Soil under nurse plants is always better than outside: a survey on soil amelioration by a complete guild of nurse plants across a long environmental gradient

Aims

Soil under nurse plants is more fertile than in the harsh surroundings. This is a primary mechanism involved in plant to plant facilitation and it is critical in structuring plant communities under stressful conditions. However we do not know how this soil enrichment process varies along complex environmental gradients and among coexisting nurse plants.

Methods

Soil properties related to structure, resource stocks and microbial activity, were compared among up to ten nurse plant species and adjacent barren soil areas, along a 1600 m elevation gradient above the treeline in central Chilean Andes. Shifts in Relative Interaction Index (RII) sensu Armas (Ecology 85: 2682–2686, 2004) and in coefficient of variation on soil properties were also modelled.

Results

Soil under nurse plants was always richer than on barren areas irrespective of altitude, except in the case of texture with more small particles in the intermediate altitude. β-glucosidase activity was higher under cushion plants than under nurse plants with other growth habit. Besides β-glucosidase and phosphatase activities were more variable at higher altitudes. Nitrogen was more variable under nurse plants than in barren areas and its RII values were lower at intermediate altitudes.

Conclusions

Soil amelioration by nurse plants occurred all along the studied environmental gradient promoting islands of fertility and a general increase on soil niches heterogeneity.

     

Local root status: a neglected bio-factor that regulates the home-field advantage of leaf litter decomposition

Background and aims

Bacterial Non-Specific Acid Phosphatase (NSAP) enzymes are capable of dephosphorylating diverse organic phosphoesters but are rarely studied: their distribution in natural and managed environments is poorly understood. The aim of this study was to generate new insight into the environmental distribution of NSAPs and establish their potential global relevance to cycling of organic phosphorus.

Methods

We employed bioinformatic tools to determine NSAP diversity and subcellular localization in microbial genomes; used the corresponding NSAP gene sequences to census metagenomes from diverse ecosystems; studied the effect of long-term land management upon NSAP diversity and abundance.

Results

Periplasmic class B NSAPs are poorly represented in marine and terrestrial environments, reflecting their association with enteric and pathogenic bacteria. Periplasmic class A and outer membrane-associated class C NSAPs are cosmopolitan. NSAPs are more abundant in marine than terrestrial ecosystems and class C more abundant than class A genes, except in an acidic peat where class A genes dominate. A clear effect of land management upon gene abundance was identified.

Conclusions

NSAP genes are cosmopolitan. Class C genes are more widely distributed: their association with the outer-membrane of cells gives them a clear role in the cycling of organic phosphorus, particularly in soils.

     

Heterogeneity in arbuscular mycorrhizal fungal communities may contribute to inconsistent plant-soil feedback in a Neotropical forest

Background and aims

Plant-soil feedback may vary across host species and environmental gradients. The relative importance of these biotic versus abiotic drivers of feedback will determine the stability of plant and microbial communities across environments. If plant hosts are the main driver of soil microbial communities, plant-soil feedback may be stable across changing environments. However, if microbial communities vary with environmental gradients, feedback may also vary, limiting its capacity to predict plant distributions.

Methods

We characterized arbuscular mycorrhizal (AM) fungi across tree plantations and a primary Neotropical rainforest. We then performed a plant-soil feedback pot experiment of AM fungi from these plantations on three plant species and related feedback and AM fungal communities in the field.

Results

In the field, temporal and spatial variation in AM fungal composition was similar in magnitude to variation across plant host species. Composition of AM fungi in the pot experiment significantly differed from the field plots. Furthermore, differential feedback was explained by shifts in AM fungal composition only for one plant host species (Hyeronima alchorneoides) in the pot experiment.

Conclusions

Natural AM fungal communities were temporally and spatially heterogeneous and AM fungal communities in the greenhouse did not reflect natural soils. These factors led to heterogeneous and unpredictable feedback responses, which suggests that applying greenhouse derived plant-soil feedback trends to predict plant coexistence in natural systems may be misleading.

     

Real-Time Vital Mineralization Detection and Quantification during In Vitro Osteoblast Differentiation

Background

In vitro studies of osteoblasts traditionally use Alizarin Red as a golden standard for the detection and quantification of mineralization, which is a marker of osteoblast differentiation. However, this method presents a number of drawbacks, including the need to fix cells, which prevents additional measurements. Years ago, Calcein Green was proposed as an alternative to Alizarin Red, with the advantage to be directly detectable in live cells. However, the protocol was still time-consuming, and it never managed to replace Alizarin Red. Now, with more efficient imaging systems, we present a protocol using Calcein Green which provides significant advantages.

