Composition Of Soil Microbiome Research Articles

Insights into the functionality of biofilm-forming bacterial consortia as bioavailability enhancers towards biodegradation of pyrene in hydrocarbon-contaminated soil.

Hydrophobic organic compounds (HOCs), such as pyrene, pose significant challenges for microbial-based remediation in soil due to limited substrate availability and the sustainability of augmented microbes. Research targets are to investigate the potential of biofilm-forming bacterial cells to enhance pyrene bioavailability and biodegradation in two different hydrocarbon-contaminated soil microcosms, employing microbiological, molecular, and chemical analysis validated through statistical tools. The microcosm augmented with strong biofilm bacterial consortia (A) significantly enhanced pyrene availability by 1-1.5% compared to the weak biofilm consortia (B) and mixed consortia (AB). Analysis of 16S rDNA amplicons revealed notable differences in bacterial community composition between consortia A and B augmented soil, with Proteobacteria as the dominant phylum. Taxonomic composition of soil microbiome predicted enhanced xenobiotic biodegradative potential of strong biofilm consortia (A) up to 20 days, exhibiting a higher abundance of functional genes related to upstream degradative pathway of PAHs, such as naphthalene dioxygenase (nahAa), PAH dioxygenase subunit genes (nidA, nidB), extradiol dioxygenase (phdF) and aldehyde dehydrogenase (nidD). Our study highlights the significant role of biofilm-forming bacteria as "bioavailability enhancers," for high molecular weight PAHs like pyrene, in contaminated soils with their implications for designing future sustainable bioremediation programs.

Soil microbiome composition is highly responsive to precipitation and plant composition manipulations in a field biodiversity experiment

Soil microbiome composition is highly responsive to precipitation and plant composition manipulations in a field biodiversity experiment

Bone Diagenesis and Extremes of Preservation in Forensic Science

Understanding the composition and diagenetic processes of the deposition environment is pivotal to understanding why bone undergoes preservation or diagenesis. This research explores the complex nexus of diagenesis at the extremes of preservation, via the interdependent chemical, and short- and long-term microbial processes that influence diagenesis. These processes include dissolution, ion exchange, hydrolysis, recrystallisation, waterlogging, acidity and alkalinity, soil composition, redox potential, bacterial activity, and microbiome composition. Diagenetic processes are discussed in relation to typical sites and sites with extremes of preservation. Understanding site conditions that impact diagenetic processes is critical to understanding the visual features presented in recovered skeletal material, ensuring an appropriate post-mortem interval is assigned, and for subsequent post hoc analysis of bone.

Effects of short-term exposure to elevated atmospheric CO2 on yield, nutritional profile, genetic regulatory pathways, and rhizosphere microbial community of common bean (Phaseolus vulgaris)

Abstract Aim Legumes are vital to agroecosystems and human nutrition, yet climate change is compromising their nutritional value. This study aims to assess how a one-month exposure to elevated CO2 (eCO2) impacts biomass yield, mineral profile, gene expression, and the soil microbiome of common bean plants (Phaseolus vulgaris L.). Methods Phaseolus vulgaris L. was grown in field conditions under ambient CO2 (control, aCO2, 400 ppm) or eCO2 (600 pm) from the start of pod filling until plant maturity and analyzed for several morphophysiological and nutritional parameters. Results Compared with aCO2, eCO2 exposure significantly increased plant and grain biomass, with fluctuations in mineral accumulation. Notably, it decreased grain iron and zinc concentrations, two essential microelements related to food security, by 59% and 49%, respectively. Additionally, grain phenolic content decreased by up to 41%. Genes involved in mineral uptake (such as FER1, ZIP1, and ZIP16), plant response to stress (TCR1, TCR2, and HLH54) and symbiosis with soil microorganisms (NRMAP7 and RAM2) seemed to regulate effects. Microbiome analysis supported these findings, with an increase in the relative abundance of Pseudomonadota by 10%, suggesting eCO2-induced alterations in microbial community structure. Conclusions This research demonstrates how eCO2 impacts the nutritional quality of common beans regarding micronutrients and phenolic content, while also affecting soil microbiome composition. Highlighting the value of shorter term eCO2 treatments, the findings provide early insights into immediate plant responses. This underscores the need for crop improvement strategies to address nutrient deficiencies that may arise under future eCO2 conditions.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

