Phytobiomes Journal

Leaf diseases pose a serious threat to faba bean production. Leaf blotch of faba bean, caused by Alternaria spp., has become increasingly widespread and destructive in several countries. Leaf diseases pose a serious threat to faba bean production. The infection of plant by pathogens can be influenced by various factors associated with the host plant, environmental conditions and presence of other microorganisms. The phyllosphere and endosphere play a critical role in plant health and disease development. This study aimed to evaluate the factors shaping the structure and diversity of fungal communities associated with faba beans. Plant samples were collected in 2004 from two intensively managed faba bean production fields in the central region of Latvia. Fungal assemblages were characterized using an ITS region metabarcoding approach based on Illumina MiSeq sequencing. Among the assigned amplicon sequence variant (AVS), 65% belonged to the phylum Ascomycota, while approximately 4% were classified as Basidiomycota. Alternaria and Cladosporium were the dominant genera across samples. The alfa and beta diversities of fungal communities was higher during flowering of faba beans to compare with ripening. The higher abundance of Basidiomycota yeasts were observed during flowering, in contrast, Cladosporium genus was significantly more abundant during ripening. Alternaria DNA was found on leaves that showed no symptoms of the disease. The diversity and composition of fungal communities were significantly influenced by sampling time and presence of leaf blotch, caused by Alternaria spp.

Microbial communities can shift under drought in ways that enhance plant performance during drought ("microbe-mediated acclimation"). However, it is also possible for microbial communities to shift in ways that worsen the effects of drought ("mal-acclimation"). It is unclear how and where microbe-mediated acclimation vs. mal-acclimation occurs, or if there are types of soils or microbial communities that are more likely to harbor microbes that enhance plant acclimation and limit mal-acclimation. We tested for microbe-mediated plant acclimation/mal-acclimation to drought in soils from 21 maize farms in the midwestern United States, spanning a range of climate, soil types, and management practices. We first conditioned soil microbial communities to drought vs. well-watered conditions in a greenhouse and then tested for microbe-mediated acclimation by growing maize in soils inoculated with the conditioned microbial communities under drought and well-watered conditions. Drought-conditioned soils did not enhance plant performance under drought. In fact, one third of the farms exhibited mal-acclimation, especially under well-watered conditions where wet-conditioned soils reduced plant performance in well-watered contemporary conditions. Farm management practices, climate, soil texture, and microbial diversity generally did not predict when this microbe-mediated mal-acclimation occurred. Overall, these results suggest that in agricultural soils, microbes may frequently impede-rather than facilitate-plant acclimation to soil moisture levels. Open research statementThe plant and soil data used in this study are available via the Environmental Data Initiative repository at https://doi.org/10.6073/pasta/f4a0db3a076cf6d8cef908947f82736e. The bacterial and fungal amplicon sequence data are available via the European Nucleotide Archive under accessions PRJEB110071 and PRJEB109827, respectively.

1.Structured Abstract1.1 AbstractSoybean red crown rot, caused by the soil-borne fungus Calonectria ilicicola, causes substantial yield losses, but the response of the root-associated bacterial microbiome remains poorly understood. Here, we combined 16S rRNA gene sequencing, shotgun metagenomics, and single-cell genomics to characterize bacterial communities in soybean root-associated soils. 16S rRNA gene sequencing showed that diseased plants had rhizosphere and, more strikingly, rhizoplane microbiomes distinct from those of healthy plants, often with increased Enterobacterales. Shotgun metagenomics further revealed enrichment of genes associated with antibiotic resistance, particularly cationic antimicrobial peptide resistance, in diseased rhizoplane samples. Single-cell genomics recovered seven nonredundant Enterobacterales genomes and showed that plant pathogenicity-related genes were broadly distributed across these lineages. In contrast, dlt genes, which are associated with cationic antimicrobial peptide resistance, were detected only in the Enterobacterales lineages enriched in diseased rhizoplane soils. These results support a model in which soybean red crown rot is accompanied by microbiome restructuring and opportunistic enrichment of specific Enterobacterales lineages carrying putative cationic antimicrobial peptide resistance genes. More broadly, this study highlights the value of strain-resolved single-cell genomics for linking disease-associated community shifts to specific bacterial traits. 1.2 ImportanceUnderstanding crop disease requires resolving not only the primary pathogen but also the root-associated bacteria that respond to infection. Here, we used 16S rRNA gene sequencing, shotgun metagenomics, and single-cell genomics to examine the soybean rhizoplane microbiome under red crown rot. Diseased plants showed reproducible shifts in bacterial composition, including frequent enrichment of Enterobacterales and antimicrobial resistance-related functions. Strain-resolved genomes further revealed that the Enterobacterales lineages enriched in diseased rhizoplane soils specifically carried putative dlt-mediated resistance to cationic antimicrobial peptides, whereas general pathogenicity-related genes were broadly shared. These findings suggest that host defense-associated selection, rather than pathogenicity genes alone, may help shape disease-associated root microbiomes. This study demonstrates how single-cell genomics can uncover strain-level traits hidden within bulk community data and thereby clarify plant-pathogen-microbiome interactions.

