influence associated rhizosphere microorganisms via root exudation and root litter quality. However, little information is known about their relationship with rhizosphere microbial taxa and functional guilds. We investigated the relationships of 11 fine root traits of 20 sub-arctic tundra meadow plant species and soil microbial community composition, using phospholipid fatty acids (PLFAs) and high-throughput sequencing. We primarily focused on the root economics spectrum, as it provides a useful framework to examine plant strategies by integrating the co-ordination of belowground root traits along a resource acquisition-conservation trade-off axis. We found that the chemical axis of the fine root economics spectrum was positively related to fungal to bacterial ratios, but negatively to Gram-positive to Gram-negative bacterial ratios. However, this spectrum was unrelated to the relative abundance of functional guilds of soil fungi. Nevertheless, the relative abundance of arbuscular mycorrhizal fungi was positively correlated to root carbon content, but negatively to the numbers of root forks per root length. Our results suggest that the fine root economics spectrum is important for predicting broader groups of soil microorganisms (i.e. fungi and bacteria), while individual root traits may be more important for predicting soil microbial taxa and functional guilds.

Plant productivity and microbial composition drive soil carbon and nitrogen sequestrations following cropland abandonment

Understanding the variations in soil organic carbon (SOC) and total nitrogen (STN) stocks in the different ages of abandoned cropland ecosystems of different ages is essential for land use decisions to maximize C sinks or improve ecosystem services. However, knowledge of the dynamics of SOC and STN stocks and their controlling factors after cropland abandonment is limited. Thus, this study investigated the changes in the SOC and STN stocks of loessal soil (Calcaric Regosols) with a chronosequence of 3, 8, 13, 18, 23 and 30 years following cropland abandonment on the Loess Plateau. As a whole, we examined 42 field plots and implemented multivariable linear regression analysis (MLRA) and structural equation modeling (SEM) using 22 influencing variables related to plant, soil and microbial properties to quantify the controls of SOC and STN stocks. The results revealed that SOC and STN stocks significantly increased after cropland abandonment for 30 years, and there were minor decreases in C and N sequestrations in the early restoration stage (<18 years). The SOC and STN changes had significant positive correlations, in which that exhibited STN stocks shifted concurrently with the rate of relative SOC stock changes. The MLRA models demonstrated that the SOC stocks were primarily controlled by aboveground biomass, STN, fungi, and the ratio of fungi to bacteria, while STN stocks were mainly driven by root biomass, above-ground biomass, STN, fungi and the ratio of fungi to bacteria after cropland abandonment. The SEM models further demonstrated that plant productivity not only directly determined the variations in SOC and STN stocks but also changed the microbial community following post-cropland restoration. These results suggest that long-term (>18 years) cropland abandonment can be a successful approach for reinstating SOC and STN stocks, while plants and microbes together mediate microbial C and N stocks during vegetation succession in a semiarid region.

Effects of Different Ages of Robinia pseudoacacia Plantations on Soil Physiochemical Properties and Microbial Communities

Robinia pseudoacacia is widely planted on the Loess Plateau as a strong drought-tolerant and salt-tolerant species for vegetation restoration. However, this mode of pure plantation has triggered great concern over the soil ecosystem. The aim of this study was to explore the effects of the plantation on soil physiochemical properties, soil microorganisms, and the relationship between them in Robinia pseudoacacia plantations of different ages. Four different ages of Robinia pseudoacacia stands, including 10-year-old, 15-year-old, 25-year-old, and 40-year-old (abbreviated as Y10, Y15, Y25, and Y40, respectively) were selected, and 20 soil physicochemical and biological indicators were determined. The variation in soil microbial biomass was influenced by sampling depth, and consistent with the variations in TN (soil total nitrogen) and SOC (soil organic carbon) during 25 years’ artificial forestation. Soil moisture increased significantly at Y15 and then decreased at Y40 but other soil properties remained relatively stable. The contents of phosphor lipid fatty acid (PLFA) of different microbial groups followed the order of B (Bacteria) > G− (Gram-negative) > G+ (Gram-positive) > A (Actinomycetes) > F (Fungi). The ratios of F/B (Fungi to Bacteria) and Sat/Mono (Saturated PLFAs to Monosaturated PLFAs) of different ages of plantations showed a similar trend, i.e., declined first, then rose, and declined again. The ratios of Cy/Pre (Cyclopropyl PLFAs to Precursor PLFAs) and G+/G− (Gram-positive to Gram-negative) of the soil of all ages of plantations showed a trend of slow growth and a trend of rapid growth, respectively. Redundancy analysis showed that the contents of individual PLFAs and total PLFA were positively correlated with SOC and TN, but variations of soil PLFA ratios mostly depended on other soil properties. After artificial forestation, the ratios of F/B and Sat/Mono were lower than before forestation, while the ratio of Cy/Pre varied with different soil layers. The ratio of G+/G− increased with the increase in afforestation time, peaking at the 25th year. The contents of individual PLFAs and total PLFA may be sensitive indicators of SOC and TN within 25 years’ plantation. Lower ratio of F/B and higher G+/G− suggest that the sustainability of the ecosystem is weaker and the fertility of the soil is lower after plantation of Robinia pseudoacacia.

The abundance of arbuscular mycorrhiza in soils is linked to the total length of roots colonized at ecosystem level

Arbuscular mycorrhizal fungi (AMF) strongly affect ecosystem functioning. To understand and quantify the mechanisms of this control, knowledge about the relationship between the actual abundance and community composition of AMF in the soil and in plant roots is needed. We collected soil and root samples in a natural dune grassland to test whether, across a plant community, the abundance of AMF in host roots (measured as the total length of roots colonized) is related to soil AMF abundance (using the neutral lipid fatty acids (NLFA) 16:1ω5 as proxy). Next-generation sequencing was used to explore the role of community composition in abundance patterns. We found a strong positive relationship between the total length of roots colonized by AMF and the amount of NLFA 16:1ω5 in the soil. We provide the first field-based evidence of proportional biomass allocation between intra-and extraradical AMF mycelium, at ecosystem level. We suggest that this phenomenon is made possible by compensatory colonization strategies of individual fungal species. Finally, our findings open the possibility of using AMF total root colonization as a proxy for soil AMF abundances, aiding further exploration of the AMF impacts on ecosystems functioning.

Blind spots in global soil biodiversity and ecosystem function research

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.

Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota

The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi, which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus, whose members are known to form nodules with legumes, was among the 10 most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall, our data documented fungal and bacterial community structure differences in three wild blueberry production fields.