Search

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.ImportanceAs the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.

Pea (Pisum sativum), a crop historically significant in the field of genetics, is regaining momentum in sustainable agriculture due to its high protein content and environmental benefits. However, its cultivation faces significant challenges from root rot, a complex disease caused by multiple soil-borne pathogens prevalent across most pea growing regions. This disease leads to substantial yield losses, further complicated by the dynamic interactions among pathogens, soil conditions, weather, and agricultural practices. Recent advancements in molecular diagnostics provide promising tools for the early and precise detection of these pathogens, which is critical for implementing effective disease management strategies. In this review, we explore how the availability of latest pea genomic resources and emerging technologies, such as CRISPR and cell-specific transcriptomics, will enable a deeper understanding of the molecular basis underlying host-pathogen interactions. We emphasize the need for a comprehensive approach that integrates genetic resistance, advanced diagnostics, cultural practices and the role of the soil microbiome in root rot. By leveraging these strategies, it is possible to develop pea varieties that can withstand root rot, ensuring the crop's resilience and its continued importance in global agriculture. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Understanding domestication's impact on crop root traits and interactions with soil microbiomes is vital for improving crop resilience and agricultural sustainability. Using this knowledge to enhance root systems, reduce chemical inputs, and adapt crops to environmental stress will help to increase global food production, promote eco‐friendly farming, and mitigate the effects of climate change. Additionally, identifying microorganisms specific to plant species may help in biodiversity conservation. Advancing scientific understanding and educating future generations on the intricate relationships between plants, soil, and microorganisms is integral to developing innovative, sustainable agricultural practices and improved food security. Summary: Domestication and intensive management practices have significantly shaped characteristics of modern crops. However, our understanding of domestication's impact had mainly focused on aboveground plant traits, neglecting root and rhizospheric traits, as well as trait–trait interactions and root‐microbial interactions.To address this knowledge gap, we grew modern (Hordeum vulgare L. var. Barke) and wild barley (Hordeum spontaneum K. Koch var. spontaneum) in large rhizoboxes. We manipulated the soil microbiome by comparing disturbed (sterilized soil inoculum, DSM) versus non‐disturbed (non‐sterilized inoculum, NSM) microbiome. Results showed that modern barley grew faster and increased organic‐carbon exudation (OCEXU) compared to wild barley.Both barley species exhibited accelerated root growth and enhanced OCEXU under DSM, indicating their ability to partially compensate and exploit the soil resources independently of microbes if need be. Plant trait network analysis revealed that modern barley had a denser, larger, and less modular network of microbes than wild barley indicating domestication's impact on trait–trait coordination. In addition, the relative abundance of bacteria did not vary between wild and modern barley rhizospheres; however, species‐specific unique bacteria were identified, with stronger effects under DSM.Overall, our findings highlight domestication‐driven shifts in root traits, trait coordination, and their modulation by the soil microbiome. [ABSTRACT FROM AUTHOR]

Background: Pecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils. Results: The results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting. Conclusions: Overall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits. [ABSTRACT FROM AUTHOR]

The soil microbiome plays a pivotal role in the functioning and resilience of agricultural ecosystems, contributing to critical processes such as organic matter decomposition, nutrient cycling, and plant growth promotion. However, the soil microbiome is constantly challenged by various environmental stresses, including drought, heavy metal contamination, salinity, and climate change, which can significantly disrupt the delicate balance of the soil ecosystem. In this context, the application of silicon (Si) has emerged as a promising strategy to mitigate the adverse effects of these environmental stresses on the soil microbiome. This review paper synthesizes the current understanding of the impacts of environmental stresses on the soil microbiome and explores the potential of Si as a mitigating agent in enhancing the resilience of the soil microbial community. Silicon can enhance the resilience of the soil microbiome through several mechanisms, such as increasing soil pH, improving nutrient and water availability and uptake, altering root exudation patterns and plant physiology, and directly stimulating the abundance, diversity, and functional potential of key microbial groups. By enhancing the resilience of the soil microbiome, Si application can help maintain the critical ecosystem services provided by soil microorganisms, ultimately contributing to the sustainability and productivity of agricultural systems. The review also highlights future research aspects, including elucidating the precise mechanisms of Si-microbiome interactions, evaluating the long-term effects of Si on soil microbiome resilience, optimizing Si application strategies for specific crop-soil systems, integrating Si management with other sustainable soil practices, and assessing the impacts of Si on soil microbiome-mediated ecosystem services. [ABSTRACT FROM AUTHOR]

