Sustainable land management enhances ecological and economic multifunctionality under ambient and future climate.

The currently dominant types of land management are threatening the multifunctionality of ecosystems, which is vital for human well-being. Here, we present a novel ecological-economic assessment of how multifunctionality of agroecosystems in Central Germany depends on land-use type and climate. Our analysis includes 14 ecosystem variables in a large-scale field experiment with five different land-use types under two different climate scenarios (ambient and future climate). We consider ecological multifunctionality measures using averaging approaches with different weights, reflecting preferences of four relevant stakeholders based on adapted survey data. Additionally, we propose an economic multifunctionality measure based on the aggregate economic value of ecosystem services. Results show that intensive management and future climate decrease ecological multifunctionality for most scenarios in both grassland and cropland. Only under a weighting based on farmers' preferences, intensively-managed grassland shows higher multifunctionality than sustainably-managed grassland. The economic multifunctionality measure is about ~1.7 to 1.9 times higher for sustainable, compared to intensive, management for both grassland and cropland. Soil biodiversity correlates positively with ecological multifunctionality and is expected to be one of its drivers. As the currently prevailing land management provides high multifunctionality for farmers, but not for society at large, we suggest to promote and economically incentivise sustainable land management that enhances both ecological and economic multifunctionality, also under future climatic conditions.

Metabolic potential of Nitrososphaera-associated clades.

Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

Extreme summers impact cropland and grassland soil microbiomes.

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.

Biofilm forming rhizobacteria affect the physiological and biochemical responses of wheat to drought.

Plant growth promoting rhizobacteria (PGPR) can attenuate the adverse effects of water deficit on plant growth. Since drought stress tolerance of bacteria has earlier been associated to biofilm formation, we aimed to investigate the role of bacterial biofilm formation in their PGPR activity upon drought stress. To this end, a biofilm-forming bacterial collection was isolated from the rhizospheres of native arid grassland plants, and characterized by their drought tolerance and evaluated on their plant growth promoting properties. Most bacterial strains formed biofilm in vitro. Most isolates were drought tolerant, produced auxins, showed 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and solubilized mineral phosphate and potassium, but at considerably different levels. Greenhouse experiments with the most promising isolates, B1, B2 and B3, under three levels of water deficit and two wheat varieties led to an increased relative water content and increased harvest index at both moderate and severe water deficit. However, the bacteria did not affect these plant parameters upon regular watering. In addition, decreased hydrogen peroxide levels and increased glutathione S-transferase activity occurred under water deficit. Based on these results, we conclude that by improving root traits and antioxidant defensive system of wheat, arid grassland rhizospheric biofilm forming bacilli may promote plant growth under water scarcity.

Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming.

Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS +) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions.

Challenges of and opportunities for protecting European soil biodiversity.

Soil biodiversity and related ecosystem functions are neglected in most biodiversity assessments and nature conservation actions. We examined how society, and particularly policy makers, have addressed these factors worldwide with a focus on Europe and explored the role of soils in nature conservation in Germany as an example. We reviewed past and current global and European policies, compared soil ecosystem functioning in- and outside protected areas, and examined the role of soils in nature conservation management via text analyses. Protection and conservation of soil biodiversity and soil ecosystem functioning have been insufficient. Soil-related policies are unenforceable and lack soil biodiversity conservation goals, focusing instead on other environmental objectives. We found no evidence of positive effects of current nature conservation measures in multiple soil ecosystem functions in Europe. In German conservation management, soils are considered only from a limited perspective (e.g., as physicochemical part of the environment and as habitat for aboveground organisms). By exploring policy, evidence, and management as it relates to soil ecosystems, we suggest an integrative perspective to move nature conservation toward targeting soil ecosystems directly (e.g., by setting baselines, monitoring soil threats, and establishing a soil indicator system).