Australia is the largest producer of Pyrethrum (Tanacetum cinerariifolium) globally. Amongst the constraints on production are the fungal pathogens Didymella tanaceti and Stagonosporopsis tanaceti, which pose a significant threat to the industry, causing substantial yield losses. While the infection biology of S. tanaceti is well characterised, knowledge of D. tanaceti and its potential interaction with S. tanaceti on plants remains limited, hindering disease management. We developed fluorescently labelled strains of both pathogens via Agrobacterium tumefaciens-mediated transformation (ATMT). Binary vectors carrying the mNeonGreen or tdTomato fluorescent protein genes were introduced into D. tanaceti and S. tanaceti, respectively, and expression of the fluorescent proteins was confirmed by microscopy. Genome sequencing revealed single-copy T-DNA insertions in all transformants, with minor genomic rearrangements at insertion sites. Detached leaf assays demonstrated that transformed strains retained pathogenicity, producing disease symptoms indistinguishable from those of the wild type. These fluorescently labelled variants enabled detailed visualisation of D. tanaceti infection biology and its interactions with S. tanaceti, including co-infection dynamics. Co-infection assays using fluorescent strains further facilitated simultaneous visualisation and differentiation of both pathogens within host tissues. Importantly, these tools also allowed the first description of the early stages of infection by D. tanaceti in pyrethrum leaves. This study represents the first successful transformation of D. tanaceti and S. tanaceti, providing valuable resources to investigate their infection processes.

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

Water scarcity is an increasing constraint on agricultural productivity and demands scalable strategies that improve crop performance under reduced irrigation. As soil microorganisms regulate key processes at the soil-plant interface, microbial inoculants may help sustain plant growth and physiological function during water limitation. Here, we assembled five functionally diverse microbial consortia containing taxa selected to support rhizosphere colonization, soil structural stabilization, and fungal-mediated nutrient and water foraging. These consortia were evaluated in greenhouse trials with lettuce and spinach grown under full irrigation or a 30% deficit irrigation regime (70% of crop water requirement). Crop responses were assessed using yield, harvest delay, root length, wilting incidence, chlorophyll content, and Water Band Index (WBI). Across both crops, microbial consortium treatments improved performance under deficit irrigation relative to untreated water-stressed controls. In lettuce, yield increased by 3-9%, while in spinach yield increased by 4-13%, with several treatments restoring performance to levels not significantly different from the fully irrigated control. Microbial treatments also reduced harvest delay by an average of three to four days, improved root length, lowered wilting incidence, and reduced WBI, indicating reduced plant water stress. In several cases, these physiological responses approached those observed under full irrigation despite 30% lower water input. Higher application rates (500 vs 250 g h-1) generally produced stronger responses, although this trend was not always statistically significant. Together, these results show that complex microbial consortia can buffer the negative effects of deficit irrigation and improve crop performance in leafy greens. These findings support the development of microbial inoculants as biologically based tools to enhance agricultural resilience under increasing water scarcity. TeaserMicrobial soil inoculants help crops maintain yield and harvest synchrony under reduced irrigation.

CoverCress is a new winter annual oilseed crop developed from field pennycress within the past 20 years. Field pennycress is commonly considered to be self-pollinated but little basic research has been published and there is some misalignment of conclusions. Our experience working with pennycress plant growth in greenhouse and field conditions over the past 13 years suggests that outcrossing is uncommon. We conducted lab, greenhouse, and field experiments to strengthen the body of work. Pollen viability kinetics analysis showed that longevity of pollen viability is negatively impacted by increasing temperatures and by direct exposure to light. Samples treated at 4C declined to 50% viability in 12 hours while it took just 2.5 hrs at 37C, and 1.6 hrs in full sunlight on a cool early April day. Cross-pollination was absent among greenhouse-grown plants flowering inside an agitated plastic pollen-containment covering. Across greenhouse tests, high rates of cross-pollination occurred only in an emasculation treatment that rendered flowers male sterile and opened the pistil to cross-fertilization. Field trials designed to measure pollen flow distance using a trackable fae1 knockout reporter gene failed to show detectable movement of pollen under field conditions in two locations. This data strongly suggests that domesticated field pennycress may be considered a self-pollinated crop and managed as such.