The intricate interplay between SMCs and agroecosystems has garnered substantial attention in recent decades due to its profound implications for agricultural productivity, ecosystem sustainability, and environmental health. Understanding the distribution of SMCs is complemented by investigations into their functional roles within agroecosystems. Soil microbes play pivotal roles in nutrient cycling, organic matter decomposition, disease suppression, and plant-microbe interactions, profoundly influencing soil fertility, crop productivity, and ecosystem resilience. Elucidating the functional diversity and metabolic potential of SMCs is crucial for designing sustainable agricultural practices that harness the beneficial functions of soil microbes while minimizing detrimental impacts on ecosystem services. Various molecular techniques, such as next-generation sequencing and high-throughput sequencing, have facilitated the elucidation of microbial community structures and dynamics at different spatial scales. These efforts have revealed the influence of factors such as soil type, land management practices, climate, and land use change on microbial community composition and diversity. Advances in high-throughput methodological strategies have revolutionized our ability to characterize SMCs comprehensively and efficiently. These include amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics, which provide insights into microbial taxonomic composition, functional potential, gene expression, and protein profiles. The integration of multiomics approaches allows for a more holistic understanding of the complex interactions within SMCs and their responses to environmental perturbations. In conclusion, this review highlights the significant progress made in mapping, understanding the distribution, elucidating the functions, and employing high-throughput methodological strategies to study SMCs in agroecosystems. [ABSTRACT FROM AUTHOR]

Aims: Plastic films efficiently control weed development in agriculture but may have environmental impacts, including alterations of the soil functioning and its microbiota. Canvases made of plant fibres are promising biodegradable alternatives showing uniform soil covering like plastic films, unlike straw mulching which is often laid unevenly on the ground. Hemp is particularly interesting for its resistance and possible effects on the soil microbiota. We tested the effect of several mulches differing in their biodegradability and homogeneity (uniform/uneven soil covering) on soil functioning and crop yield. Methods: In greenhouse, we assessed the effects of different mulching on lettuce yields, soil properties (temperature, moisture, enzymatic activities) and the soil microbiota. We cropped lettuces either on bare soil (control), a homogeneous non-biodegradable mulch (plastic film), a biodegradable heterogeneous mulch (hemp straw) and a biodegradable and homogenous mulch (hemp canvas). Results: Plastic film increased soil temperature, decreased most enzymatic activities, and altered the soil microbiota composition. The hemp canvas decreased fungal diversity, while increasing soil moisture, laccase activity, and the abundance of specific Ascomycota, Proteobacteria and Actinobacteria taxa. Plastic and hemp canvas gave similar lettuce yields. Conclusions: Mulching with plastic films and hemp canvases changed soil functioning (C cycle enzymatic activities) and the soil microbiota. Although similar lettuce yields were obtained, effects of the plastic film were likely mediated by the increased soil temperature and accelerated organic matter degradation, while effects of the hemp canvas resulted from increased soil moisture and recalcitrant matter degradation, combined with the stimulation of potentially beneficial soil microorganisms. [ABSTRACT FROM AUTHOR]

Halophyte-based desalinization is emerging as a promising technology for saline agriculture. However, few studies have integrated halophytes into intercropping systems. This study investigated Suaeda salsa and soybean intercropping and the associated mechanisms, including changes in salt, nutrients, and bacterial communities at three salt treatments (control, 3‰, and 5‰). The results showed that regardless of salt treatment, soybean biomass and P content significantly increased in intercropping compared with monocropping, by an average of 32% and 51%, respectively (p < 0.05), indicating interspecific facilitation. Under 5‰ salt, soybean mortality decreased from 37% in monocropping to 10% in intercropping, and shoot Na decreased by over 60% in intercropping; the rhizosphere Na+, Cl−, and NO3−–N decreased in intercropping by over 75% compared with monocropping, and the response ratios correlated negatively with S. salsa biomass (p < 0.01). The soybean rhizosphere bacterial community in intercropping was enriched with the genera Sphingomonas, Salinimicrobium, Lysobacter, Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium, and Ramlibacter, and the bacterial co-occurrence network exhibited increases in the number of nodes and edges, average degree, and average clustering coefficient. Considering the combined effects, the soybean biomass of intercropping correlated positively with bacterial co-occurrence network parameters, including average degree and number of edges, independent of tissue salt and nutrient content, and that of monocropping correlated negatively with tissue salt content. These results demonstrate that S. salsa intercropping could alleviate salt stress in soybean by creating a low-salt environment and improving its nutrient accumulation and rhizosphere bacterial community, and emphasize the importance of microbial communities in influencing soybean growth. [ABSTRACT FROM AUTHOR]

Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices. [ABSTRACT FROM AUTHOR]

