The impact of <Emphasis Type="Italic">Carpobrotus</Emphasis> cfr. <Emphasis Type="Italic">acinaciformis</Emphasis> (L.) L. Bolus on soil nutrients,microbial communities structure and native plant communities in Mediterranean ecosystems

Background and aims

Carpobrotus spp. are amongst the most impactful and widespread plant invaders of Mediterranean habitats. Despite the negative ecological impacts on soil and vegetation that have been documented, information is still limited about the effect by Carpobrotus on soil microbial communities. We aimed to assess the changes in the floristic, soil and microbial parameters following the invasion by Carpobrotus cfr. acinaciformis within an insular Mediterranean ecosystem.

Methods

Within three study areas a paired-site approach, comparing an invaded vs. a non-invaded plot, was established. Within each plot biodiversity indexes, C and N soil content, pH and microbial biomass and structure (bacterial and fungal) were assessed.

Results

Invaded plots showed a decrease of α-species richness and diversity. The least represented plant species in invaded plots were those related to grassland habitats. In all invaded soils, a significant increase of carbon and nitrogen content and a significant decrease of pH were registered. Carpobrotus significantly increased bacterial and fungal biomass and altered soil microbial structure, particularly favoring fungal growth.

Conclusions

Carpobrotus may deeply impact edaphic properties and microbial communities and, in turn, these strong modifications probably increase its invasive potential and its ability to overcome native species, by preventing their natural regeneration.

     

Do litter-mediated plant-soil feedbacks influence Mediterranean oak regeneration? A two-year pot experiment

Background & Aims

Oak seedling establishment is difficult and may be partly explained by litter-mediated interactions with neighbors. Litter effects can be physical or chemical and result in positive or negative feedback effects for seedlings. Mediterranean species leaves contain high levels of secondary metabolites which suggest that negative litter effects could be important.

Methods

Seedlings of Quercus ilex and Quercus pubescens were grown for two years in pots with natural soil and litter inputs from 6 Mediterranean woody species, artificial litter (only physical effect) or bare soil.

Results

Litter types had highly different mass loss (41–80%), which correlated with soil organic C, total N and microbial activity. Litter of Q. pubescens increased soil humidity and oak seedlings aerial biomass. Litters of Cotinus coggygria and Rosmarinus officinalis, containing high quantities of phenolics and terpenes respectively, decomposed fast and led to specific soil microbial catabolic profiles but did not influence oak seedling growth, chemistry or mycorrhization rates.

Conclusions

Physical litter effects through improved soil humidity seem to be predominant for oak seedling development. Despite high litter phenolics content, we detected no chemical effects on oak seedlings. Litter traits conferring a higher ability to retain soil moisture in dry periods deserve further attention as they may be critical to explain plant-soil feedbacks in Mediterranean ecosystems.

     

Interaction between contrasting rice genotypes and soil physical conditions induced by hydraulic stresses typical of alternate wetting and drying irrigation of soil

Background and aims

Drought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.

Methods

In a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.

Results

The soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.

Conclusion

In subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.

     

Identity of plant,lichen and moss species connects with microbial abundance and soil functioning in maritime Antarctica

Background and aims

Plant breeding activities shape the rhizosphere microbiome but less is known about the relationship of both with the seed microbiome. We analyzed the composition of bacterial communities of seeds and rhizospheres of Styrian oil pumpkin genotypes in comparison to bulk soil to elucidate specific microbial signatures to support a concept involving plant-microbe interactions in breeding strategies.

Methods

The seed and rhizosphere microbiomes of 14 genotypes of oilseed pumpkin and relatives were analyzed using a 16S rRNA gene amplicon sequencing approach, which was assessed by bioinformatics and statistical methods.

Results

All analyzed microhabitats were characterized by diverse bacterial communities, but the relative proportions of phyla and the overall diversity was different. Seed microbiomes were characterized by the lowest diversity and dominant members of Enterobacteriaceae including potential pathogens (Erwinia, Pectobacterium). Potential plant-beneficial bacteria like Lysobacter, Paenibacillus and Lactococcus contributed to the microbial communities in significant abundances. Interestingly, strong genotype-specific microbiomes were detected for seeds but not for the rhizospheres.