Microbial engineering offers potential for improving the sustainability of agriculture by providing greater control of desired microbial functions. However, successful control of engineered functions requires greater understanding of their robustness under diverse conditions including those used for plant hydroponics. Here, we studied biomass accumulation and surfactin biosynthesis by an engineered derivative of Bacillus subtilis PY79 in common plant culture media as a model system for interrogating metabolic robustness. We report the observation that PY79 and all other B. subtilis strains that we tested, including natural isolates, exhibited difficulty growing under shaking incubation in defined media where the only nitrogen sources were inorganic. In contrast, assimilation of inorganic nitrogen sources functioned relatively robustly under static incubation in these same media. Our findings may offer some guidance for use of B. subtilis in controlled environment agriculture and could aid future efforts to identify the molecular basis for the agitation-dependent effect on nitrogen assimilation.

Beyond the significant impact of Cassava witches broom disease (CWBD), caused by the fungus Rhizoctonia (syn. Ceratobasidium) theobromae on cassava cultivation in French Guiana and Brazil, this disease also poses a potential threat to cacao trees in the region, since the fungus is responsible for Vascular Streak Dieback (VSD) of cacao in South East Asia. Cross-pathogenicity trials were conducted in several cassava fields in French Guiana by planting young cacao plants adjacent to diseased cassava plants. Vascular necrosis was observed in some cacao plants, and the presence of R. theobromae in the cacao tissues was confirmed through PCR diagnostics using primers specific to the fungus. Sequence analysis indicated 100% similarity between samples from both hosts and 97.53 to 99.74% identity with R. theobromae isolates previously reported from cassava in the Americas and Southeast Asia. Additionally, symptomatic cacao in a mixed cacao-cassava farm yielded R. theobromae-positive PCR results, suggesting a natural infection. Ongoing work includes artificial inoculations and controlled cross-pathogenicity trials under screenhouse conditions to attempt reproduction of the symptoms. While current data do not yet establish definitive causality, the findings indicate potential host jump and warrant rapid communication to researchers, policy makers, and farmers to safeguard cacao production and Theobroma biodiversity in the Amazon region.

O_LIPhyllosphere microbiomes are subject to microbial import from various sources and undergo substantial changes during phenological changes of plants. However, these processes are still poorly understood for forest canopies. We propose that phenology-driven changes in host properties, and rainwater-mediated, within-canopy transport shape the phyllosphere microbiome in temperate forests. Leaves and throughfall samples were collected from oak, ash and linden trees at top, mid, and bottom canopy positions at the Leipzig canopy crane facility (Germany) at time points representing early, mid and late phenological stages. Bacterial community composition was assessed by 16S rRNA gene amplicon sequencing. C_LIO_LIPhenological stages explained 19% of phyllosphere bacterial community variation, followed by tree species identity (12%) and canopy position (2%). Later phenological stages exhibited more homogeneous and functionally redundant phyllosphere communities along with a strong decline of plant pathogens and increasing potential for microbially mediated biocontrol mechanisms. Throughfall transported up to 1011 bacterial cells per litre with maximum bacterial fluxes at the canopy top. C_LIO_LIOur findings demonstrate that in temperate forests, phenology-driven effects on the phyllosphere microbiome are far more important than tree species specific effects. Extent and selectivity of throughfall-mediated mobilization may play a crucial role for the spatial heterogeneity of microbial communities in tree crowns. C_LI

AI-driven data search and integration represent an emerging research direction. Although several LLM-based backend frameworks and agentic frameworks have emerged, significant gap remains in developing a one-stop, configurable agent framework that supports various data sources and provides a web interface for efficient data retrieval using natural language. To address this, we present Dingent, a novel and configurable agent framework that facilitates data access from various resources and enables the flexible constructions of agent applications. We demonstrate its capabilities across three distinct application scenarios, achieving promising results. The Dingent framework can be readily applied to other fields, such as earth sciences and ecology, to facilitate data discovery.