Camelina (Camelina sativa (L.) Crantz) is a valuable source of essential amino acids, especially sulphur-containing ones, which are generally lacking in leguminous crops, thus representing an alternative source of protein for both humans and farm animals. Rhizosphere soil samples from five experimental plots with mono- and mixed cultivations of three camelina cultivars, including two introduced varieties Cs1.Pro (Luna) and Cs2.Pro (Lenka) and one Bulgarian variety Cs3.Pro (local Bulgarian landrace) with variety 666 of vetch (Vicia sativa L.) (Cs3-Vs.Pro) and variety Mir of pea (Pisum sativum L.) (Cs3-Ps.Pro), were collected and analysed. The total DNA was isolated from the rhizosphere soils and the presence of the 16S rRNA gene was confirmed by amplification with the universal primer 16SV34. In the present study, the structure of the soil bacterial community in five different plots (Cs1.S.Pro, Cs2.S.Pro, Cs3.S.Pro, Cs3.Vs.S.Pro, and Cs3.Ps.S.Pro) where camelina was grown alone and by being intercropped with pea and vetch was analysed via a metagenomic approach. The number of observed species was highest in the local genotype of the camelina Cs3 grown alone, followed by soil from the intercropped variants Cs3-Vs and CsS-Ps. The soil bacterial communities differed between the sole cultivation of camelina and that grown with joint cultivation with vetch and peas, indicating that legumes considerably affected the growth and development of beneficial microorganisms by aspects such as nitrogen fixing, levels of nitrifying bacteria, and levels of phosphorus-dissolving bacteria, thus helping to provide better plant nutrition. The α-diversity indicated that bacterial communities in the rhizosphere were higher in soils intercropped with vetch and pea. The optical properties of cereals and legumes were determined by their energy structure, which includes both their occupied and free electronic energy levels and the energy levels of the atomic vibrations of the molecules or the crystal lattice. [ABSTRACT FROM AUTHOR]

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes. [ABSTRACT FROM AUTHOR]

Background: Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. T his study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient. Results: A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well. Conclusion: Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. 5_PfxzZNKyxgT3zPqUmUdg Video Abstract [ABSTRACT FROM AUTHOR]

Background: The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. Results: We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. Conclusions: By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens. [ABSTRACT FROM AUTHOR]

Soil microbiome characterization is typically achieved with next-generation sequencing (NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity. These techniques have been instrumental in microbiology, but they have limitations. They require extensive time, funding, expertise, and computing power to be effective. Moreover, these techniques are restricted to controlled laboratory conditions; they are not applicable in field settings, nor can they rapidly generate data. This hinders using NGS as an environmental monitoring tool or an in-situ checking device. Biosensing technology can be applied to soil microbiome characterization to overcome these limitations and to complement NGS techniques. Biosensing has been used in biomedical applications for decades, and many successful commercial products are on the market. Given its previous success, biosensing has much to offer soil microbiome characterization. There is a great variety of biosensors and biosensing techniques, and a few in particular are better suited for soil field studies. Aptamers are more stable than enzymes or antibodies and are more ready for field-use biosensors. Given that any microbiome is complex, a multiplex sensor will be needed, and with large, complicated datasets, machine learning might benefit these analyses. If the signals from the biosensors are optical, a smartphone can be used as a portable optical reader and potential data-analyzing device. Biosensing is a rich field that couples engineering and biology, and applying its toolset to help advance soil microbiome characterization would be a boon to microbiology more broadly. [ABSTRACT FROM AUTHOR]

Anaerobic soil disinfestation (ASD) is a novel, eco-friendly method to improve soil health. This method creates oxygen-free conditions by adding organic amendments as a carbon source, saturating the soil to field capacity, and then covering it with plastic. These anaerobic conditions reduce soilborne pathogens, enhance microbial diversity, and increase crop productivity. This review provides an overview of the different organic amendments used in ASD, their impact on managing soilborne pathogens, the role of beneficial microbiomes, and the challenges associated with adopting ASD. It also emphasizes the potential benefits of ASD and the innovative approach to advancing it for sustainable agriculture. [ABSTRACT FROM AUTHOR]