Conclusions

Our study indicates a strong impact of the Cucurbita pepo genotype on the composition of the seed microbiome. This should be considered in breeding of new cultivars that are more capable of exploiting beneficial indigenous microbial communities.

     

Temporal dynamics of ultraviolet radiation impacts on litter decomposition in a semi-arid ecosystem

Background and aims

The emerging consensus posits that ultraviolet (UV) radiation accelerates litter decomposition in xeric environments mainly by preconditioning litter for subsequent microbial decomposition. However, how UV radiation affects the interactions among litter chemistry, microbes, and eventually litter mass during different decomposition stages is still poorly understood.

Methods

Here, we conducted a 29-month in situ decomposition experiment with litter exposed to ambient and reduced UV in a semi-arid grassland.

Results

The decomposition rate for Cleistogenes squarrosa and Stipa krylovii under ambient UV was 82 and 111% greater than that under reduced UV, respectively. UV’s positive effect showed three-stage temporal dynamics. During the early stage, UV had no impact on either litter chemistry or mass loss. During the intermediate stage, UV decreased litter carbon concentration and increased dissolved organic carbon concentration, but still had no effect on litter mass. During the late stage, UV exposure increased microbial population size in the surface soil and significantly increased litter mass loss.

Conclusions

Overall, our study suggested that UV exposure accelerated litter decomposition first by improving litter biodegradability during the intermediate stage and then by enhancing microbial decomposition during the late stage. More long-term photodegradation experiments are needed to explore the biotic and abiotic interactions during different decomposition stages.

     

Effects of phosphorus-mobilizing bacteria on tomato growth and soil microbial activity

Aims

The aim of our study was to clarify whether inoculating a soil with Pseudomonas sp. RU47 (RU47) bacteria would stimulate the enzymatic cleavage of organic P compounds in the rhizosphere and bulk soil, promoting plant growth. Adding either viable or heat treated RU47 cells made it possible to separate direct from indirect effects of the inoculum on P cycling in soil and plants.

Methods

We performed a rhizobox experiment in the greenhouse with tomato plants (Solanum lycopersicum) under low P soil conditions. Three inoculation treatments were conducted, using unselectively grown soil bacteria (bacterial mix), heat treated (HT-RU47) and viable RU47 (RU47) cells, and one not inoculated, optimally P-fertilized treatment. We verified plant growth, nutrient availability, enzyme activities and microbial community structure in soil.

Results

A plant growth promotion effect with improved P uptake was observed in both RU47 treatments. Inoculations of RU47 cells increased microbial phosphatase activity (PA) in the rhizosphere.

Conclusions

Plant growth promotion by RU47 cells is primarily associated with increased microbial PA in soil, while promotion of indigenous Pseudomonads as well as phytohormonal effects appear to be the dominant mechanisms when adding HT-RU47 cells. Thus, using RU47 offers a promising approach for more efficient P fertilization in agriculture.

     

Seed weight affects shoot and root growth among and within soybean genotypes beyond the seedling stage: implications for low P tolerance screening

Background and aims

Invasive plants have been associated with alterations to soil properties, functions, and organisms, with the potential to impact ecosystem processes. An observational study was conducted to determine how the invasive plant Frangula alnus affects soil microbial communities and biogeochemical processes in Wisconsin forests.

Methods

Paired invaded/non-invaded sites (n = 10), including high (n = 5) and low (n = 5) density invasions, were sampled in spring, summer, and fall. Soil was analyzed for extractable and total nitrogen (N), N mineralization rate, total carbon, microbial biomass carbon and N, and microbial community structure using terminal restriction fragment length polymorphisms.

Results

Linear regression analysis with robust variance estimation revealed higher N mineralization rates in invaded sites than non-invaded sites in summer, and in high density invaded sites than non-invaded sites overall (p < 0.05). There was not a corresponding increase in extractable N. No differences between invaded and non-invaded sites were observed for other variables.