Results

The osteoblast mineralization was efficiently detected and accurately quantified in real time at any desired time point across the entire differentiation period, with a minimum time expenditure.

Conclusions

The combination of Calcein Green and the real-time imaging station IncuCyte ZOOM can efficiently replace the Alizarin Red method, and allows very accurate and time-saving assessment of the level and the dynamics of matrix mineralization.

     

Metabolomic study of the response to cold shock in a strain of <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> isolated from cloud water

Introduction

Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level.

Objectives

The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock.

Methods

Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA).

Results

Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function.

Conclusions

This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.

     

Investigation of the relationship between cell surface hydrophobicity and demulsifying capability of biodemulsifier-producing bacteria

Background

Cell surface hydrophobicity (CSH) is one of the key physicochemical features of biodemulsifier-producing bacteria that influence their demulsification capability maintenance in petroleum contaminated environments.

Methods

In present study, biodemulsifier-producing bacteria were isolated from petroleum contaminated environments using different isolation media and the correlation between their CSH and demulsifying ability was investigated. The demulsifying ability of isolates was measured through demulsification tests on water in kerosene emulsions. The microbial adhesion to the hydrocarbon (MATH) assay was used to denote their CSH.

Results

The evaluation of CSH showed that majority of biodemulsifier producing bacteria have high CSH which indicating a positive correlation between CSH and demulsifying capability.

Conclusions

According to these results it can be concluded that CSH can be used as an indicator for assessment of biodemulsifier-producing bacteria and screening of new isolates for their biodemulsifier production.

     

Metabolomic profiling of maternal hair suggests rapid development of intrahepatic cholestasis of pregnancy

Introduction

Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.

Objective

Investigate the maternal hair metabolome for predictive biomarkers of ICP.

Methods

The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.

Results

Of 105 metabolites detected in hair, none were significantly associated with ICP.

Conclusion

Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.

     

Fruit metabolite networks in engineered and non-engineered tomato genotypes reveal fluidity in a hormone and agroecosystem specific manner

Introduction

Metabolomics provides a view of endogenous metabolic patterns not only during plant growth, development and senescence but also in response to genetic events, environment and disease. The effects of the field environment on plant hormone-specific metabolite profiles are largely unknown. Few studies have analyzed useful phenotypes generated by introducing single or multiple gene events alongside the non-engineered wild type control at field scale to determine the robustness of the genetic trait and its modulation in the metabolome as a function of specific agroecosystem environments.

Objectives

We evaluated the influence of genetic background (high polyamine lines; low methyl jasmonate line; low ethylene line; and isogenic genotypes carrying double transgenic events) and environments (hairy vetch, rye, plastic black mulch and bare soil mulching systems) on the metabolomic profile of isogenic reverse genetic mutations and selected mulch based cropping systems in tomato fruit. Net photosynthesis and fruit yield were also determined.

Methods

NMR spectroscopy was used for quantifying metabolites that are central to primary metabolism. We analyzed both the first moment (means) of metabolic response to genotypes and agroecosystems by traditional univariate/multivariate methods, and the second moment (covariances) of responses by creating networks that depicted changes in correlations of paired metabolites. This particular approach is novel and was necessary because our experimental material yielded highly variable metabolic responses that could not be easily understood using the traditional analytical approaches for first moment statistics.

Results

High endogenous spermidine and spermine content exhibited strong effects on amino acids, Krebs cycle intermediates and energy molecules (ADP + ATP) in ripening fruits of plants grown under different agroecosystem environments. The metabolic response to high polyamine genotypes was similar to the response to hairy vetch cover crop mulch; supported by the pattern of changes in correlation between metabolites. Changes in primary metabolites of genotypes mutated for the deficiency of ethylene or methyl jasmonate were unique under all growth conditions and opposite of high polyamine genotype results. The high polyamine trait was found to dominate the low ethylene and low jasmonate mutations under field conditions. For several metabolites low ethylene and low methyl jasmonate genotypes had an inverse relationship. Collectively, these results affirm that interactions between metabolite pathways and growth environments are affected by genotype, and influence the metabolite quality of a crop.

Conclusion

This study portrays how metabolite relationships change, both in mean and in correlation, under different genotypic and environmental conditions. Although these networks are surprisingly dynamic, we also find examples of selectively conserved associations.

     

Serpentine ecotypic differentiation in a polyploid plant complex: shared tolerance to Mg and Ni stress among di- and tetraploid serpentine populations of <Emphasis Type="Italic">Knautia arvensis</Emphasis> (Dipsacaceae)

Background and aims

Serpentine soils impose limits on plant growth and survival and thus provide an ideal model for studying plant adaptation under environmental stress. Despite the increasing amount of data on serpentine ecotypic differentiation, no study has assessed the potential role of polyploidy. We tested for links between polyploidy and the response to serpentine stress in Knautia arvensis, a diploid-tetraploid, edaphically differentiated complex.