The Organisation for Economic Co‐operation and Development (OECD) 216 test guideline investigates the impact of agrochemicals on soil nitrogen transformation. After an evaluation of 465 OECD 216 studies, we describe two distinct yet contrasting outcomes in control nontreated samples that are possible in this testing framework, which we term the "rise" (consistent increases in nitrate concentrations throughout the test period) and "dip" (initial decline in nitrate concentration between Days 0–7, followed by a net‐generation of nitrate across Days 7–28) responses. We raise significant concerns that control data from standardized, internationally recognized test guidelines can demonstrate such dissimilar patterns. We propose that, when present, the dip response undermines the intended functioning of the test system and removes the ability to draw appropriate ecotoxicological inferences from the data. In this work, we hypothesize the dip response is a product of conducting the study in low nitrogen content soils. Our results indicate that the dip response can be alleviated by using ammonium sulfate as an immediately available inorganic nitrogen source in place of the guideline‐mandated complex, organic lucerne meal, demonstrating the influence of nitrogen availability and accessibility. However, not all low nitrogen soils exhibited the dip response, indicating the involvement of additional unidentified factors. Using our data and real‐world regulatory examples, we advocate that datasets displaying the dip response should not be considered valid OECD 216 studies due to the influence of soil properties precluding an assessment of whether any impacts observed are driven solely by the test compound in question or are instead a product of the soil used. We propose methods to account for these soil‐specific responses that could be integrated into the conduct and interpretation of OECD 216 studies. Such amendments will improve the reliability and robustness of the study system and enhance confidence in ecotoxicological conclusions derived from OECD 216 datasets. Integr Environ Assess Manag 2024;20:1611–1624. © 2024 SETAC Key Points: We report on two soil‐specific outcomes within control data originating in the OECD 216 Nitrogen Transformation Test, which we term the "dip" and "rise" responses.We suggest the dip response represents the test system behaving in an adverse and unintended manner and can affect ecotoxicological inferences made from the data.We demonstrate the dip response is linked to nitrogen availability and accessibility; however, our data also demonstrate the involvement of additional, unidentified factors.We propose amendments to the OECD 216 guideline to better account for the differential performance of soils within the test system and improve the reliability and robustness of OECD 216 data. [ABSTRACT FROM AUTHOR]

Climate change presents an unprecedented global challenge, demanding collective action to both mitigate its effects and adapt to its consequences. Soil health and function are profoundly impacted by climate change, particularly evident in the sensitivity of soil microbial respiration to warming, known as Q10. Q10 measures the rate of microbial respiration's increase with a temperature rise of 10 degrees Celsius, playing a pivotal role in understanding soil carbon dynamics in response to climate change. Leveraging machine learning techniques, particularly explainable artificial intelligence (XAI), offers a promising avenue to analyze complex data and identify biomarkers crucial for developing innovative climate change mitigation strategies. This research aims to evaluate the extent to which chemical, physical, and microbiological soil characteristics are associated with high or low Q10 values, utilizing XAI approaches. The Extra Trees Classifier algorithm was employed, yielding an average accuracy of 0.923 ± 0.009 , an average AUCROC of 0.964 ± 0.004 , and an average AUCPRC of 0.963 ± 0.006 . Additionally, through XAI techniques, we elucidate the significant features contributing to the prediction of Q10 classes. The XAI analysis shows that the temperature sensitivity of soil respiration increases with microbiome variables but decreases with non-microbiome variables beyond a threshold. Our findings underscore the critical role of the soil microbiome in predicting soil Q10 dynamics, providing valuable insights for developing targeted climate change mitigation strategies. [ABSTRACT FROM AUTHOR]

Phytophthora diversity was examined in eight forest and ornamental nurseries in the Czech Republic. A leaf baiting isolation technique and, in two nurseries, also Illumina DNA metabarcoding were used to reveal the diversity of Phytophthora in soil and irrigation water and compare the efficacy of both approaches. In total, baiting revealed the occurrence of 12 Phytophthora taxa in 59.4% of soil samples from seven (87.5%) nurseries. Additional baiting of compost was carried out in two nurseries and two Phytophthora species were recovered. Irrigation water was examined in three nurseries by baiting or by direct isolation from partially decomposed floating leaves collected from the water source, and two Phytophthora species were obtained. Illumina sequencing of soil and water samples was done in two and one nurseries, respectively. Phytophthora reads were identified as 45 Phytophthora taxa, 15 of them previously unknown taxa from Clades 6, 7, 8 and 9. Another 11 taxa belonged to known or undescribed species of the oomycete genera Globisporangium, Hyaloperonospora, Nothophytophthora, Peronospora and Plasmopara. Overall, with both techniques 50 Phytophthora taxa were detected with five taxa (P. taxon organica, P. plurivora, P. rosacearum, P. syringae and P. transitoria) being exclusively detected by baiting and 38 only by DNA metabarcoding. Particularly common records in DNA barcoding were P. cinnamomi and P. lateralis which were not isolated by baiting. Only seven species were detected by both techniques. It is recommended to use the combination of both techniques to determine true diversity of Phytophthora in managed or natural ecosystems and reveal the presence of rare or unknown Phytophthora taxa. [ABSTRACT FROM AUTHOR]

Abstract Background Pecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils. Results The results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting. Conclusions Overall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits. Graphical Abstract

Abstract Background Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. T his study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient. Results A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well. Conclusion Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. Video Abstract

Abstract Soil microbiome characterization is typically achieved with next-generation sequencing (NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity. These techniques have been instrumental in microbiology, but they have limitations. They require extensive time, funding, expertise, and computing power to be effective. Moreover, these techniques are restricted to controlled laboratory conditions; they are not applicable in field settings, nor can they rapidly generate data. This hinders using NGS as an environmental monitoring tool or an in-situ checking device. Biosensing technology can be applied to soil microbiome characterization to overcome these limitations and to complement NGS techniques. Biosensing has been used in biomedical applications for decades, and many successful commercial products are on the market. Given its previous success, biosensing has much to offer soil microbiome characterization. There is a great variety of biosensors and biosensing techniques, and a few in particular are better suited for soil field studies. Aptamers are more stable than enzymes or antibodies and are more ready for field-use biosensors. Given that any microbiome is complex, a multiplex sensor will be needed, and with large, complicated datasets, machine learning might benefit these analyses. If the signals from the biosensors are optical, a smartphone can be used as a portable optical reader and potential data-analyzing device. Biosensing is a rich field that couples engineering and biology, and applying its toolset to help advance soil microbiome characterization would be a boon to microbiology more broadly.

