Applied Soil Ecology

Phosphorus (P) availability affects soil carbon (C) cycling such as microbial C use efficiency (CUE) and priming effects (PEs). While non-allophanic Andosols are characterized by high organic C content and strong P retention, the effects of different P fertilization regime on C dynamics in these soils remain poorly understood. In this study, we conducted a 20-day incubation experiment using 13C-enriched glucose to investigate how different soil P levels (Truog-P: 157 mg P kg-1 and 12 mg P kg-1) impacted microbial C dynamics in non-allophanic Andosols from contrasting field management practices. Our results showed that soil organic matter (SOM) priming is associated with P fertilization management, with total primed CO2-C emissions remaining low in these soils. In the high-P soils, glucose and nitrogen (N) addition resulted in negative PEs, whereas in the low-P soils, the same treatment stimulated microbial SOM mining, resulting in positive PEs. Additionally, higher glucose-derived CUE was found in the high-P soils than in low-P soils after 20 days of incubation. These findings suggest that long-term P fertilization influences both substrate-induced microbial assimilation and SOM decomposition, with P limitation potentially promoting SOM mining which, along with concurrent soil acidity and exchangeable Al toxicity, modulates CUE. This study provides insights for improving C sequestration in non-allophanic Andosols through soil fertility management.

The growing worlds population, expected to surpass 9 billion by 2050, demands a 70-100% increase in farm productivity, posing significant challenges for sustainable agriculture. Conventional farming, reliant on chemical fertilizers and pesticides, negatively impacts environmental sustainability and food quality. Metagenomics, a culture-independent technique, has revolutionized the study of microbial communities by enabling comprehensive analysis of microbial diversity and function. This study evaluated the effects of combined nutrient management practices--including farmyard manure (FYM), wheat straw, green manure, and NPK fertilizers--on soil bacterial diversity using 16S rRNA-based metagenomic analysis. Key findings revealed the dominance of bacterial phyla such as Proteobacteria, Actinobacteria, and Firmicutes, which play critical roles in nutrient cycling, organic matter decomposition, and plant growth promotion. Distinct taxonomic distributions were observed across the samples, with Proteobacteria and Firmicutes dominating in control (T1), NPK (T2), and NPK_Green Manure (T5) treatments, while a shift in phyla composition was noted in NPK_FYM (T3) and NPK_WheatStraw (T4). Genus-level analysis revealed that Pseudomonas and Bacillus species were abundant in control (T1) and NPK (T2), while Sphingomonas species were dominant in NPK_FYM (T3). Further diversity analyses revealed significant variation across the samples, with T3 showing the highest richness and control (T1) showing the lowest richness. The rarefaction curve confirmed sufficient sampling for capturing microbial diversity, while beta diversity analysis, including Principal Coordinate Analysis (PCA) and Bray-Curtis clustering, indicated distinct microbial community structures across different treatments. The combined use of organic amendments with NPK fertilizer enhanced microbial diversity and population, indicating their potential to support resilient and productive soil ecosystems.

AimsHarnessing rhizosphere processes offers a valuable opportunity to optimize nutrient use efficiency in agroecosystems. In nutrient-limited soils, plants discharge part of photosynthate surplus via root exudation, including carboxylates, which may enhance mineral dissolution and nutrient mobilization. We aimed to assess how plant responses to nutrient limitation translated into changes in exudate profiles, and how these exudates, in turn, drive bioweathering across soils of contrasting mineralogy and weathering degree. MethodsWe conducted a hydroponic experiment with Lupinus albus grown in a phosphorus (P) gradient over seven weeks. We measured plant biomass and root traits, performed a metabolomics analysis and quantified seven carboxylates in root exudates using gas chromatography-mass spectrometry. To assess bioweathering across contrasted soil domains, we conducted batch dissolution tests with exudates using three soil horizons--each with distinct physicochemical properties: enriched in organic matter, iron oxides, or primary silicates. ResultsAt the intermediate level of P supply, shoot biomass was comparable to that under high P, but plants produced more root biomass and a higher total carboxylate exudation rate. Despite low carboxylate concentrations (<100 ppb), exudates promoted the dissolution of Ca, Mg, Si, Fe, P and K in all soils. Yet, the degree of element released varied among soil types. ConclusionThese findings highlight the importance of root exudates in enhancing mineral dissolution, with effects dependent on soil physicochemical properties. The results suggest that managing agroecosystems under moderate nutrient limitation could be a sustainable strategy to increase root-to-shoot ratios, enhance bioweathering and nutrient release in rhizosphere.

