Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

Green-resilient supply chain network design for perishable products considering route risk and horizontal collaboration under robust interval-valued type-2 fuzzy uncertainty: A case study in food industry

A green and resilient (G-Resilient) supply chain network is designed for perishable products under disruption risks and epistemic uncertainties. This study aims to minimize effects of the disruption by presenting new strategies, such as multiple sourcing, financial suppliers, horizontal collaboration, route risk, and coverage radius, in designing a new multi-objective mixed-integer linear programming model for multi-product, multi-period, multi-modal G-Resilient supply chain. Then, a novel robust possibilistic programming (RPP) approach is presented using credibility measure and membership functions of generalized interval-valued type-2 fuzzy variables to face the epistemic uncertainties, such as supply capacity of facilities, customer demand, transportation cost, and CO₂ emission factor, in the proposed mathematical model. An improved version of augmented ε-constraint method (AUGMECON2) is also employed to produce separate Pareto-optimal solutions. Moreover, the study compares the proposed RPP with possibilistic chance-constrained programming model and illustrates its advantages; in the standard deviation of CO₂ emission objective function, its performance has improved by about 44.91%. Finally, the model's performance has been verified by a real case study in the food industry, and managerial implications have been provided.

Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

The specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

Background

The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.

Results

BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.

Conclusions

The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.

Assessment of fungi proliferation and diversity in cultural heritage: Reactions to UV-C treatment

Fungi are present in natural and non-touristic caves due to the presence of organic matter provided mainly by insects or animals such as bats. In show caves, however, tourist infrastructure and the visitors themselves are an important source of organic matter. In addition, photosynthetic biofilms provide a high amount of carbon and nitrogen sources for fungi. This study was conducted to identify the fungal communities present in caves along with the potential use of UV-C treatment against their proliferation. Thus, fungal communities proliferating in biofilms in six French and Swiss show caves were analyzed using high throughput sequencing. The results show 385 species recorded, some of them previously described in cases of fungal outbreak. This preliminary study also aimed to test the use of UV-C light as an environmentally friendly method to treat fungal proliferation. Six fungal strains, from three different sources (Lascaux cave, La Glacière cave, a church in Vicherey, France), were cultivated in an agar dish. Spores, mycelia and the entire colony were irradiated using several UV-C intensities. Results showed that four of the six fungi spores and mycelium died following a low-intensity UV-C treatment (2 kJ m^-2, 160 s), though Ochroconis lascauxensis and Penicillium bilaiae spores showed higher resistance. Finally, it was demonstrated that the fungal colony could resist the UV-C light due to a shadow effect. The structure of the fungal colony was affected from the periphery to its inner part. However, after four 30 kJ m^-2 treatments (39 min irradiation) all strains there definitively eradicated. Further studies will be necessary to examine the potential of UV-C light under cave conditions as a preventive and curative treatment.

Biogeography of soil bacteria and archaea across France

Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.

Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale

Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long‐term research study catchment (12 km²) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape‐scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.

High Microbial Diversity Promotes Soil Ecosystem Functioning

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO₂ emission by up to 40%, and (ii) shaped the source of CO₂ emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data

In recent decades, show caves have begun to suffer from microorganism proliferation due to artificial lighting installations for touristic activity. In addition to the aesthetic problem, light encourages microorganisms that are responsible for physical and chemical degradation of limestone walls, speleothems and prehistoric paintings of cultural value. Microorganisms have previously been described by microscopy or culture-dependent methods, but data provided by new generation sequencing are rare. The authors identified, for the first time, microorganisms proliferating in one Swiss and in four French show caves using three different primers. The results showed that both photosynthetic and non-photosynthetic bacteria were the dominant taxa present in biofilms. Microalgae were heavily represented by the Trebouxiophyceae, Eustigmatophyceae and Chlorophyceae groups. Twelve diatoms were also recorded, with dominance of Syntrichia sp. (96.1%). Fungi were predominantly represented by Ascomycota, Zygomycota and Basidiomycota, fully half of the sampled biofilms where Fungi were detected. Comparing microbial communities from bleach-treated caves to those in untreated caves showed no significant difference except for a low-level change in the abundance of certain taxa. These findings provided by Illumina sequencing reveal a complex community structure in the 5 caves based on the assembly of bacteria, cyanobacteria, algae, diatoms, fungi and mosses.

Correction: Mapping and predictive variations of soil bacterial richness across France

[This corrects the article DOI: 10.1371/journal.pone.0186766.].

UV-C as an efficient means to combat biofilm formation in show caves: evidence from the La Glacière Cave (France) and laboratory experiments

Ultra-violet C (UV-C) treatment is commonly used in sterilization processes in industry, laboratories, and hospitals, showing its efficacy against microorganisms such as bacteria, algae, or fungi. In this study, we have eradicated for the first time all proliferating biofilms present in a show cave (the La Glacière Cave, Chaux-lès-Passavant, France). Colorimetric measurements of irradiated biofilms were then monitored for 21 months. To understand the importance of exposition of algae to light just after UV radiation, similar tests were carried out in laboratory conditions. Since UV-C can be deleterious for biofilm support, especially parietal painting, we investigated their effects on prehistoric pigment. Results showed complete eradication of cave biofilms with no algae proliferation observed after 21 months. Moreover, quantum yield results showed a decrease directly after UV-C treatment, indicating inhibition of algae photosynthesis. Furthermore, no changes in pigment color nor in chemical and crystalline properties has been demonstrated. The present findings demonstrate that the UV-C method can be considered environmentally friendly and the best alternative to chemicals. This inexpensive and easily implemented method is advantageous for cave owners and managers.