Abstract Background The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. Results We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. Conclusions By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.

Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarchaeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). Our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats. IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.

Aim: Previous local‐scale research (within plots or landscapes) has shown that invasive plants can alter the composition and diversity of soil microbial communities, with potential feedback effects on their own invasion success. However, the broader ecological patterns of these interactions across different invasion timescales and geographic regions remain poorly understood. This study investigated whether the composition and diversity of soil microbial communities associated with Solidago canadensis (Canada goldenrod) invasion vary across both population residence times and geographic locations. Location: South‐eastern China. Taxon: Soil fungal and bacterial communities and S. canadensis. Methods: We collected rhizospheric soil of S. canadensis, nonrhizospheric soil and adjacent uninvaded soil from each of 36 populations of S. canadensis with varying residence times (8–89 years), totalling 108 samples. We extracted DNA from these samples and sequenced the V3–V4 region of the bacterial 16S rRNA gene and the ITS2 region of the fungal rDNA. We analysed the DNA sequences to assess whether variation in α‐diversity, β‐diversity, arbuscular mycorrhizal fungi (AMF) richness and the ratio of AMF to plant pathogens in the soil microbial communities varied with S. canadensis population residence time, latitude and longitude. Results: The α‐diversity and β‐diversity of soil fungal and bacterial communities significantly varied with S. canadensis residence times, latitude and longitude. In locations where S. canadensis had been established for longer periods, there was an increase in AMF richness and a decrease in plant pathogens in the rhizospheric soil. Fungal diversity in rhizospheric soils was positively correlated with longitude, while bacterial diversity in rhizospheric and nonrhizospheric soils was positively correlated with both latitude and longitude. Main Conclusions: These findings indicate that the time since invasion and geographical location can both significantly influence the composition and diversity of soil microbial communities associated with invasive plant species. [ABSTRACT FROM AUTHOR]

Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses. [ABSTRACT FROM AUTHOR]

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Climate change presents an unprecedented global challenge, demanding collective action to both mitigate its effects and adapt to its consequences. Soil health and function are profoundly impacted by climate change, particularly evident in the sensitivity of soil microbial respiration to warming, known as Q10. Q10 measures the rate of microbial respiration’s increase with a temperature rise of 10 degrees Celsius, playing a pivotal role in understanding soil carbon dynamics in response to climate change. Leveraging machine learning techniques, particularly explainable artificial intelligence (XAI), offers a promising avenue to analyze complex data and identify biomarkers crucial for developing innovative climate change mitigation strategies. This research aims to evaluate the extent to which chemical, physical, and microbiological soil characteristics are associated with high or low Q10 values, utilizing XAI approaches. The Extra Trees Classifier algorithm was employed, yielding an average accuracy of 0.923±0.009, an average AUCROC of 0.964±0.004, and an average AUCPRC of 0.963±0.006. Additionally, through XAI techniques, we elucidate the significant features contributing to the prediction of Q10 classes. The XAI analysis shows that the temperature sensitivity of soil respiration increases with microbiome variables but decreases with non-microbiome variables beyond a threshold. Our findings underscore the critical role of the soil microbiome in predicting soil Q10 dynamics, providing valuable insights for developing targeted climate change mitigation strategies.

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

The article explores how to enhance ecosystem services in urban soils, focusing on managing the microbiome of Technosols to improve soil health and biodiversity. Topics include the impact of urban development on soil quality, the potential benefits of microbial inoculation and diverse plant communities, and strategies for integrating nature-based solutions into urban landscapes.