Conclusions

Nitrogen-rich F. alnus leaf litter (3.2 % of dry mass) may contribute to elevated N mineralization at these sites, though pre-existing conditions may be responsible. Results suggest that F. alnus alters N cycling but has little impact on soil carbon pools and microbial communities.

     

Plant growth-promoting bacterium <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> FR1 secrets a novel type of extracellular polyhydroxybutyrate polymerase involved in abiotic stress response in plants

Objectives

Identification of novel microbial factors contributing to plant protection against abiotic stress.

Results

The genome of plant growth-promoting bacterium Pseudomonas fluorescens FR1 contains a short mobile element encoding a novel type of extracellular polyhydroxybutyrate (PHB) polymerase (PhbC) associated with a type I secretion system. Genetic analysis using a phbC mutant strain and plants showed that this novel extracellular enzyme is related to the PHB production in planta and suggests that PHB could be a beneficial microbial compound synthesized during plant adaptation to cold stress.

Conclusion

Extracellular PhbC can be used as a new tool for improve crop production under abiotic stress.

     

Total and active microbial communities and <Emphasis Type="Italic">phoD</Emphasis> as affected by phosphate depletion and pH in soil

Background and Aims

Soil microbial communities contribute to organic phosphorus cycling in a variety of ways, including secretion of the PhoD alkaline phosphatase. We sampled a long-term grassland fertilization trial in Switzerland characterized by a natural pH gradient. We examined the effects of phosphate depletion and pH on total and active microbial community structures and on the structure and composition of the total and active phoD-harboring community.

Methods

Archaeal, bacterial and fungal communities were investigated using T-RFLP and phoD-harboring members of these communities were identified by 454-sequencing.

Results

Phosphate depletion decreased total, resin-extractable and organic phosphorus and changed the structure of all active microbial communities, and of the total archaeal and phoD-harboring communities. Organic carbon, nitrogen and phosphorus increased with pH, and the structures of all total and active microbial communities except the total fungal community differed between the two pH levels. phoD-harboring members were affiliated to Actinomycetales, Bacilliales, Gloeobacterales, Planctomycetales and Rhizobiales.

Conclusions

Our results suggest that pH and associated soil factors are important determinants of microbial and phoD-harboring community structures. These associated factors include organic carbon and total nitrogen, and to a lesser degree phosphorus status, and active communities are more responsive than total communities. Key players in organic P mineralization are affiliated to phyla that are known to be important in organic matter decomposition.

     

Microbial community and associated enzymes activity influence soil carbon chemical composition in <Emphasis Type="Italic">Eucalyptus urophylla</Emphasis> plantation with mixing N<Subscript>2</Subscript>-fixing species in subtropical China

Background and aims

Microbial communities and their associated enzyme activities affect the quantity and chemical quality of carbon in soil. We aimed to evaluate the biochemical mechanisms underlying how N₂-fixing species influences soil organic carbon chemical composition through soil microbial functional groups and enzyme activities.

Methods

We examined the effects of N₂-fixing species mixed with Eucalyptus on soil carbon storage, and the chemical composition of an 8-year-old pure Eucalyptus urophylla plantation (PP) and a mixed E.urophylla and Acacia mangium plantation (MP).

Results

The soil carbon stock and recalcitrant carbon chemical component significantly increased in surface soil in MP. The total PLFAs and bacterial PLFAs increased by 29.1% and 27.0% in cool-dry season, while in the warm-wet season, the total PLFAs and bacterial PLFAs increased by 13.1% and 27.3%, respectively. However, the fungal PLFAs decreased significantly in warm-wet season in MP. The total activity of the cellulose-degrading enzyme β-glucosidase was significantly greater with mixed N₂-fixing species in both dry-cool and wet-warm season. The increase in the Alk-C/O-Alk-C ratio and SOC was strongly associated with both C-acquisition activity and bacterial community.

Conclusions

Our findings highlight the importance of N₂-fixing species in regulating both soil microbial communities and their functioning in association with soil extracellular enzyme activities, which contribute to the increased soil carbon storage and recalcitrant carbon composition in Eucalyptus plantations.