Phytophthora species are globally significant soilborne oomycetes responsible for widespread ecosystem decline. Standard soil sampling protocols, originally developed for qualitative baiting assays, typically require collecting substantial soil volumes in order to capture viable propagules. While effective for culture-based detection, these protocols are labour-intensive and can damage the shallow root systems of sensitive host species such as New Zealand kauri (Agathis australis). Phytophthora agathidicida (PA), the pathogen associated with kauri dieback disease, is routinely surveyed using these methods. However, quantitative data describing the vertical distribution of PA in natural forest soils are lacking. Consequently, it remains unclear whether extensive depth sampling is necessary to ensure consistent molecular detection. In this study, we applied a quantitative oospore DNA (oDNA) qPCR assay to characterise the fine-scale vertical distribution of PA across four soil depth increments (0-5, 5-10, 10-15, 15-20 cm) from 12 kauri trees representing a range of disease stages. Results revealed distinct vertical stratification, with PA DNA concentrations peaking within the upper 0-10 cm of soil in non-symptomatic and possibly symptomatic trees. In symptomatic trees, the absolute peak occasionally reached 10-15 cm, while pathogen signals remained consistently detectable within the top 10 cm. Field validation from an additional eight trees confirmed that targeted 0-10 cm "shallow" sampling yielded higher PA concentrations than deeper sampling protocols. These findings provide a data-driven basis for refining soil sampling strategies, enabling more sensitive molecular detection while minimising disturbance and logistical effort in fragile ecosystems. IMPORTANCEPhytophthora species are among the most destructive soilborne pathogens globally, requiring robust diagnostic protocols for both agricultural and conservation settings. Traditional sampling frameworks were established to meet the biological requirements of baiting assays, which often necessitate collecting large soil volumes from broad depth profiles to ensure the capture of viable, infectious propagules. However, these extensive requirements are labour-intensive and can cause significant soil disturbance in sensitive forest ecosystems. Using P. agathidicida as a model, this study provides a high-resolution quantitative assessment of how pathogen DNA is distributed vertically across different disease stages. We demonstrate that while absolute peak abundance can shift within the 0-15 cm range as infection progresses, the pathogen signal remains consistently detectable within the top 10 cm. This evidence-based approach suggests that targeted, shallow sampling enhances sensitivity by reducing signal dilution, offering a lower-impact path for monitoring soilborne oomycetes worldwide.

Emergence of multi-drug resistant (MDR) pathogens is facilitated by the mobilization of resistance genes from bacteria in animal and environmental habitats, a process often mediated by plasmids. While fertilization of agricultural soils with manure is hypothesized to serve as a pathway for transferring antimicrobial resistance plasmids to soil and crop bacteria, evidence is limited. In this study, we aimed to determine whether MDR-plasmids from manure transfer in soil, leading to the formation of long-term agricultural resistance reservoirs. To this end, we introduced a known MDR plasmid to agricultural soil where barley was subsequently grown and monitored spread of the plasmid over the course of a growing season (up to 190 days). Our experimental design mimicked conventional agricultural practices at a microcosm scale. A digital droplet PCR approach indicated plasmid transfer in the rhizosphere, which was confirmed by a targeted Hi-C method (termed Hi-C+). This demonstrated transfer of the plasmid to soil bacteria 10 days after barley planting but was not observed afterwards. The new plasmid hosts could not be identified, as plasmid-associated host Hi-C reads were absent from existing databases. This implies these hosts were rare and likely unculturable members of the soil microbiome. Our findings demonstrate that plasmid transfer from manure to soil can occur under conditions reflecting those found in agricultural settings. Furthermore, rare and uncharacterized members of the soil microbiomes may participate in acquiring MDR plasmids from manure bacteria, raising important questions about their role in spreading resistance plasmids.

Favoured by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economical and public health challenges. Microcystis, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialised interactions with its microbiome occur, and are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomic, metabolomic and metabolic modelling, we characterised the phycospheres of twelve Microcystis strains isolated from a French pond. The distribution of metabolic reactions within Microcystis was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny indicating functional decoupling between cyanobacteria and their associated microbiomes. Phycosphere-associated bacteria substantially expand the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, metabolomic profiles were largely driven by cyanobacterial metabolic outputs. Metabolic modelling, together with the identification of toxic specialised metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of Microcystis phycosphere functioning, demonstrate the value of multi-omics systems biology approaches, and underscore the ecological relevance of interspecies and inter-phycosphere metabolic interactions as a structuring process in bloom-associated microbiomes.