Microplastics (MPs) in soils have recently emerged as a significant environmental concern because of their potential impacts on ecosystems and human health. In this study, MPs have been determined in genetic soil horizons to a maximum depth of 140 cm along four transects that encompass various land uses (managed and unmanaged) in Fars Province, southwest Iran. Soils have also been characterised in terms of texture and chemistry using established methods. With little contemporary or historical application through agricultural practices, MPs were dominated by fibres of various colours and sizes and polymeric construction (mainly polyamides, polyesters and polyolefins), with remaining particles largely consisting of sheet-like fragments. MP abundance (up to about 200 per kg of dry soil) and size were heterogeneously distributed throughout the region and with respect to soil depth, regardless of land use, with inverse correlations with soil particle size observed at two locations. We infer that atmospheric deposition is the principal source at the soil surface and that MPs that evade erosion are able to readily migrate downwards to depths extending to at least that of the lowest horizon sampled. Migration appears to be independent of particle size or density and is likely driven by percolating precipitation but facilitated through bioturbation and soil cracking during dry periods. The persistence and vertical migration of MPs in soils may have adverse impacts on subterranean ecosystems and ground water quality. HighlightsO_LIMicroplastics (MPs) determined in soil horizons covering different land uses in Fars Province C_LIO_LIMPs dominated by fibres and derived largely from atmospheric deposition C_LIO_LIMPs distributed heterogeneously with depth, land use, soil texture C_LIO_LIRegardless of size and density, MPs able to migrate to at least 140 cm C_LIO_LIMigration may have adverse impacts on subterranean ecosystems and ground water C_LI

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of a dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species range in Colby Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after ten years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western KS as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after ten years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought.

Urban greenspaces, encompassing parks, golf courses, roundabouts, and urban crops, have potential to offset urban carbon footprints by storing soil organic carbon (SOC). This study analyzed particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) stocks in topsoil across 27 Iberian cities, comparing urban greenspaces with natural ecosystems under varying climatic and edaphic conditions. Results revealed that urban greenspaces store comparable SOC stocks to natural ecosystems, with MAOC stocks being more dominant and stable across land-use types. POC stocks showed variability, particularly lower in roundabouts and parks compared to natural ecosystems, but remained similar in golf courses and urban crops. SOC fractions correlated inversely with mean annual temperature (MAT), emphasizing the need for cooling strategies in urban areas to preserve stable carbon pools. While MAOC exhibited saturation at higher SOC levels, POC showed a linear increase. This study highlights the importance of tailored management practices to enhance carbon storage in urban soils for climate change mitigation.

Chitosan reduced soil pH, conductivity (CE) and cation exchange capacity (CEC) in pots when applied at field capacity. However, chitosan did not affect these soil physicochemical properties, when applied monthly to agricultural fields. Chitosan did not affect field respiration. Increases in field soil respiration found in chitosan plots, especially in spring-midsummer, were not significant. Although, no differences in soil mineral nitrogen were found, chitosan influenced field soil microbiota. Metabarcoding showed chitosan significantly modifies fungal genera composition of ecologically managed field soil. On the contrary, chitosan caused no significant differences in bacterial taxa composition of field soil. Chitosan coacervates increase naturally occurring nematophagous fungus Purpureocillium in soil respect to chitosan solution treated soil and untreated controls. Besides chitosan reduces inoculum of plant pathogenic fungi Alternaria and Fusarium in field soil. Soil microbial co-occurrence network analysis clustering coefficient (CC) for ITS+V1-V2 regions show that the nematophagous fungus Pochonia promoted network clustering into modules. In addition, CC in ITS+V3-V4 regions show that the nematode trapping-fungus Orbilia and bacteria belonging to Acidimicrobiales and Cytophagales also significantly contributed to microbial network clustering in field soil. Our results show that chitosan coacervates increase soil nematophagous microbiota and that both nematode egg-parasites and trapping-fungi help to structure soil microbiota.