     

Ethnicity influences gut metabolites and microbiota of the tribes of Assam,India

Introduction

The human gut microbes and their metabolites are involved in multiple host metabolic pathways. Dysbiosis in the gut microbiota and altered metabolite profiles were reported in diseased state. In a region like Assam, where 12.4% of the populations are tribal population, evaluating the influence of ethnicity on gut microbiota and metabolites has become important to further differentiate it from the diseased state.

Objective

To study the influence of ethnicity on fecal metabolite profile and their association with the gut microbiota composition.

Methods

In this study, we determined the untargeted fecal metabolites from five ethnic groups of Assam (Tai-Aiton, Bodo, Karbi, Tea-tribe and Tai-Phake) using GC–MS and compared them among the tribes for common and unique metabolites. Metabolites of microbial origin were related with the available metagenomic data on gut bacterial profiles of the same ethnic groups and functional analysis were carried out based on HMDB.

Results

The core fecal metabolite profile of the Tea-tribe contained aniline, benzoate and acetaldehyde. PLS-DA based on the metabolites suggested that the individuals grouped based on their ethnicity. PCA plot of the data on bacterial abundance at the level of genus indicated clustering of individuals based on ethnicity. Positive correlations were observed between propionic acid and the genus Clostridium (R?=?0.43 and p?=?0.03), butyric acid and the genus Lactobacillus (R?=?0.45 and p?=?0.024), acetic acid and the genus Bacteroides (R?=?0.63 and p?=?0.001) and methane and the genus Escherichia (R?=?0.58 and p?=?0.002).

Conclusion

Results of this study indicated that ethnicity influences both gut bacterial profile and their metabolites.

     

Plant-soil feedbacks and root responses of two Mediterranean oaks along a precipitation gradient

Aims

Plant-soil feedbacks (PSFs) have been shown to be relevant drivers of forest community dynamics. However, few studies have explored variation of PSFs along environmental gradients. In a framework of climate change, there is a great need to understand how interactions between plants and soil microbes respond along climatic gradients. Therefore, we compared PSFs along a precipitation gradient in Mediterranean oak forests and included trait responses. Following the Stress Gradient Hypothesis (SGH), we expected less negative or even positive PSFs in the physically harsh dry end of our gradient and more negative PSFs in the wettest end.

Methods

We grew Quercus ilex and Quercus suber acorns on soil inoculated with microbes sampled under adults of both species in six sites ranging in annual precipitation. After 4 months, we measured shoot biomass and allocation and morphological traits above and belowground.

Results

We found negative PSFs for Q. ilex independent of precipitation, whereas for Q. suber PSFs ranged from positive in dry sites to negative in wet sites, in agreement with the SGH. The leaf allocation showed patterns similar to shoot biomass, but belowground allocation and morphological traits revealed responses which could not be detected aboveground.

Conclusions

We provide first evidence for context-dependent PSFs along a precipitation gradient. Moreover, we show that measuring root traits can help improve our understanding of climate-dependent PSFs. Such understanding helps to predict plant soil microbe interactions, and their role as drivers of plant community dynamics under ongoing climate change.

     

Bacterial endophytes from rice cut grass (<Emphasis Type="Italic">Leersia oryzoides</Emphasis> L.) increase growth,promote root gravitropic response,stimulate root hair formation,and protect rice seedlings from disease

Background and Aims

Leersia oryzoides, a wild relative of rice (Oryza sativa), may carry potential seed-borne bacterial endophytes which could be used to enhance growth of rice. We hypothesized that seed-associated bacteria from L. oryzoides would be compatible with rice and promote seedling growth, development, and survival.

Methods

We isolated bacteria from seed of L. oryzoides and checked compatibility with rice as well as Bermuda grass seeds for seedling growth promotion. Internal colonisation of bacteria into root cells was observed by ROS staining and microscopic observation. Growth promoting bacteria were evaluated for IAA production, phosphate solubilization and antifungal activities.