La biodiversidad del suelo y las funciones ambientales relacionadas se dejan de lado en la mayoría de las evaluaciones de la biodiversidad y de las acciones de conservación de la naturaleza. Analizamos cómo la sociedad, y particularmente los formuladores de políticas, han abordado estos factores a nivel mundial con un enfoque en Europa y exploramos como ejemplo el papel de los suelos en la conservación de la naturaleza en Alemania. Revisamos las políticas mundiales y europeas en el pasado y en la actualidad, comparamos el funcionamiento ambiental del suelo dentro y fuera de las áreas protegidas y examinamos el papel de los suelos en la gestión de la conservación por medio del análisis de textos. La protección y la conservación de la biodiversidad y el funcionamiento ambiental del suelo han sido insuficientes. Las políticas relacionadas con el suelo son inaplicables y carecen de objetivos de conservación para su biodiversidad, pues se enfocan más bien en otros objetivos ambientales. No descubrimos evidencias de los efectos positivos de las medidas actuales de conservación en múltiples funciones ambientales del suelo en Europa. En la gestión alemana de la conservación, los suelos sólo se consideran desde una perspectiva limitada (p. ej.: como una parte físico química del ambiente y como hábitat para los organismos que habitan por encima de él). Mediante la exploración de la política, evidencias y gestión conforme se relaciona con los ecosistemas del suelo, sugerimos una perspectiva integrada para dirigir a la conservación hacia el enfoque directo sobre los ecosistemas del suelo (p. ej.: al establecer líneas base, monitorear las amenazas para el suelo y establecer un sistema indicador del suelo).

Designing Synergistic Biostimulants Formulation Containing Autochthonous Phosphate-Solubilizing Bacteria for Sustainable Wheat Production.

Applying phosphate-solubilizing bacteria (PSB) as biofertilizers has enormous potential for sustainable agriculture. Despite this, there is still a lack of information regarding the expression of key genes related to phosphate-solubilization (PS) and efficient formulation strategies. In this study, we investigated rock PS by Ochrobactrum sp. SSR (DSM 109610) by relating it to bacterial gene expression and searching for an efficient formulation. The quantitative PCR (qPCR) primers were designed for PS marker genes glucose dehydrogenase (gcd), pyrroloquinoline quinone biosynthesis protein C (pqqC), and phosphatase (pho). The SSR-inoculated soil supplemented with rock phosphate (RP) showed a 6-fold higher expression of pqqC and pho compared to inoculated soil without RP. Additionally, an increase in plant phosphorous (P) (2%), available soil P (4.7%), and alkaline phosphatase (6%) activity was observed in PSB-inoculated plants supplemented with RP. The root architecture improved by SSR, with higher root length, diameter, and volume. Ochrobactrum sp. SSR was further used to design bioformulations with two well-characterized PS, Enterobacter spp. DSM 109592 and DSM 109593, using the four organic amendments, biochar, compost, filter mud (FM), and humic acid. All four carrier materials maintained adequate survival and inoculum shelf life of the bacterium, as indicated by the field emission scanning electron microscopy analysis. The FM-based bioformulation was most efficacious and enhanced not only wheat grain yield (4-9%) but also seed P (9%). Moreover, FM-based bioformulation enhanced soil available P (8.5-11%) and phosphatase activity (4-5%). Positive correlations were observed between the PSB solubilization in the presence of different insoluble P sources, and soil available P, soil phosphatase activity, seed P content, and grain yield of the field grown inoculated wheat variety Faisalabad-2008, when di-ammonium phosphate fertilizer application was reduced by 20%. This study reports for the first time the marker gene expression of an inoculated PSB strain and provides a valuable groundwork to design field scale formulations that can maintain inoculum dynamics and increase its shelf life. This may constitute a step-change in the sustainable cultivation of wheat under the P-deficient soil conditions.

Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements.

Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.

Priming effects in soils across Europe.

Land use is a key factor driving changes in soil carbon (C) cycle and contents worldwide. The priming effect (PE)-CO2 emissions from changed soil organic matter decomposition in response to fresh C inputs-is one of the most unpredictable phenomena associated with C cycling and related nutrient mobilization. Yet, we know very little about the influence of land use on soil PE across contrasting environments. Here, we conducted a continental-scale study to (i) determine the PE induced by 13 C-glucose additions to 126 cropland and seminatural (forests and grasslands) soils from 22 European countries; (ii) compare PE magnitude in soils under various crop types (i.e., cereals, nonpermanent industrial crops, and orchards); and (iii) model the environmental factors influencing PE. On average, PEs were negative in seminatural (with values ranging between -60 and 26 µg C g-1 soil after 35 days of incubation; median = -11) and cropland (from -55 to 27 µC g-1 soil; median = -4.3) soils, meaning that microbial communities preferentially switched from soil organic C decomposition to glucose mineralization. PE was significantly less negative in croplands compared with seminatural ecosystems and not influenced by the crop type. PE was driven by soil basal respiration (reflecting microbial activity), microbial biomass C, and soil organic C, which were all higher in seminatural ecosystems compared with croplands. This cross European experimental and modeling study elucidated that PE intensity is dependent on land use and allowed to clarify the factors regulating this important C cycling process.

Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.

Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (ß-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.

Drought and Plant Community Composition Affect the Metabolic and Genotypic Diversity of Pseudomonas Strains in Grassland Soils.

Climate and plant community composition (PCC) modulate the structure and function of microbial communities. In order to characterize how the functional traits of bacteria are affected, important plant growth-promoting rhizobacteria of grassland soil communities, pseudomonads, were isolated from a grassland experiment and phylogenetically and functionally characterized. The Miniplot experiment was implemented to examine the mechanisms underlying grassland ecosystem changes due to climate change, and it investigates the sole or combined impact of drought and PCC (plant species with their main distribution either in SW or NE Europe, and a mixture of these species). We observed that the proportion and phylogenetic composition of nutrient-releasing populations of the Pseudomonas community are affected by prolonged drought periods, and to a minor extent by changes in plant community composition, and that these changes underlie seasonality effects. Our data also partly showed concordance between the metabolic activities and 16S phylogeny. The drought-induced shifts in functional Pseudomonas community traits, phosphate and potassium solubilization and siderophore production did not follow a unique pattern. Whereas decreased soil moisture induced a highly active phosphate-solubilizing community, the siderophore-producing community showed the opposite response. In spite of this, no effect on potassium solubilization was detected. These results suggest that the Pseudomonas community quickly responds to drought in terms of structure and function, the direction of the functional response is trait-specific, and the extent of the response is affected by plant community composition.

Interactions between soil properties, agricultural management and cultivar type drive structural and functional adaptations of the wheat rhizosphere microbiome to drought.

Rhizosphere microbial communities adapt their structural and functional compositions to water scarcity and have the potential to substantially mitigate drought stress of crops. To unlock this potential, it is crucial to understand community responses to drought in the complex interplay between soil properties, agricultural management and crop species. Two winter wheat cultivars, demanding and non-demanding, were exposed to drought stress in loamy Chernozem and sandy Luvisol soils under conventional or organic farming management. Structural and functional adaptations of the rhizosphere bacteria were assessed by 16S amplicon sequencing, the predicted abundance of drought-related functional genes in the bacterial community based on 16S amplicon sequences (Tax4Fun) and the activity potentials of extracellular enzymes involved in the carbon cycle. Bacterial community composition was strongly driven by drought and soil type. Under drought conditions, Gram-positive phyla became relatively more abundant, but either less or more diverse in Luvisol and Chernozem soil respectively. Enzyme activities and functional gene abundances related to carbon degradation were increased under drought in the rhizosphere of the demanding wheat cultivar in organic farming. We demonstrate that soil type, farming system and wheat cultivar each constitute important factors during the structural and/or functional adaptation of rhizobacterial communities in response to drought.

Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns.

Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50-70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterized using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices.

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect.

Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). Then, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions.

The wheat growth-promoting traits of Ochrobactrum and Pantoea species, responsible for solubilization of different P sources, are ensured by genes encoding enzymes of multiple P-releasing pathways.

Production and release of organic acids and phosphatase enzymes by microbes are important for inorganic and organic phosphorus cycling in soil. The presence of microorganisms with corresponding traits in the plant rhizosphere lead to improved plant P uptake and ultimately growth promotion. We studied the potential of two rhizosphere-competent strains, Pantoea sp. MR1 and Ochrobactrum sp. SSR, for solubilization of different organic and inorganic P sources in vitro. In a pot experiment we further revealed the impact of the two strains on wheat seedling performance in soil amended with either phytate, rock phosphate or K2HPO4 as solely P source. To directly link P-solubilizing activity to the strain-specific genetic potential, we designed novel primers for glucose dehydrogenase (gcd), phosphatase (pho) and phytase (phy) genes, which are related to the organic and inorganic P solubilization potential. Quantitative tracing of these functional genes in the inoculated soils of the conducted pot experiment further allowed to compare strain abundances in the soil in dependency on the present P source. We observed strain- and P source-dependent patterns of the P solubilization in vitro as well as in the pot experiment, whereby P release, particularly from phytate, was linked to the strain abundance. We further revealed that the activity of microbial phosphatases is determined by the interplay between functional gene abundance, available soil P, and substrate availability. Moreover, positive impacts of microbial seed inoculation on wheat root architecture and aboveground growth parameters were observed. Our results suggest that screening for rhizosphere-competent strains with gcd, pho and phy genes may help to identify new microbial taxa that are able to solubilize and mineralize inorganic as well as organic bound P. Subsequently, the targeted use of corresponding strains may improve P availability in agricultural soils and consequently reduce fertilizer application.

