Aridity drives the variability of desert soil microbiomes across north-western China

Dryland covers >35 % of the terrestrial surface and the global extent of dryland increases due to the forecasted increase in aridity driven by climate change. Due to the climate change-driven aridity ecosystems, deserts provide one of the most hostile environments for microbial life and survival. Therefore, a detailed study was carried out to explore the deserts with different aridity levels (exposed to severe climate change) influence on microbial (bacteria, fungi, and protist) diversity patterns, assembly processes, and co-occurrence. The results revealed that the aridity (semi-arid, arid, and hyper-arid) patterns caused distinct changes in environmental heterogeneity in desert ecosystems. Similarly, microbial diversities were also reduced with increasing the aridity pattern, and it was found that environmental heterogeneity is highly involved in affecting microbial diversities under different ecological niches. Interestingly, it was found that certain microbes, including bacterial (Firmicutes), fungal (Sordariomycetes), and protistan (Ciliophora) abundance increased with increasing aridity levels, indicating that these microbes might possess the capability to tolerate the environmental stress conditions. Moreover, microbial community turnover analysis revealed that bacterial diversities followed homogenous selection, whereas fungi and protists were mostly driven by the dispersal limitation pattern. Co-occurrence network analysis showed that hyper-arid and arid conditions tightened the bacterial and fungal communities and had more positive associations compared to protistan. In conclusion, multiple lines of evidence were provided to shed light on the habitat specialization impact on microbial (bacteria, fungi, and protists) communities and composition under different desert ecosystems.

Weathering and soil production under trees growing on sandstones - The role of tree roots in soil formation

Rock weathering drives both landform formation and soil production/evolution. The less studied biological component of weathering and soil production caused by tree root systems is the main focus of the present study. Weathering by trees, which likely has been important in soil formation since the first trees emerged in the middle and late Devonian, is accomplished through both physical and biological means, like acids excreted by plants and exudates from associated bacterial communities. However, these processes are relatively poorly known. We assessed the impact of tree roots and associated microbiota on the potential level of biological weathering. Three research plots were selected in two sandstone regions in Poland. Two plots were in the Stołowe Mountains (Złotno, Batorów), a tableland built of Cretaceous sandstones. The third plot (Żegiestów) was in the Sącz Beskidy Mountains, the Carpathians. Soil samples were taken from tree root zones of Norway spruces from predefined sampling positions. Soils from non-tree control positions were also sampled. Soil samples were a subject of laboratory analyses which included the content of Fe and Al (amorphous and labile forms), carbon (C), nitrogen (N), and soil pH. The microbial functional diversity of soil microorganisms was determined using the Biolog (EcoPlate) system. Rock fragments were collected for mineralogical and a subject of optical microscopy and cathodoluminescence analyses in order to examine their mineralogical composition. Significant differences (pHolm-corrected < 0.05) between sample locations were found mostly for the Żegiestów plot: Soils at control positions differed from the crack and bulk soil sample positions in terms of C, N, C/N, and pH. Tree roots were able to develop a great variety of sizes and forms by following the existing net of bedrock discontinuities and hillslope microrelief. They developed along the most accessible surfaces, and caused rockcliff retreat and scree slope formation. These two features can be considered as initial stages of soil production. Trees add to the complexity of the soil system and allow formation of rhizospheric soils, and horizons rich in organic matter which are zones of a high microbial activity. However, as our study shows, rock cracks with roots cannot be considered as zones of microbial weathering. In addition, C content and microbial activity decreases with depth but can stay on a high level along living and dead roots. When entering rock fractures, they change the intensity of biomechanical weathering and soil properties. The highest biological activity of microorganisms was found in the control samples. Overall, tree roots do change the pattern of soil formation and explain the existing pattern of soil chemical properties, microbial activity, and potentially biological weathering intensity, and the intensity of those processes in correlation with root presence varies in space.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Potential of algal-based products for the management of potato brown rot disease

BACKGROUND

Ralstonia solanacearum causes potato brown rot disease, resulting in lower crop's production and quality. A sustainable and eco-friendly method for controlling the disease is required. Algae's bioactive chemicals have shown the potential to enhance plant defenses. For the first time, the efficacy of foliar application of Acanthophora spicifera and Spirulina platensis seaweed extracts, along with the utilization of dried algal biomasses (DABs) of Turbinaria ornata and a mixture of Caulerpa racemosa and Cystoseira myrica (1:1)on potato yield and brown rot suppression were investigated under field conditions. Field experiments were conducted in three locations: Location 1 (Kafr Shukr district, Kaliobeya governorate), Location 2 (Moneira district, Kaliobeya governorate), and Location 3 (Talia district, Minufyia governorate). Locations 1 and 2 were naturally infested with the pathogen, while location 3 was not. The study evaluated potato yield, plant nutritive status and antioxidants, soil available nitrogen-phosphorus-potassium (N-P-K), and organic matter percentage. Additionally, the shift in soil microbial diversity related to R. solanacearum suppression was examined for the most effective treatment.