Mapping and predictive variations of soil bacterial richness across France

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.

A comparative study on the effects of ultrathin luminescent graphene oxide quantum dot (GOQD) and graphene oxide (GO) nanosheets on the interfacial interactions and mechanical properties of an epoxy composite

The reinforcement effect of graphene oxide nanosheets on the mechanical properties of an epoxy coating has been extensively studied. However, the effect of graphene oxide quantum dot (GOQD) as a new unique carbon based nanomaterial (with lateral dimension of 5-6nm and thickness of one carbon atom) on the mechanical properties of epoxy coating has not been reported and compared with GO yet. So this study aims at fabrication of a high-performance polymer composite with unique mechanical properties using GOQD nanosheets. GO and GOQD were obtained through two different strategies of "top-down" synthesis from an expandable graphite by a modified Hummers' method and an easy "bottom-up" method by carbonizing citric acid, respectively. The morphology, size distribution, microstructure and chemistry of the GO and GOQD were compared by utilizing X-ray diffraction (XRD) analysis, atomic force microscopy (AFM), high resolution-transmission electron microscopy (HR-TEM), high resolution field-emission scanning electron microscopy (FE-SEM), thermal gravimetric analysis (TGA), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS). Results obtained from these analyses confirmed successful synthesize of GOQD and GO nanosheets. The reinforcement effect of GO and GOQD nanosheets on the mechanical properties of the epoxy coating was studied by dynamic mechanical thermal analysis (DMTA) and tensile test. It was found that the GOQD could remarkably enhance the energy of break, Young's modulus, tensile stress and interfacial interactions compared to the neat epoxy and the one reinforced with GO nanosheets. GOQD improved the fracture toughness by factor of 175% and 700% compared to the GO/Epoxy and neat epoxy, respectively.

Periodic mesoporous organosilica with ionic-liquid framework supported manganese: an efficient and recyclable nanocatalyst for the unsymmetric Hantzsch reaction

We have described the catalytic application of a manganese containing ionic liquid-based ordered mesoporous organosilica in the synthesis of polyhydroquinolines.

Comparison of effect of sex hormone manipulation during neonatal period, on mRNA expression of Slc9a4, Nr3c2, Htr5b and Mas1 in hippocampus and frontal cortex of male and female rats

It has long been known that spatial memory and the ability to navigate through space are sexually dimorphic traits among mammals, and numerous studies have shown that these traits can be altered by means of sex hormone manipulation. Hippocampus, the main organ involved in this kind of memory, has specific signature genes with high expression level compared to other regions of the brain. Based on their expression levels and the role that products of these genes can play in processes like signal transduction, mediation of hormone effects and long term potentiation, these genes can be considered as genes necessary for routine tasks of hippocampus. Male and female rat pups were injected with estradiol and testosterone respectively. at early stage of their lives to examine the effect of sex hormone manipulation on mRNA expression of Slc9a4, Nr3c2, Htr5b and Mas1 using comparative quantitative real-time polymerase chain reaction. The results showed that expressions of these genes are strongly influenced by sex hormones in both the frontal cortex and hippocampus, especially in male hippocampus, in which expression of all genes were up-regulated. Htr5b was the only gene that was affected only in the males. Expression of Mas1 was contrary to expectations, showed stronger changes in its expression in cortex than in hippocampus. Nr3c2 was down regulated in all samples but up regulated in male hippocampus, and Slc9a4 also showed a huge up-regulation in male hippocampus compared to other samples.

Contrasting levels of heavy metals in the feathers of urban pigeons from close habitats suggest limited movements at a restricted scale

Despite restrictions in emissions, heavy metals may remain a major environmental issue due to their numerous sources and their persistence. Here, we assessed current levels of 4 metals (Copper, Cadmium, Lead, Zinc) in the feathers of 91 feral pigeons (Columba livia) from 7 sites in the urbanized region of Paris. Elements were detected in all pigeons, indicating that metals persist in urbanized areas. The ratio between metal concentrations in the feathers vs. in the environment calculated using data from other studies was 2-90 times higher for cadmium than for other metals, underlying its ecological importance. Concentrations in the feathers depended on locality, suggesting that pigeons remain in local habitats at this restricted scale, as expected from previous observations. Overall, our study suggests that urban feral pigeons may represent a good model system for metal biomonitoring.

An annual survey of successful suicide incidence in hamadan, Western iran

BACKGROUND

Suicide has constituted a critical public health problem for many decades. The number of completed suicide is traditionally high in Iran. The objective of the present study was to describe the patterns of methods of suicide among registered deaths due to suicide in Hamada, western Iran.

METHODS

In this cross-sectional study, all completed suicide cases (n=146) were included from March 2004 through March 2005 based on Hamadan's Forensic center registered deaths because of suicide. Supplementary data were gauged through a questionnaire from the attempters’ relatives. All statistical analyses were performed using version 13 of the statistical software package SPSS and an alpha level of .05 for all statistical tests.

RESULTS

Prevalence of completed suicide was 8.3 per 100,000 in Hamadan, Iran. From 146 cases, the male-to-female ratio was 7.1:1. Average age of cases was 33.9 yr (Min=10, Max=94) across all age groups, males show consistently higher completed suicide rates than females. Of the 69.2% were from urban population versus 30.8% form rural population. The most common method of suicide was hanging (78.1 %). Other common methods were poisoning (11.6%), and self-burning (6.2%).

CONCLUSION

Suicide rate in Hamadan is high among males through hanging which can be due tosubstance dependency and unemployment.