Fungal guilds and soil functionality respond to tree community traits rather than to tree diversity in European forests.

At the global scale, most forest research on biodiversity focuses on aboveground organisms. However, understanding the structural associations between aboveground and belowground communities provides relevant information about important functions linked to biogeochemical cycles. Microorganisms such as soil fungi are known to be closely coupled to the dominant tree vegetation, and we hypothesize that tree traits affect fungal guilds and soil functionality in multiple ways. By analysing fungal diversity of 64 plots from four European forest types using Illumina DNA sequencing, we show that soil fungal communities respond to tree community traits rather than to tree species diversity. To explain changes in fungal community structure and measured soil enzymatic activities, we used a trait-based ecological approach and community-weighted means of tree traits to define 'fast' (acquisitive) versus 'slow' (conservative) tree communities. We found specific tree trait effects on different soil fungal guilds and soil enzymatic activities: tree traits associated with litter and absorptive roots correlated with fungal, especially pathogen diversity, and influenced community composition of soil fungi. Relative abundance of the symbiotrophic and saprotrophic guilds mirrored the litter quality, while the root traits of fast tree communities enhanced symbiotrophic abundance. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon-cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorous. Our findings highlight that tree trait effects of either 'fast' or 'slow' tree communities drive different fungal guilds and influence biogeochemical cycles.

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact.

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

Diversity and geographic distribution of soil streptomycetes with antagonistic potential against actinomycetoma-causing Streptomyces sudanensis in Sudan and South Sudan.

BACKGROUND: Production of antibiotics to inhibit competitors affects soil microbial community composition and contributes to disease suppression. In this work, we characterized whether Streptomyces bacteria, prolific antibiotics producers, inhibit a soil borne human pathogenic microorganism, Streptomyces sudanensis. S. sudanensis represents the major causal agent of actinomycetoma - a largely under-studied and dreadful subcutaneous disease of humans in the tropics and subtropics. The objective of this study was to evaluate the in vitro S. sudanensis inhibitory potential of soil streptomycetes isolated from different sites in Sudan, including areas with frequent (mycetoma belt) and rare actinomycetoma cases of illness. RESULTS: Using selective media, 173 Streptomyces isolates were recovered from 17 sites representing three ecoregions and different vegetation and ecological subdivisions in Sudan. In total, 115 strains of the 173 (66.5%) displayed antagonism against S. sudanensis with different levels of inhibition. Strains isolated from the South Saharan steppe and woodlands ecoregion (Northern Sudan) exhibited higher inhibitory potential than those strains isolated from the East Sudanian savanna ecoregion located in the south and southeastern Sudan, or the strains isolated from the Sahelian Acacia savanna ecoregion located in central and western Sudan. According to 16S rRNA gene sequence analysis, isolates were predominantly related to Streptomyces werraensis, S. enissocaesilis, S. griseostramineus and S. prasinosporus. Three clusters of isolates were related to strains that have previously been isolated from human and animal actinomycetoma cases: SD524 (Streptomyces sp. subclade 6), SD528 (Streptomyces griseostramineus) and SD552 (Streptomyces werraensis). CONCLUSION: The in vitro inhibitory potential against S. sudanensis was proven for more than half of the soil streptomycetes isolates in this study and this potential may contribute to suppressing the abundance and virulence of S. sudanensis. The streptomycetes isolated from the mycetoma free South Saharan steppe ecoregion show the highest average inhibitory potential. Further analyses suggest that mainly soil properties and rainfall modulate the structure and function of Streptomyces species, including their antagonistic activity against S. sudanensis.

Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice.

Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 µg mL-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 µg mL-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.