An understanding of the distribution of soil microorganisms and enzyme activities at different soil aggregate level could help to understand the mechanisms operating behind different tillage management on soil structure and function. Our objective was to determine if the microbial community structure and soil enzymes activity (EA) associated with different aggregate fractions changed within the transition at switching between no-till and conventional tillage at 30 months after the switch of management on a base line field of 27 years long were no-till (NT) and conventional tillage (CT) were side by side compared. Part of NT plot was turned into new CT (n-CT) while part of CT plot was turned into new NT (n-NT). Aggregate fractions of 2000-250, 250-63, 63-20, 20-2 and 2-0.1m were obtained from soil samples taken at 30 months after the switch. Specific microbial abundances, measured by qPCR, and EAs were greatest on 2-0.1m following by 20-2and 2000-250m. The EAs showed the highest activities in the CT ({beta}-Glucosidase and {beta}-D-cellobiosidase) and in the nCT (Phosphatase and N-acetyl-{beta}-Glucosaminidase) in 2000-250m. In contrast, in the intermediate fractions (250-63m and 63-20m), the highest activities were observed in NT soil. Microbial communities were significantly different among different aggregates. In the 20-2m fraction, fungi were able to differentiate between current treatments, and bacteria and archaea showed similar trends. In 2000-250m, the treatments were associated by their historical management, and the abundances in CT samples were superior to those of the NT. In contrast, in the fractions 250-63 and 63-20m, the NT samples showed greater abundances to those of the CT and the new treatment samples have suffered differences from historical treatments. In conclusion, tillage systems influenced the spatial distribution of soil enzymes as well as the abundances of microbial communities in the different soil aggregate size fractions. HighlightsO_LISoil microbial structure and functional activity showed a heterogeneous distribution within aggregate soil fraction. C_LIO_LIDistribution of functions and microbial structure is shaped by tillage soil management C_LIO_LIThe greater values of microbial abundance and soil activity appeared at smaller aggregates. C_LIO_LIFungi abundance significantly enhanced under NT than the CT at 20-2 m. C_LI

Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (>500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2x500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar - a bioinformatics pipeline presented here - had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.

IntroductionSeveral Desmodium spp. are used as intercrops in push-pull pest management systems to repel insect herbivores. In addition, Desmodium suppresses the parasitic weed Striga, and diversifies the soil microbiome with negative impacts on fungi. We investigated the impact of a 2-year cropping of five Desmodium species on soil microbiome populations. MethodologyTotal DNA was obtained from root zone soil samples collected from a two-years-old common garden experiment with replicated plots of five Desmodium spp. at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Subsequently, 16S and ITS DNA sequencing were performed and the data was analysed by using QIIME2 and Calypso. ResultsOur findings show significant differences in composition and abundance of specific microbial taxa among the Desmodium plots and the bulk soil, with a stronger shift observed for fungal community profiles than bacteria. There was, however, no significant difference in overall diversity, richness and evenness of microbial communities among the Desmodium plots and the bulk soil. Similarly, beta diversity analysis did not reveal a significant association of variation to specific Desmodium spp. plots. Discussion and conclusionThis is the first study to compare impact and association of whole soil microbiomes to different Desmodium species. Whereas long-term Desmodium cropping clearly shifts whole microbiome communities, no significant difference in overall diversity and richness of microbial populations was observed among the studied plots. However, there was a divergence of individual taxa reflected on their increased abundance in association to specific Desmodium spp., pointing towards potential impact on ecosystem services. These findings indicate that significant shifts in whole microbial populations due to Desmodium spp. and thus potentially provision of associated ecosystem services require longer cultivation periods to solidify. Future studies should focus on techniques that monitor real-time changes in microbial populations such as RNA-seq to ascertain live and dead microbes, and thus infer ecological services.