Methods

Variation in growth, biomass yield and tissue Mg and Ni accumulation in response to high Mg and Ni concentrations were experimentally tested using hydroponic cultivation of seedlings from eight populations of different ploidy and edaphic origin.

Results

Regardless of ploidy level, serpentine populations exhibited higher tolerance to both Mg and Ni stress than their non-serpentine counterparts, suggesting an adaptive character of these traits in K. arvensis. The effect of ploidy was rather weak and confined to a slightly better response of serpentine tetraploids to Mg stress and to higher biomass yields in tetraploids from both soil types.

Conclusions

The similar response of diploid and tetraploid serpentine populations to edaphic stress corresponded with their previously described genetic proximity. This suggests that serpentine tolerance might have been transmitted during the local autopolyploid origin of serpentine tetraploids.

     

Outer membrane protein C (OmpC) of <Emphasis Type="Italic">Escherichia coli</Emphasis> induces neurodegeneration in mice by acting as an amyloid

Objectives

Involvement of the outer membrane protein C (OmpC) of Escherichia coli in neurodegeneration was investigated using a mouse model.

Results

OmpC formed protease-resistant fibres that exhibited the diagnostic features of an amyloid. The spectral shift in the Congo Red and the thioflavin T assays produced features similar to neurotoxic peptides. Intramuscular administration of OmpC in mice resulted in spongiform neurodegeneration of the brain through calcium-dependent apoptosis and also showed upregulation of apoptosis related genes. Immunolocalization of OmpC in brain demonstrated the direct involvement of the porin in neurodegeneration and formation of spongiform encephalopathy.

Conclusion

We have demonstrated the ability of OmpC of E. coli to induce neurodegeneration in mice.

     

Expression of <Emphasis Type="Italic">Ciona intestinalis</Emphasis> AOX causes male reproductive defects in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Background

Mitochondrial alternative respiratory-chain enzymes are phylogenetically widespread, and buffer stresses affecting oxidative phosphorylation in species that possess them. However, they have been lost in the evolutionary lineages leading to vertebrates and arthropods, raising the question as to what survival or reproductive disadvantages they confer. Recent interest in using them in therapy lends a biomedical dimension to this question.

Methods

Here, we examined the impact of the expression of Ciona intestinalis alternative oxidase, AOX, on the reproductive success of Drosophila melanogaster males. Sperm-competition assays were performed between flies carrying three copies of a ubiquitously expressed AOX construct, driven by the α-tubulin promoter, and wild-type males of the same genetic background.

Results

In sperm-competition assays, AOX conferred a substantial disadvantage, associated with decreased production of mature sperm. Sperm differentiation appeared to proceed until the last stages, but was spatially deranged, with spermatozoids retained in the testis instead of being released to the seminal vesicle. High AOX expression was detected in the outermost cell-layer of the testis sheath, which we hypothesize may disrupt a signal required for sperm maturation.

Conclusions

AOX expression in Drosophila thus has effects that are deleterious to male reproductive function. Our results imply that AOX therapy must be developed with caution.

     

Responses of rice to chronic and acute iron toxicity: genotypic differences and biofortification aspects

Background and aims

Iron (Fe) toxicity is a wide-spread stress in lowland rice production. The aim of this study was to differentiate between responses to acute Fe stress during the vegetative stage and chronic Fe stress throughout the growing period.

Methods

Six rice genotypes were tested in a semi-artificial greenhouse setup, in which acute (almost 1500 mg L^?1 Fe in soil solution during the vegetative stage) and chronic (200 to 300 mg L^?1 Fe throughout the season) Fe toxicity were simulated.

Results

Acute Fe stress induced early development of heavy leaf bronzing, whereas moderate symptoms occurred in the chronic treatment throughout the season. Grain yields were only reduced in the chronic stress treatment (?23 %) due to reductions in spikelet fertility, grain number and grain weight. Symptom formation during the early growth stages did not reflect yield responses in all genotypes. Only one genotype showed increases in grain Fe concentrations (24 % in the acute stress and 44 % in the chronic stress) compared to the control.

Conclusions

Contrasting genotypes responded differently to acute and chronic Fe toxicity, and one genotype showed consistent tolerance and the ability to translocate excess Fe into grains. These traits can be useful in the adaptive breeding of rice for Fe toxic environments.