Morocco is a leading citrus producer with a Mediterranean climate and fertile soil. The diversity of microbial communities is a subtle indicator of this fertility and lends insights into soil function and sustainability. We compare the soil microbiome under oranges in the Taroudant and Béni Mellal regions: 90 samples were analysed by genetic sequencing using Illumina MiSeq. Several groups of microorganisms play a key role in soil health, tree growth, and the production of good quality fruit. Proteobacteria dominate the bacterial phyla, Ascomycota the fungal phyla, but ANOVA reveals a highly significant difference between the two studied areas (R = 0.164, p = 0.001) in terms of bio-sustainability and microbiome. According to the Similarity Percentage Test, the Taroudant region is characterised by high biodiversity, contributing 55% to the other parameters, whereas Béni-Mellal region exhibits high resistance of microbial communities, contributing 43% to the other parameters. [ABSTRACT FROM AUTHOR]

The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years. [ABSTRACT FROM AUTHOR]

Overgeneralization and a lack of baseline data for microorganisms in high‐latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind‐driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10–12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long‐term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally. [ABSTRACT FROM AUTHOR]

Establishing geographical location is a crucial aspect of forensic sciences, distinguishing between primary and secondary crime scenes, linking an individual to a crime scene, or detecting sources of disease. Microorganisms can be used as geolocation indicators since microbial communities vary according to climatic factors (e.g. temperature, humidity, soil properties, altitude). Therefore, this systematic review aimed to investigate whether the human or environmental microbiomes help to determine a crime's geolocation. Articles were searched in PubMed,Scopus and Web of Science using keywords and data fields. The final selection included seven (of 172) manuscripts. The results showed that the microbial profile of either human or environmental samples have the potential to link a cadaver or a crime scene to a given location, highlighting microbes' usefulness in obtaining information from geographical locations (e.g. soil samples from a suspect's shoe matched to a source). However, research is required before applying this forensic strategy to real scenarios. For instance, optimizing and standardizing the microbiome analysis methods and determining several factors that may influence the results. [ABSTRACT FROM AUTHOR]

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses. [ABSTRACT FROM AUTHOR]

Drought is one of the major yield‐limiting factors under climatic adversaries. The positive role of silicon (Si) in drought tolerance of plants has unfolded a new avenue for enhancing crop productivity through better Si use efficiency. It is hence interesting to understand the mechanistic insights pertaining to its beneficial roles under drought stress conditions. Higher plants sense drought stress via roots which, regulate aboveground plant growth under stress. Cellular and molecular modulations occurring at the root and soil interphases influence the survival and growth of plants under drought stress; therefore, it is intriguing to know how Si influences the soil–root interphase and how this interaction augments overall plant growth under drought. In this review, we summarised the roles of Si in the root systems, rhizosphere and their interactions that could improve plant's growth and development under drought conditions. We have discussed the direct and indirect effects of Si‐induced belowground changes on plant roots, soil physical, chemical and biological properties, and their mutual interactions in eliciting defence signalling, including hormone signalling pathways. A mechanistic model of Si‐induced beneficial effects in water‐limited environments is suggested, which could help improve the management of rainfed croplands through Si fertilisation. [ABSTRACT FROM AUTHOR]

Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16-, and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities. [ABSTRACT FROM AUTHOR]

Soil microbiomes play a pivotal role in shaping plant health and their ability to suppress the pathogens. However, the specific microbial features that confer disease suppression in agricultural soils have remained unknown. In this study, we aim to elucidate the mechanistic roles of soil key bacteria contributing to disease suppression in banana Panama disease by using a comprehensive soil survey focusing on suppressive, and conducive soils. Through an initial field survey across twelve paired locations, we identified five fields with significantly lower pathogen abundances compared to their co-located counterparts. Subsequent greenhouse experiments validated the disease-suppressive nature of soils collected from Jianfeng (JF) and Lingao (LG), both exhibiting low pathogen densities. Furthermore, four OTUs classified as Massilia (OTU44), Flavisolibacter (OTU396), Brevundimonas (OTU632) and Pseudomonas (OTU731), respectively, were identified as key players in suppressing pathogen invasion as they were significantly enriched in suppresive groups and pathogen inoculated treatments. The present results might suggest a vital link between these soil bacteria and pathogen inhibition in banana rhizosphere via a greenhouse experiment. The abundance of nonribosomal peptide synthetase (NRPS) genes, which was responsible for antibiotic synthesis and significantly enriched in the banana rhizosphere after beneficial microorganism inoculation, displayed a significant and negative correlation with pathogen abundance while a positive correlation with relative abundance of Pseudomonas. This result suggests that the up-regulation of NRPS genes may play a key role in bolstering banana plant immunity. These findings not only provide promising biocontrol strategies but also offer valuable insights into the dynamic relationship between soil microbiomes and plant physiology, paving the way for sustainable agriculture and disease management. [ABSTRACT FROM AUTHOR]