Soil microorganisms play a vital role in the regulation of the transformation and cycle of soil nutrients, thereby improving soil fertility and crop productivity. These microbes, associated with plants, contribute significantly to plant growth and development by improving nutrient cycling and crop productivity by improving soil fertility. This systematic review aims to assess the impact of microbial activity on nutrient cycle and transformation, which includes soil fertility and crop productivity improvement. The PRISMA flow methodology systematically included articles from various geographic regions. Through analyzing 120 articles, this review sought to address the question at hand. Among the articles analyzed, 31.4% indicate that soil microbial activity directly regulates nutrient cycling, while 68.6% suggest that microbial activity enhances soil fertility and crop productivity. The systematic review concludes that microbial activity has a significant effect on nutrient cycle and transformation, as well as on improving soil fertility and crop productivity. Farmers, policymakers, and experts are encouraged to manage soil microorganisms to regulate nutrient cycling, directly influencing soil fertility and crop productivity, thus promoting sustainable agricultural development.

O_LIPlastic pollution has become a global environmental problem. Alternative use of biodegradable plastics has been proposed to mitigate the pollution problem caused by the traditional non-biodegradable plastics but the relative impacts of both types of microplastics on plant community productivity and diversity remain unknown. Microplastics can affect growth of individual plants directly by altering plant physiological processes and indirectly by altering soil biota that in turn influence plant growth. However, it remains unknown whether soil biota can mediate impact of biodegradable and non-biodegradable microplastics on plant community productivity and diversity due to a lack of studies on the topic. C_LIO_LIHere, we performed a greenhouse experiment with six plant communities and five biodegradable and five non-biodegradable microplastics to test whether: 1) biodegradable microplastics have a less negative effect on plant community biomass production and diversity than non-biodegradable microplastics, and 2) soil microorganisms differentially mediate the effects of non-biodegradable and biodegradable microplastics on plant community biomass production and diversity. We employed a fully crossed factorial design to grow the six plant communities in the presence vs. absence of the 10 microplastics individually and in live soil vs. sterilized soil. C_LIO_LIResults show that live soil ameliorated the negative effects of biodegradable microplastics on shoot biomass of the plant communities, but microplastics suppressed plant community diversity more strongly in live soil than in sterilized soil regardless of microplastics types under averaged across all treatments. Furthermore, the specific microplastics polymers were the main drivers of these results. C_LIO_LISynthesis and applications: Overall, our findings indicate that even biodegradable microplastics, e.g. PBS, which are considered environmentally friendly, still pose significant ecological risks to the structure and productivity of plant communities with potential implications for functioning of terrestrial ecosystems. Future studies may identify the specific taxa of soil microorganisms that may have degraded the microplastics that we studied, their rates of biodegradation, and the effects thereof on plant community structure and productivity under more natural field conditions in contrasting climatic conditions. C_LI

Long-term monoculture agriculture systems could lead to soil degradation and yield decline. The ways in which soil microbiotas interact with one another, particularly in response to long-term tea monoculture systems are currently unclear. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 years to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function and co-occurrence network of soil microbial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that structures and functions of soil bacterial communities were significantly affected by different stand ages of tea plantations, but sampling sites and land-use conversion (from forest to tea plantation) still outcompeted stand age to control the diversity and structure of soil bacterial communities. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to variation of structure and function in soil microbial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with the increasing stand age of respective tea stands. Overall, this study provides a comprehensive understanding of the impact of long-term monoculture stand age on soil nutrient dynamics and bacterial communities in tea production.

Soils harbor diverse microbial communities crucial for ecosystem functioning, but poor genomic representation of many uncultured soil microorganisms limits the utility of existing databases to address some of the most pressing questions in environmental microbiology. To address this, we developed the SoilMicrobeDB, a comprehensive, genome-based reference database to enhance metagenomic classification for soil ecosystems, with a focus on previously underrepresented fungal taxa and uncultured organisms. We evaluated the database using a large soil metagenome dataset, comparing classification rates, analyzing fungal-bacterial ratios against phospholipid fatty acid (PLFA) estimates, and validating lineage abundances with rRNA amplicon sequencing data. Mock community analysis was also conducted to test the precision of community classification and the prevalence of false positives. The SoilMicrobeDB workflow improved metagenomic read classification by over 20% and provided more accurate fungal abundance estimates, particularly for nutrient cycling groups such as ectomycorrhizal fungi. Metagenomic-derived fungal-bacterial ratios were correlated with PLFA and qPCR estimates, and lineage proportions were aligned with relative abundances estimates from rRNA amplicon sequencing. Uncultured taxa represented up to 50% of classifiable soil microbial communities in certain biomes. SoilMicrobeDB offers robust taxonomic and functional profiling of soil communities and provides a scalable and updatable tool for soil microbial ecology research. SoilMicrobeDB is accessible through an interactive platform linking genomes to environmental factors, enabling researchers to explore microbial distributions across soil conditions and potentially leading to new insights into soil ecology and management practices.