     

Concordant morphological and molecular clines in a contact zone of the Common and Spined toad (<Emphasis Type="Italic">Bufo bufo</Emphasis> and <Emphasis Type="Italic">B. spinosus</Emphasis>) in the northwest of France

Background

Hybrid zones are regions where individuals of two species meet and produce hybrid progeny, and are often regarded as natural laboratories to understand the process of species formation. Two microevolutionary processes can take place in hybrid zones, with opposing effects on population differentiation. Hybridization tends to produce genetic homogenization, reducing species differences, whereas the presence of mechanisms of reproductive isolation result in barriers to gene flow, maintaining or increasing differences between taxa.

Results

Here we study a contact zone between two hybridizing toad species, Bufo bufo and B. spinosus, through a combination of molecular (12 polymorphic microsatellites, four nuclear and two mitochondrial SNP markers) and morphological data in a transect in the northwest of France. The results show largely concordant clines across markers, defining a narrow hybrid zone of ca. 30 km wide. Most hybrids in the centre of the contact zone are classified as F₂ or backcrossed individuals, with no individuals assigned to the F₁ hybrid class.

Conclusions

We discuss the implications of these results for our understanding of the evolutionary history of these species. We anticipate that the toad contact zone here described will become an important asset in the study of hybrid zone dynamics and evolutionary biology because of its easy access and the abundance of the species involved.

     

Mapping data elements to terminological resources for integrating biomedical data sources

Background

Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration.

Methods

We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings.

Results

82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed.

Conclusion

Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

     

Ecofriendly demulsification of water in oil emulsions by an efficient biodemulsifier producing bacterium isolated from oil contaminated environment

Objective

Water in oil emulsions increase oil processing costs and cause damage to refinery equipment which necessitates demulsification. Since chemical demulsifiers cause environmental pollution, biodemulsifiers have been paid more attention. This study aims to identify biodemulsifier-producing bacteria from petroleum contaminated environments.

Results

As a result, several biodemulsifier producing strains were found that Stenotrophomonas sp. strain HS7 (accession number: MF445088) which produced a cell associated biodemulsifier showed the highest demulsifying ratio, 98.57% for water in kerosene and 66.28% for water in crude oil emulsion after 48 h. 35 °C, pH 7, 48 h incubation and ammonium nitrate as nitrogen source were optimum conditions for biodemulsifier production. Furthermore, it was found that hydrophobic carbon sources like as liquid paraffin is not preferred as the sole carbon source while a combination of various carbon sources including liquid paraffin will increase demulsification efficiency of the biodemulsifier.

Conclusions

The appropriate potential of this biodemulsifier strengthens the possibility of its application in industries especially petroleum industry.

     

Human health characterization factors of nano-TiO<Subscript>2</Subscript> for indoor and outdoor environments

Purpose

The increasing use of engineered nanomaterials (ENMs) in industrial applications and consumer products is leading to an inevitable release of these materials into the environment. This makes it necessary to assess the potential risks that these new materials pose to human health and the environment. Life cycle assessment (LCA) methodology has been recognized as a key tool for assessing the environmental performance of nanoproducts. Until now, the impacts of ENMs could not be included in LCA studies due to a lack of characterization factors (CFs). This paper provides a methodological framework for identifying human health CFs for ENMs.

Methods

The USEtox? model was used to identify CFs for assessing the potential carcinogenic and non-carcinogenic effects on human health caused by ENM emissions in both indoor (occupational settings) and outdoor environments. Nano-titanium dioxide (nano-TiO₂) was selected for defining the CFs in this study, as it is one of the most commonly used ENMs. For the carcinogenic effect assessment, a conservative approach was adopted; indeed, a critical dose estimate for pulmonary inflammation was assumed.

Results and discussion

We propose CFs for nano-TiO₂ from 5.5E?09 to 1.43E?02 cases/kg_emitted for both indoor and outdoor environments and for carcinogenic and non-carcinogenic effects.

Conclusions

These human health CFs for nano-TiO₂ are an important step toward the comprehensive application of LCA methodology in the field of nanomaterial technology.

     

A versatile <Emphasis Type="Italic">Trichoderma reesei</Emphasis> expression system for the production of heterologous proteins

Objectives

To develop a versatile Trichoderma reesei (teleomorph Hypocrea jecorina) expression system for the high-purity production of heterologous proteins.

Results

The versatile T. reesei expression system is based on xyn1 and xyn2 promoters, A824V transition in XYRI, and a bicomponent carbon source strategy. Red fluorescent protein gene rfp and alkaline endoglucanase EGV gene egv3 from Humicola insolens were used as reporter genes to test our versatile expression system

Conclusions

The versatile T. reesei expression system can be applied to produce heterologous proteins with high purity and high yield.

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.