Phosphate-solubilising fungi (PSF) are beneficial microorganisms that play a pivotal role in plant growth by increasing the availability of phosphorus (P) in soil. Although phosphorus is an essential nutrient for plants, it often becomes inaccessible as it binds into insoluble forms. PSF effectively facilitate the release of this bound phosphorus through diverse mechanisms. Numerous fungal species demonstrate the ability to solubilise various types of phosphate compounds. Among the commonly researched PSF are Penicillium, Aspergillus, Rhizopus, Fusarium, Trichoderma, and Sclerotium. Moreover, yeasts such as Saccharomyces cerevisiae can potentially be leveraged as PSF. PSF secrete organic acids that chelate phosphate ions, thereby increasing their solubility in the soil. Moreover, PSF contribute to the decomposition of organic phosphorus compounds in soil by employing enzymes such as phosphatases, phytases, and phosphonatases. Furthermore, PSF can interact with other soil microorganisms, including nitrogen-fixing bacteria and arbuscular mycorrhizal fungi (AM-fungi), fostering synergistic effects that further enhance plant growth and nutrient absorption. The utilisation of PSF as biofertilisers offers numerous advantages over chemical fertilisers, including environmental friendliness, cost-effectiveness, and enhanced fertiliser utilisation efficiency. Furthermore, PSF can prove beneficial in challenging environments characterised by high phosphate sorption. Hence, this review serves as an updated study aimed at broadening the understanding of PSF and its potential applications in P solubilisation. This review also focuses on the diversity of PSF, the mechanisms underlying solubilisation, ecological roles of PSF in soil microbiome, and the benefits of sustainable agriculture. By delving into the ecological roles of PSF and their potential as biofertilisers, this study contributes to a deeper understanding of sustainable agriculture practices and addresses challenges in phosphate-scarce environments. [ABSTRACT FROM AUTHOR]

Simple Summary: Soil and its quality are becoming more and more important. Healthy and fertile soil allows for the cultivation of high-quality food plants, is resistant to erosion, and contributes to the mitigation of climate change. Researchers are intensively working on research that would allow not only to maintain the quality of the soil, but also to achieve the highest possible yield. Recently, a number of studies have been conducted to determine the benefits of organic fertilizers on soil properties and yield. Our research is about how organic fertilizers and biological inputs affect one of the most important soil components, soil bacteria and fungi, and how other agrochemical parameters change after the application of organic fertilizers. We present a lot of information on how the values of the studied agrochemical and microbiological indicators changed, depending on the use of different organic fertilizers. We also talk about the established effects of the studied biological inputs. Our results contribute to the body of knowledge and can be used to implement sustainable agriculture. The application of organic fertilizers and biological inputs to soil inevitably affects its quality, agrochemical indicators, and microbiota. Sustainable agriculture is based on continuously learning about how to properly manage available soil, water, and biological resources. The aim of the study was to determine changes in microorganism communities and carbon stocks in infertile soils for fertilization using different organic fertilizers and their combinations with bio-inputs. Genetic analysis of microorganism populations was performed using the NGS approach. Our study showed that the application of organic fertilizers affects the soil microbiota and the taxonomic structure of its communities. Specific groups of bacteria, such as Bacillota, were promoted by organic fertilization, meanwhile the abundance of Pseudomonadota and Ascomycota decreased in most treatments after the application of poultry manure. Metagenomic analysis confirmed that the use of bio-inputs increased the relative abundance of Trichoderma spp. fungi; meanwhile, a significant change was not found in the representatives of Azotobacter compared to the treatments where the bio-inputs were not used. The positive influence of fertilization appeared on all the studied agrochemical indicators. Higher concentrations of Corg and Nmin accumulated in the soil when we used granulated poultry manure, and pHKCl when we used cattle manure. [ABSTRACT FROM AUTHOR]

The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume–rhizobium dynamics in soil communities. [ABSTRACT FROM AUTHOR]

Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections. [ABSTRACT FROM AUTHOR]

Tasmanian eucalypt forests are among the most carbon‐dense in the world, but projected climate change could destabilize this critical carbon sink. While the impact of abiotic factors on forest ecosystem carbon dynamics have received considerable attention, biotic factors such as the input of animal scat are less understood. Tasmanian devils (Sarcophilus harrisii)—an osteophageous scavenger that can ingest and solubilize nutrients locked in bone material—may subsidize plant and microbial productivity by concentrating bioavailable nutrients (e.g., nitrogen and phosphorus) in scat latrines. However, dramatic declines in devil population densities, driven by the spread of a transmissible cancer, may have underappreciated consequences for soil organic carbon (SOC) storage and forest productivity by altering nutrient cycling. Here, we fuse experimental data and modeling to quantify and predict future changes to forest productivity and SOC under various climate and scat‐quality futures. We find that devil scat significantly increases concentrations of nitrogen, ammonium, phosphorus, and phosphate in the soil and shifts soil microbial communities toward those dominated by r‐selected (e.g., fast‐growing) phyla. Further, under expected increases in temperature and changes in precipitation, devil scat inputs are projected to increase above‐ and below‐ground net primary productivity and microbial biomass carbon through 2100. In contrast, when devil scat is replaced by lower‐quality scat (e.g., from non‐osteophageous scavengers and herbivores), forest carbon pools are likely to increase more slowly, or in some cases, decline. Together, our results suggest often overlooked biotic factors will interact with climate change to drive current and future carbon pool dynamics in Tasmanian forests. [ABSTRACT FROM AUTHOR]