Decomposition of organic matter is a key process in soils contributing to carbon and nutrient cycling. To identify management strategies for agroecosystems that reduce nutrient losses while maximizing plant growth, it is important to understand which parameters determine decomposition rates. This study therefore investigated how the presence of winter wheat (Triticum aestivum var. Asory) affects decomposition in a controlled Ecotron setup with two soil types with varying organic matter content across three simulated climates (2013, 2068, 2085). Using the tea bag index, interstitial soil pore water analyses, microbial biomass quantification, bacterial and fungal gene abundance, and soil respiration measurements, we tested the hypotheses that plant exudates would enhance decomposition rate and microbial biomass, while plant nitrogen uptake would deplete soil nitrate, potentially mitigated by fertilization. Contrary to expectations, decomposition rates were lower in planted than in unplanted soils, suggesting resource competition between plants and microbes. No significant differences were observed in microbial biomass or respiration due to plant presence, and fertilization effects on nitrate or microbial mineralization were undetectable, likely due to rapid turnover of organic molecules including uptake by plants and microbes. Mechanistically, fungi and soil humidity were more important for decomposition than bacteria or temperature. The findings corroborate climate impacts on decomposition but also indicate microbial resilience and highlight the potential of management strategies like cover crops, adjusted planting dates and crop residual management which can contribute to healthy soils by sustaining carbon and nutrient cycling.

Microplastics are a diverse and ubiquitous contaminant, a global change driver with potential to alter ecosystem properties and processes. Microplastic-induced effects in soils are manifold as microplastics differ in a variety of properties among which the shape is of special interest. Microplastic shapes can resemble natural forms or be dissimilar from natural objects. Our knowledge is limited regarding the impact of various microplastic shapes on soil processes. Therefore, we conducted this two-part research comprising a meta-analysis on published literature and a lab experiment focusing on microplastic shapes- and polymer-induced effects on soil aggregation and organic matter decomposition. We here focus on fibers, films, foams and fragments as microplastic shapes. In the meta-analysis, we revealed a strong research focus on fibrous and particulate microplastic materials, with films and foams neglected. Our experiment showed that microplastic shapes are important modulators of responses in soil aggregation and organic matter decomposition. Fibers, irrespective of their chemistry, negatively affected the formation of aggregates. This supported the shape dissimilarity hypothesis. However, for other shapes like foams and fragments, the polymer identity is clearly an important factor co-modulating the soil responses. Further research is needed to generate a data-driven foundation to build on our developing mechanistic understanding of the importance and consequences of microplastic shapes added to our soils.

Crop rotation and intercropping with Allium spp. (e.g. garlic, onion) are recognized as biological controls of Fusarium wilt in several crops. However, the non-target effects of this strategy on the soil microbiome are largely unknown. We evaluated the effect of cultivating Musa basjoo, Allium tuberosum (Chinese leek), and their co-cultivation on the rhizosphere and bulk soil microbiome under glasshouse conditions. We do not report the impact of Chinese leek on Foc abundances, as this has been previously reported. The bacterial and fungal communities in the rhizosphere and bulk soil varied depending on the plant type. The microbiomes of allium and bananas were consistently dissimilar, and the co-cultivation treatment contained constituent taxa from both. However, the effect of allium on soil community composition was outweighed by that of bananas in the co-cultivation scenario. Discriminative taxa for allium included members of the genera Sphingomonas, Microbacterium, Flavihumibacter, Brevundimonas, Pseudolabrys, Ramlibacter, Trichoderma, Mortierella and Fusarium. In the case of bananas, predominant biomarkers encompassed members of Rhizobacter, Noviherbaspirillum, Pseudarthrobacter, Aquabacterium, Pseudomonas, Tausonia and Humicola Biomarkers and predictions of functional gene abundances suggest that shifts in the soil microbiome induced by allium are correlated with increases in microorganisms exhibiting potential disease suppression and antibiotic or antifungal traits, whereas those in bananas are associated with plant-growth-promoting microorganisms. The biocontrol efficacy of allium co-cultivation may there involve shifts in the soil microbiome as well as direct impacts of root exudate chemistry on Fusarium plant pathogens.