Omics-centric evidences of fipronil biodegradation by Rhodococcus sp. FIP_B3

The widespread use of the pesticide fipronil in domestic and agriculture sectors has resulted in its accumulation across the environment. Its use to assure food security has inadvertently affected soil microbiome composition, fertility and, ultimately, human health. Degradation of residual fipronil present in the environment using specific microbial species is a promising strategy for its removal. The present study delves into the omics approach for fipronil biodegradation using the native bacterium Rhodococcus sp. FIP_B3. It has been observed that within 40 days, nearly 84% of the insecticide gets degraded. The biodegradation follows a pseudo-first-order kinetics (k = 0.0197/d with a half-life of ∼11 days). Whole genome analysis revealed Cytochrome P450 monooxygenase, peroxidase-related enzyme, haloalkane dehalogenase, 2-nitropropane dioxygenase, and aconitate hydratase are involved in the degradation process. Fipronil-sulfone, 5-amino-1-(2-chloro-4-(trifluoromethyl)phenyl)-4- ((trifluoromethyl)sulfonyl)-1H-pyrazole-3-carbonitrile, (E)-5-chloro-2-oxo-3- (trifluoromethyl)pent-4-enoic acid, 4,4,4-trifluoro-2-oxobutanoic acid, and 3,3,3- trifluoropropanoic acid were identified as the major metabolites that support the bacterial degradation of fipronil. In-silico molecular docking and molecular dynamic simulation-based analyses of degradation pathway intermediates with their respective enzymes have indicated stable interactions with significant binding energies (−5.9 to −9.7 kcal/mol). These results have provided the mechanistic cause of the elevated potential of Rhodococcus sp. FIP_B3 for fipronil degradation and will be advantageous in framing appropriate strategies for the bioremediation of fipronil-contaminated environment.

Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes

Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.

Species-specific impact of protists in controlling litter decomposition

Protists affect soil microbiome composition and functioning, potentially increasing litter decomposition and plant growth. Yet, the role of different protist species, individually or in combinations, in regulating microbial-mediated litter decomposition remains unknown, as well as if these interactions feedback to plant growth. Using a full-factorial design of three protist species combinations with bacterial and fungal communities, we found that only one protist species reduced litter decomposition by 19%, with other species and combinations not affecting litter decomposition. Despite a positive correlation between plant growth and litter decomposition, we did not observe protist-induced changes in plant growth. Overall, our results highlight that protists affect litter decomposition in a species-specific manner, including reducing litter decomposition.

Soil and root microbiome analysis and isolation of plant growth-promoting bacteria from hybrid buffaloberry (Shepherdia utahensis 'Torrey') across three locations.

The effects of climate change are becoming increasingly hazardous for our ecosystem. Climate resilient landscaping, which promotes the use of native plants, has the potential to simultaneously decrease the rate of climate change, enhance climate resilience, and combat biodiversity losses. Native plants and their associated microbiome form a holo-organism; interaction between plants and microbes is responsible for plants' growth and proper functioning. In this study, we were interested in exploring the soil and root microbiome composition associated with Shepherdia utahensis, a drought hardy plant proposed for low water use landscaping, which is the hybrid between two native hardy shrubs of Utah, S. rotudifolia and S. argentea. The bulk soil, rhizosphere, root, and nodule samples of the hybrid Shepherdia plants were collected from three locations in Utah: the Logan Campus, the Greenville farm, and the Kaysville farm. The microbial diversity analysis was conducted, and plant growth-promoting bacteria were isolated and characterized from the rhizosphere. The results suggest no difference in alpha diversity between the locations; however, the beta diversity analysis suggests the bacterial community composition of bulk soil and nodule samples are different between the locations. The taxonomic classification suggests Proteobacteria and Actinobacteriota are the dominant species in bulk soil and rhizosphere, and Actinobacteriota is solely found in root and nodule samples. However, the composition of the bacterial community was different among the locations. There was a great diversity in the genus composition in bulk soil and rhizosphere samples among the locations; however, Frankia was the dominant genus in root and nodule samples. Fifty-nine different bacteria were isolated from the rhizosphere and tested for seven plant growth-promoting (PGP) traits, such as the ability to fix nitrogen, phosphates solubilization, protease activity, siderophore, Indole Acetic Acid (IAA) and catalase production, and ability to use ACC as nitrogen source. All the isolates produced some amount of IAA. Thirty-one showed at least four PGP traits and belonged to Stenotrophomonas, Chryseobacterium, Massilia, Variovorax, and Pseudomonas. We shortlisted 10 isolates that showed all seven PGP traits and will be tested for plant growth promotion.