RESULTS

The results revealed that seaweed extracts significantly increased potato yield at all locations, which correlated with higher phosphorus absorption, while T. ornate DAB increased potato yield only at location 2, accompanied by noticeable increases in soil nitrogen and plant phosphorus. The mixed DABs of C. racemosa and C. myrica demonstrated greater disease suppression than foliar applications. The disease-suppressive effect of the mixed DABs was accompanied by significant increases in flavonoids and total antioxidant capacity (TAC). Moreover, the application of mixed DABs increased soil bacterial biodiversity, with a higher abundance of oligotrophic marine bacterial species such as Sphingopyxis alaskensis and growth-promoting species like Glutamicibacter arilaitensis, Promicromonospora sp., and Paenarthrobacter nitroguajacolicus in all three locations compared to the untreated control. Klebsiella sp., Pseudomonas putida, and P. brassicacearum abundances were increased by the mixed DABs in Location 1. These species were less abundant in locations 2 and 3, where Streptomyces sp., Bacillus sp., and Sphingobium vermicomposti were prevalent.

CONCLUSIONS

The results demonstrated that the used seaweed extracts improved potato yield and phosphorous absorption, while the mixed DABs potentially contributed in disease suppression and improved soil microbial diversity.

Multi-year seabed environmental baseline in deep-sea offshore oil prospective areas established using microbial biodiversity

Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial microbial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along the Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar in space and time, with members of the family Woeseiaceae detected consistently in >1 % relative abundance, similar to seabed sediments in other parts of the world. Anomalous biodiversity results at one site featured lower Woeseiaceae as well as higher levels of bacterial groups specifically associated with cold seeps such as Aminicenantes. This was unexpected given that site selection was based on sediment geochemistry not revealing any petroleum hydrocarbons in these locations. This finding highlights the sensitivity and specificity of microbial DNA sequencing in environmental monitoring. Microbiome assessments like this one represent an important strategy for incorporating microbial biodiversity as a new and useful metric for establishing robust environmental baselines that are necessary for understanding ecosystem responses to marine pollution.

Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration

Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes

BACKGROUND

Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.

RESULTS

The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.

CONCLUSION

This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.

Rotation cropping and organic fertilizer jointly promote soil health and crop production

Identifying field management practices to promote crop production, while conserving soil health is essential to maintain long-term food production in a changing world. Also, providing experimental evidence to support the use of traditional agricultural practices is necessary to secure sustainable agriculture. Here, we conducted a long-term 12-year experiment to investigate the impact of different combinations of fertilization type (control, inorganic fertilizer, organic fertilizer) and cropping regimes (continuous cropping and rotation cropping) on the crop (tobacco) production and multiple soil attributes associated with soil health, including proportions of soil-borne pathogens and decomposers, soil microbial diversity, microbial network stability and biomass, nutrient pools and microbial resource limitations. Our long-term experiment supports that the combination of organic fertilizer with rotation cropping increased crop production by at least 40% compared to the other management combinations and improved soil nutrient pools (e.g. the content of soil organic matter), improved the relative proportion of soil decomposers, and promoted bacterial and fungal network stability and biodiversity. Furthermore, this combination treatment relieved microbial resource limitation and reduced the abundance of potential fungal plant pathogens by at least 20% compared to other management combinations. In summary, we provide experimental evidence to support that the combined use of organic fertilization and rotation cropping management can help maintain long-term soil health, crop production, and economic outputs.

The influence of flow rates and water depth gradients on the growth process of submerged macrophytes and the biomass composition of the phytoplankton assemblage in eutrophic water: an analysis based on submerged macrophytes photosynthesis parameters