Considerable microbial diversity has been discovered in soil through genomic sequencing. Despite its role in biogeochemical cycling, relatively little is known about the proteomic diversity of the soil microbiome as most commercially available soil kits focus on DNA/RNA extractions. Consequently, a plethora of protein extraction techniques have been developed for soil but have yet to be integrated into simplified, modern sample preparation techniques such as the S-Trap. Furthermore, classical data analysis strategies for soil metaproteomics rely on genomically-informed databases for peptide/protein identification. This assumes that DNA/RNA extracts adequately represent the soil proteome. Within this study, we systematically assess several extraction techniques, developing a data processing pipeline which is driven by both proteomics and genomics to fully characterize the soil microbiome. Both pipelines reveal remarkably complementary data, with [~]60% of the protein identifications coming from Proteomically-derived databases. Sodium dodecyl sulfate-based extractions proved to provide the most unique protein identifications ([~]3000 proteins), and by combining both proteomic and genomic-based results, the total protein identifications increased approximately 2-fold for each extraction. Combining these complementary data pipelines with improved extraction techniques can allow for drastically improved proteomic results (12,307 unique protein identifications), even from minute (50 mg) sample volumes. These enhancements to previous workflows can better describe the microbial diversity within soil and provide a deeper functional understanding of the soil microbiome.

Arbuscular mycorrhizal fungi (AMF) form symbioses with approximately 80% of plant species and potentially benefit their hosts (e.g. nutrient acquisition) and the soil environment (e.g. soil aggregation). AMF also affect soil microbiota and soil multifunctionality. We manipulated AMF presence (via inoculation of non-sterile soil with Rhizophagus irregularis and using a hyphal compartment design) and used RNA-seq and metaproteomics to assess AMF roles in soil. The results indicated that AMF drove an active soil microbial community expressing transcripts and proteins related to nine metabolic functions, including the metabolism of C and N. We suggest two possible mechanisms: 1) the AMF hyphae produce exudates that select a beneficial community, or, 2) the hyphae compete with other soil microbes for available nutrients and consequently induce the community to mineralize nutrients from soil organic matter. We also identified candidate proteins that are potentially related to soil aggregation, such as Lpt and HSP60. Our results bridge microbial ecology and ecosystem functioning. We show that the AMF hyphosphere contains an active community related to soil respiration and nutrient cycling, thus potentially improving nutrient mineralization from soil organic matter and nutrient supply to the plants.

Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which facilitates better understanding of metabolic and other traits without having to culture the microorganism. We applied the MAG technique using the nf-core/mag pipeline on shotgun metagenome sequences obtained from a soil ecosystem that has long-term co-contamination with radionuclides (mainly uranium), heavy metals (mercury, nickel etc.) and organic compounds. Annotation of MAGs was performed using SPAdes and MEGAHIT and genomes were binned and taxonomically classified using the GTDBTk and CAT toolkits within nf-core/mag. Additional annotations were done using Prokka and Prodigal and the dRep program was used to choose specific MAGs for further analysis. Initial analysis resulted in a total of 254 MAGs which met the high-quality standard with the completeness > 95% and contamination < 5%, accounting for 26.67% of all the MAGs (Fig SI-1). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Summer season) were reconstructed. These 27 MAGs span across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Overall, the Arthrobacter MAG was found to be one that was robust for further analysis. Over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorous, sulfur and 598 genes encoding enzymes for metals resistance from cadmium, zinc, chromium, arsenic and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium contaminated soils. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/563326v1_figS1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@1da3b60org.highwire.dtl.DTLVardef@70570borg.highwire.dtl.DTLVardef@162d300org.highwire.dtl.DTLVardef@10abf5b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. SI-1.C_FLOATNO Overall winner MAGs produced from the SRS soils reported in this study. C_FIG