Purpose: Soil Phosphorous (P) availability is critical for many important ecological processes and oil-contaminated soil remediation. Despites a few studies confirmed directly effects of crude oil exposure on soil Phosphorus-cycling (P-cycling), how soil microbes and functional genes affiliated with P-cycling respond to crude oil remains poorly understood. Methods: Here, metagenomics was implemented to analyze variations in the microbial community structure and potential functions associated with P transformation in the coastal soil contaminated by crude oil. Results: Results showed a dramatic scarcity of P in the contaminated soil. Microbial inorganic P solubilization was governed by genes gcd and ppx in CK soil. In contrast, genes encoding C-P lyase (phnGHIJKLN) and alkaline phosphatase (phoA) displayed significantly greater abundances in the contaminated soils. Taxa annotation revealed that oil contamination altered the structure of the P-cycling microbial community with a bias towards those with oligotrophic characteristics. Specifically, the oil-contaminated soils were characterized by a stronger contribution of Proteobacteria, Ascomycota and Firmicutes. Overall, the strategy for acquiring P in the CK is inorganic P solubilization, while it converted to organic P mineralization under petroleum contamination. Soil N/P ratio played a key role in affecting P-cycling functional genes. Conclusion: Our results highlighted that oil contamination with unbalanced N/P ratio greatly altered the microbial strategy for obtaining available P (AP) in soil. A better understanding of P-cycling mechanism exposed to oil contamination and further scientifically regulating it may set the stage for in-depth improvement for current bioremediation practices. [ABSTRACT FROM AUTHOR]

Sustainable agricultural management practices aimed at improving soil health can alter the soil microbiome, which can influence plant health and defenses against insects. The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is a major belowground pest of corn. Pest management relies heavily on the planting of transgenic crops expressing Bacillus thuringiensis (Bt) toxins. In this study, we ask how corn-WCR interactions via the soil microbiome are affected by a conservation management system (extended corn-soybean-wheat rotation with cover crops under no-till) compared with a conventional management system (corn-soybean rotation under mulch tillage and no cover crops) when combined with transgenic Bt corn. To do this, we applied soil microbes from the conservation and conventional management systems to two corn lines, one producing Bt and one non-Bt. We then reared Bt-resistant and Bt-susceptible WCR on inoculated seedlings to examine plant and insect changes in fitness. We found that Bt was effective against susceptible larvae in both soil treatments. Bt-resistant larvae were ~ 20% smaller when reared in the presence of soil microbes from the conservation management system. Thus, control of Bt-resistant WCR may be improved in a conservation system without sacrificing Bt effectiveness in susceptible insects. Comparing the microbial communities using 16S rRNA sequencing revealed that management practices influenced the microbiomes associated with the soil and the plant rhizosphere, but not WCR. Our findings suggest value for growers in utilizing conservation management practices, such as no-till and cover crops, in agricultural systems through bottom-up changes to plant–insect interactions via the soil microbiome. [ABSTRACT FROM AUTHOR]

Food production must undergo systems change to meet the sustainable development goals (SDGs). For example, organic farming can be empowered by soil microorganisms with plant growth promotion (PGP) and biocontrol features. In this context, there have been limited studies on pomegranate. We investigated microbial diversity in rhizosphere of the pomegranate "Bhagwa" variety and its potential role in PGP and biocontrol. Both bulk and rhizosphere soil samples were analyzed for their physicochemical properties. Whole metagenome sequencing was conducted using the Illumina NovaSeq6000 platform. Surprisingly, we found that bulk and rhizosphere soil samples had comparable microbial diversity. Metagenome sequencing revealed the abundance of Streptomyces indicus, Bradyrhizobium kalamazoonesis, and Pseudomonas cellulosum in the rhizosphere that are reported here for the first time in agricultural literature. Pathway prediction analysis using KEGG (Kyoto Encyclopedia for Genes and Genomes) and COG (clusters of orthologous genes) databases identified metabolic pathways associated with biocontrol properties against pathogens. We confirmed the metagenome data in vitro, which demonstrated their PGP potential and antimicrobial properties. For instance, S. indicus produced high concentration of indole-3-acetic acid, a PGP phytohormone, that can stimulate plant growth. In addition, an antimicrobial susceptibility assay suggested that bacterial extracts displayed activity against Xanthomonas, a primary pathogen causing the pomegranate wilt disease. In conclusion, this study suggests that S. indicus, B. kalamazoonesis, and P. cellulosum can potentially be PGP and biocontrol agents that may contribute to increased crop productivity in pomegranate cultivation. These agents and their combinations warrant future research with an eye on SDGs and so as to enable and innovate organic farming and pomegranate agricultural practices. [ABSTRACT FROM AUTHOR]