Bacterial interactions-whether positive or negative - are crucial for the functioning of microbial communities. Though bacterial interactions are mainly expected to be negative, the sign and strength of interactions are predicted to be context dependent, with interactions typically being more positive in more stressful and nutrient-poor conditions. However, systematic studies investigating how the environment affects interactions between multiple taxa are lacking. Here, we determine if interactions between a panel of natural soil isolates change in response to the environment in which they are grown, with two different artificial media used (one simple and one complex) and a more ecologically relevant soil wash. To maximise natural variation in interactions, we collected multiple isolates from multiple sites: co-occurring (sympatric) isolates were predicted to show more negative interactions than allopatric isolates because of greater overlap in resource use. Pairwise interactions were in general negative, but more negative when grown in a complex lab-derived medium (Tryptic Soy Broth). Mutually beneficial interactions were most common in a simple resource medium (M9 minimal media) and exploitative interactions were most frequent in a soil broth. These patterns were independent of whether species originated from the same or a different site. The study supports the prediction that nutrient rich environments promote more negative interactions, and that measuring interactions of soil isolates in standard lab media is likely to misrepresent interactions occurring in natural environments.

BackgroundGlobally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. ResultsOur cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts. ConclusionOur work provides a detailed genomic and phenotypic analysis of bacteria isolated from Z. marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.

Xylella fastidiosa is a xylem-limited phytopathogen bacterium responsible for severe diseases in numerous plant species of major agricultural importance. Despite its economic impact, its metabolism remains poorly characterized due to the bacteriums fastidious growth and the limited availability of defined culture media. In this work, we reconstructed the first pangenome-based genome-scale metabolic model for X. fastidiosa, integrating the conserved metabolic capabilities of 18 strains representing five described subspecies. The resulting core metabolic model, Xfcore, was manually curated and used to investigate the metabolic potential of the species. Model simulations predict minimal nutritional requirements that guide the formulation of defined media capable of supporting biofilm formation in vitro. Analysis of the metabolic network also suggests an undescribed metabolic pathway that enables growth on acetate as a sole carbon source. Furthermore, the model predicts that X. fastidiosa could overproduce polyamines, compounds previously associated with virulence in other phytopathogens. Experimental analyses confirm the production and secretion of polyamines in several X. fastidiosa strains, providing the first in vitro evidence of polyamine production in this pathogen. These findings suggest that polyamine biosynthesis may represent an uncharacterized virulence factor in X. fastidiosa, potentially contributing to bacterial protection against host-induced oxidative stress. Overall, the Xfcore model provides a systems-level framework to explore the metabolism of X. fastidiosa, generate testable hypotheses about its physiology and virulence, and establish a basis for future strain-specific reconstructions and host-pathogen metabolic interaction studies.

The human microbiome plays a critical role in health and disease, and its dynamic nature has made longitudinal sampling a key strategy for elucidating microbiome-disease relationships. Although the gut microbiome generally stabilizes over time, a subset of samples frequently shows marked deviations from an individuals baseline profile. We refer to these as abnormal samples. To analyze these abnormal samples, we developed a three-stage workflow to identify and classify these abnormal samples to figure out the underlying causes of these abnormal samples. Moreover, we systematically investigated abnormal samples across 16 publicly available metagenomic datasets, comprising a total of 5,171 metagenomes. Our analysis revealed that abnormal samples are often the result of mislabeling during sample collection, processing, or sequencing. Of which, fecal samples from family are more likely mislabeled. We found evidence of mislabeling in 75% of longitudinal datasets, involving up to dozens of samples per study, and in 25% of randomly selected cross-sectional datasets. Additional factors such as disease status (e.g., inflammatory bowel disease), sampling intervals, and sampling density may also contribute to sample abnormalities owing to true biological variations. These findings highlight that mislabeling is a common yet underrecognized issue in microbiome research. Our work underscores the importance of identifying and correcting abnormal samples to ensure data integrity in microbiome studies and provides a practical solution for quality control in large-scale metagenomic datasets.

Agriculture has modified the soil structure due to the influence of external factors and processes that affect microbial biodiversity. Metagenomics is a fundamental tool for the study of soil microbial diversity because it provides information about the ecosystem diversity, including both the microorganisms that cannot be isolated in culture media and those that are no longer viable in the analyzed sample. In this work, six soil samples obtained from agroecosystems of central and northern Argentina were subjected to a preliminary 16S metagenomic analysis. Copiotrophic bacteria (Proteobacteria and Actinobacteria) were dominant and one of the samples had a dominance of an oligotrophic Phylum (Acidobacteria). Our findings support previous evidence from traditionally managed agroecosystems and provide new insights into the diversity of soil microbiomes in Argentine regions outside the Pampas. Finally, we analyzed the most common genera with relevant species to agronomy, both beneficial and pathogenic, and their abundance and diversity in the sequenced samples.

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.