No tillage and organic fertilization improved kiwifruit productivity through shifting soil properties and microbiome

AbstractThe preservation of edaphic quality and productivity is critical for the ecological sustainability of vine orchards. The heavy utilization of intensified tillage and singular chemical fertilizers can shift changes in edaphic physicochemical and biological features, thus exerting significant pressure on agroecosystems. In current research, we assessed the shifts in soil physicochemical features and soil microbiome composition over 11 years carrying out no tillage and organic fertilizer substitution in a typical Chinese Guanzhong kiwifruit production area, and explore the fundamental factors that contribute to alterations in the microbial community and the influence on kiwifruit performance. Results showed that long‐term no tillage and organic fertilizer improved the soil condition by significantly increasing the proportion of soil macroaggregates, bulk density, and nutrient content (e.g., organic matter, nitrogen, and ammonia), as compared to conventional tillage with chemical fertilization. Moreover, no tillage significantly increased soil bacterial α‐diversity but had no significant effects on fungal. No tillage also enhanced the abundance of potential beneficial soil bacteria (e.g., Acidobacteria, Actinobacteria, and Nitrospira), while decreasing the abundance of Proteobacteria, Pseudomonas, and Fusarium. In addition, no tillage and mixed fertilized soil microbial network exhibited higher complexity (i.e., node and edge numbers, and positive edge proportion) and connectivity (i.e., average number of neighbors) than conventional tillage and chemical fertilization group. Changes in nitrate, ammonia, available phosphorus, and pH values accounted for the variation in the structure of soil microbial community. Hence, the utilization of both no tillage and organic fertilization practices could serve as a suitable and sustainable approach for managing kiwifruit production in the fragile environmental conditions of the Chinese Guanzhong region, and lead to an improvement in soil nutrient levels and help regulate the soil microbial community.

The Impact of Climate Change on Immunity and Gut Microbiota in the Development of Disease.

According to the definition provided by the United Nations, "climate change" describes the persistent alterations in temperatures and weather trends. These alterations may arise naturally, such as fluctuations in the solar cycle. Nonetheless, since the 19th century, human activities have emerged as the primary agent for climate change, primarily attributed to the combustion of fossil fuels such as coal, oil, and gas. Climate change can potentially influence the well-being, agricultural production, housing, safety, and employment opportunities for all individuals. The immune system is an important interface through which global climate change affects human health. Extreme heat, weather events and environmental pollutants could impair both innate and adaptive immune responses, promoting inflammation and genomic instability, and increasing the risk of autoimmune and chronic inflammatory diseases. Moreover, climate change has an impact on both soil and gut microbiome composition, which can further explain changes in human health outcomes. This narrative review aims to explore the influence of climate change on human health and disease, focusing specifically on its effects on the immune system and gut microbiota. Understanding how these factors contribute to the development of physical and mental illness may allow for the design of strategies aimed at reducing the negative impact of climate and pollution on human health.

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments.

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.

Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.

Single and combined effects of secondary polyethylene microplastic on the growth of Pak choi and the soil microbiome composition

Single and combined effects of secondary polyethylene microplastic on the growth of Pak choi and the soil microbiome composition

Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.

Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.

Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling.

The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.

High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation.

The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.