Submerged macrophytes and phytoplankton assemblage play significant roles in the functioning of aquatic ecosystems. An experiment was carried out in Beijing in order to further evaluate the environmental factors that affect the growth of submerged macrophytes and phytoplankton assemblage. Submerged macrophytes (i.e., Vallisneria natans, Hydrilla verticillata, and Ceratophyllum demersum) constructed the growth system with some controllable influencing factors (i.e., the flow rate and water depth gradient). The flow rates were set separately as 4 L/h (1#), 6 L/h (2#), and 12 L/h (3#), while the water depth gradient was of 0.5-1.7 m in eutrophic water. Generally, all macrophytes could grow normally in the experiment, and the system could maintain and improve the effluent quality. The average removal rates of NH3-N, COD, NO3-N, TN, and TP were about 90%, 33%, 65%, 45%, and 40%, respectively. Seen from the results of the water depth gradient experiments, it is indicated that Vallisneria natans grows better in shallow water (0.5 m) and moderate shallow water (0.7 m) area, with an average relative growth rate (ARGA) of 57%. Hydrilla verticillata and Ceratophyllum demersum grow better in moderate deep water (1.2 m) and deep water (1.7 m) area (ARGA of 66% and 64%, respectively). Results of the flow rate experiments showed that the moderate flow rate (6 L/h) was the best for those three macrophytes' growth. As the fitting results of the rapid light curves (RLCs) showed that the utilization of light and the tolerance to strong light were different for these macrophytes, if they are ranked in the order of the utilization and the tolerance from strong to weak, they are Hydrilla verticillata, Ceratophyllum demersum, and Vallisneria natans. Microbial analyses indicated that the overall system diversity of the experimental groups have been improved after cultivation of macrophytes. However, the accumulated Cyanobacteria caused by the low flow rate (1#) would lead to the suppression of microbial organics decomposition and nutrient metabolism in the macrophytes. To sum up, the results of this study provided theoretical guidance and technical support for the restoration of submerged macrophytes in eutrophic water.

Enhanced isophthalonitrile complexation-reduction removal using a novel anaerobic fluidized bed reactor in a bioelectrochemical system based on electric field activation (AFBR-EFA)

On account of the recalcitrant and highly toxicity of organonitrile substrates, traditional processes are limited by HCN poisoning thus inefficient. This article proposed a novel anaerobic fluidized bed reactor with electric field activation (AFBR-EFA) which had a 260-day continuous operation. The operation aims to explore the practicability of the enhanced reduction of isophthalonitrile (IPN), with emphasis on the optimum operation parameters and synergistic effect between electric field and anaerobic processes. The results showed that relatively higher voltage (1.0 V < V < 1.6 V) had a positive impact on reduction enhancement. High removal could be obtained at high initial concentration, low methanol dosage and short HRT which indicated that tolerance to shock loading was significantly enhanced in AFBR-EFA. Furthermore, EFA visibly motivated the enrichment of electrochemically active bacteria and various autotrophic IPN degradation-related species. The significantly efficient performance makes the potential for full-scale application of the AFBR-EFA markedly improved, particularly for treating hard-biodegraded contaminants.

Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles

Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.

Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics

High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.

The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes

Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always

BACKGROUND

Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments.

RESULTS

This study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well.

CONCLUSIONS

The results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.

Text mining tools for extracting information about microbial biodiversity in food

Information on food microbial diversity is scattered across millions of scientific papers. Researchers need tools to assist their bibliographic search in such large collections. Text mining and knowledge engineering methods are useful to automatically and efficiently find relevant information in Life Science. This work describes how the Alvis text mining platform has been applied to a large collection of PubMed abstracts of scientific papers in the food microbiology domain. The information targeted by our work is microorganisms, their habitats and phenotypes. Two knowledge resources, the NCBI taxonomy and the OntoBiotope ontology were used to detect this information in texts. The result of the text mining process was indexed and is presented through the AlvisIR Food on-line semantic search engine. In this paper, we also show through two illustrative examples the great potential of this new tool to assist in studies on ecological diversity and the origin of microbial presence in food.

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We present new text-mining tools to extract information in food microbiology.

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The results of the extraction are available in an on-line semantic search engine.

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Taxa, habitats, phenotypes and links between them can be queried in PubMed abstracts.

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Text-mining tools could assist to browse past and recent scientific literature.

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Two use-cases are presented: fruit microbiota and spore-forming bacteria in food.

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments

Saffron may be spoiled by a variety of microorganisms during cultivation, harvesting, and post harvesting. As saffron can be dried and stored in different ways, this preliminary study explored the natural microbiota present in Moroccan saffron when subjected to different drying techniques. An analysis of the carotenoid-derived volatiles present in the saffron was also carried out. The culturable microbiota of the saffron samples dried using different methods, namely in the shade (also called natural), in the sun, or in the oven, were studied using classical and molecular approaches. The effect of the drying methods on head-space chemical volatiles was also determined. Eighty-two isolates grown in the different culture media were chosen from the colonies, and genotype analysis grouped the microorganisms into 58 clusters, revealing a wide diversity. Out of the 82 isolates, 75 belonged to the Bacillaceae family. The other isolates were distributed within the Dietziaceae, Paenibacillaceae and Carnobacteriaceae families. The dominant species was Bacillus simplex, which was detected in all samples, regardless of the drying method used. Lysinibacillus macroides was dominant in the sun-dried saffron. No pathogens were isolated, but an isolate belonging to Dietzia maris, a potential human pathogenic species, was detected. The biodiversity indexes were linked to the drying method and generally decreased as the intensity of the treatment increased. The results of this preliminary work show that the different drying methods strongly influenced the microbiota and affect the saffron volatile profile. Further analysis will be needed to determine possible effects of selected microbiota on saffron volatiles.