New perspectives on microbiome and nutrient sequestration in soil aggregates during long‐term grazing exclusion

AbstractGrazing exclusion alters grassland soil aggregation, microbiome composition, and biogeochemical processes. However, the long‐term effects of grazing exclusion on the microbial communities and nutrient dynamics within soil aggregates remain unclear. We conducted a 36‐year exclusion experiment to investigate how grazing exclusion affects the soil microbial community and the associated soil functions within soil aggregates in a semiarid grassland. Long‐term (36 years) grazing exclusion induced a shift in microbial communities, especially in the <2 mm aggregates, from high to low diversity compared to the grazing control. The reduced microbial diversity was accompanied by instability of fungal communities, extended distribution of fungal pathogens to >2 mm aggregates, and reduced carbon (C) sequestration potential thus revealing a negative impact of long‐term GE. In contrast, 11–26 years of grazing exclusion greatly increased C sequestration and promoted nutrient cycling in soil aggregates and associated microbial functional genes. Moreover, the environmental characteristics of microhabitats (e.g., soil pH) altered the soil microbiome and strongly contributed to C sequestration. Our findings reveal new evidence from soil microbiology for optimizing grazing exclusion duration to maintain multiple belowground ecosystem functions, providing promising suggestions for climate‐smart and resource‐efficient grasslands.

The Microbiomes of Various Types of Abandoned Fallow Soils of South Taiga (Novgorod Region, Russian North-West)

More than 30 years have passed after the collapse of the Soviet Union, and huge areas of soil were left in a fallow state. The study of the microbiological status of fallow soils is an extremely urgent task because fallow soils represent the “hidden” food basket of Eurasia. In this context, we studied the influence of land use type (pasture, vegetable garden, hayfield, or secondary afforestation) on key agrochemical parameters and parameters of soil microbial biodiversity. All anthropogenically transformed soils included in the analysis showed increased humus content and pH shift to a more neutral side compared to the mature soil; the same seemed to be the case for all nutrient elements. It was established that the key factor regulating soil microbiome composition shift was the duration and degree of irreversibility of an agrogenic impact. The key phyla of soil microorganisms were Pseudomonadota, Acidobacteriota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. The proportion of other phyla was quite variative in soils of different land use. At the same time, all the 30-year-old abandoned soils were more similar to each other than to mature reference soil and 130-year-old soils of monoculture vegetable gardens. Thus, the first factor, regulating soil microbiome composition, is a continuation of soil agrogenic transformation. The second factor is the type of land use if the soil age was equal for fallow territory in the case of one initial podzol soil and one type of landscape. Thus, 30-year-old abandoned soils are intermediate in terms of microbial biodiversity between pristine natural podzols and plaggic podzol. It could be suggested that in the case of secondary involvement of soils in agriculture, the composition of the microbiome may turn to mature soil or to plaggic soil under intensive amelioration.

Shifts of the soil microbiome composition induced by plant–plant interactions under increasing cover crop densities and diversities

Interspecific and intraspecific competition and facilitation have been a focus of study in plant-plant interactions, but their influence on plant recruitment of soil microbes is unknown. In this greenhouse microcosm experiment, three cover crops (alfalfa, brassica, and fescue) were grown alone, in paired mixtures, and all together under different densities. For all monoculture trials, total pot biomass increased as density increased. Monoculture plantings of brassica were associated with the bacteria Azospirillum spp., fescue with Ensifer adhaerens, and alfalfa with both bacterial taxa. In the polycultures of cover crops, for all plant mixtures, total above-ground alfalfa biomass increased with density, and total above ground brassica biomass remained unchanged. For each plant mixture, differential abundances highlighted bacterial taxa which had not been previously identified in monocultures. For instance, mixtures of all three plants showed an increase in abundance of Planctomyces sp. SH-PL14 and Sandaracinus amylolyticus which were not represented in the monocultures. Facilitation was best supported for the alfalfa-fescue interaction as the total above ground biomass was the highest of any mixture. Additionally, the bulk soil microbiome that correlated with increasing plant densities showed increases in plant growth-promoting rhizobacteria such as Achromobacter xylosoxidans, Stentotrophomonas spp., and Azospirillum sp. In contrast, Agrobacterium tumefaciens, a previously known generalist phytopathogen, also increased with alfalfa-fescue plant densities. This could suggest a strategy by which, after facilitation, a plant neighbor could culture a pathogen that could be more detrimental to the other.