Results

Overall, ten bacteria were found to be growth promoting in rice seedlings with effects including restoration of root gravitropic response, increased root and shoot growth, and stimulation of root hair formation. All bacteria were identified by 16S rDNA sequencing. Six bacteria were found to become intracellular in root parenchyma and root hairs in rice and in Bermuda grass seedlings. Six bacteria were able to produce IAA in LB broth with highest (47.06 ± 1.99 μg ml^?1) by LTE3 (Pantoea hericii). Nine isolates solubilized phosphate and inhibited at least one soil borne fungal pathogen.

Conclusions

Seed bacteria of L. oryzoides are compatible with rice. Many of these bacteria become intracellular, induce root gravitropic response, increase root and shoot growth, and stimulate root hair formation in both rice and Bermuda grass seedlings. Presence of bacteria protects seedlings from soil pathogens during seedling establishment. This research suggests that bioprospecting microbes on near relatives of rice and other crop plants may be a viable strategy to obtain microbes to improve cultivation of crops.

     

The bacterial community associated with rose-scented geranium (<Emphasis Type="Italic">Pelargonium graveolens</Emphasis>) leaves responds to anthracnose symptoms

Background

The fungus Colletotrichum is a plant pathogen that causes the anthracnose disease, resulting in huge losses in various crops including the rose-scented geranium (Pelargonium graveolens). Although the bacterial community associated with plants has an important role in the establishment of plant diseases, little is known about what happens in P. graveolens.

Aims

To increase the knowledge about the bacterial community associated with P. graveolens and its relationship with anthracnose disease symptoms.

Methods

Quantitative PCR and high-throughput sequencing were combined to determine the presence of the fungus Colletotrichum and to reveal the bacterial communities associated with different plant parts – root, stem and leaf – and in the rhizosphere and bulk soil, and also to determine the respective bacterial communities associated with P. graveolens leaves symptomatic and asymptomatic for anthracnose disease.

Results

The fungus Colletotrichum was detected in all plant parts and in the surrounding soil. Bacterial communities varied spatially in plants, and the disease symptoms also influenced the composition of the bacterial community. Abundances of operational taxonomic units (OTUs) assigned to the phylum Actinobacteria and to the genus Streptococcus were greatly increased in asymptomatic leaves.

Conclusions

The bacterial community associated to geranium leaves responds to anthracnose symptoms.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

Nitrogen competition between three dominant plant species and microbes in a temperate grassland

Background and aims

To test the hypothesis that dominant plant species could acquire different nitrogen (N) forms over a spatial scale and they also have the ability to compete for available N with microbes.

Methods

A short-term ¹⁵N labeling experiment was conducted in the temperate grassland ecosystem of North China in July of 2013. Three N forms (NO₃ ^? _, NH₄ ⁺ and glycine) labeled with ¹⁵N were injected into the two soil depths (0–5 and 5–15 cm) surrounding each plant to explore N acquisition by plants and microbes. Three dominant plant species (Artemisia frigida, Cleistogenes squarrosa and Artemisia capillaris) were investigated.

Results

Two hours after ¹⁵N labeling, all three dominant plant species absorbed both organic and inorganic N, but different patterns were observed at two soil depths. Uptake of NO₃ ^? was significantly higher at 0–5 cm than at 5–15 cm soil depth among all the dominant plant species. ¹⁵N recovery by microbes was significantly higher than plants. However, ¹⁵N recovery by plants showed different patterns over soil depths.

Conclusions

Dominant plant species in the temperate grassland have different patterns in acquisition of N added to soil in organic form and absorption of inorganic N, and microbes were more effectively than plants at competing for N in a short-term period.

     

Phosphorus dynamics in a tropical forest soil restored after strip mining

Background and aims

We hypothesized that successful early ecosystem and soil development in these P-deficient soil materials will initially depend on effective re-establishment of P storage and cycling through organic matter. This hypothesis was tested in a 26-year chronosequence of seven lightly fertilized, oxidic soil materials restored to eucalypt forest communities after bauxite mining.

Methods

Total P (Pt) status, Hedley P fractions and partial chemical speciation (NaOH-EDTA extraction and analysed using solution ³¹P NMR spectroscopy) were determined in the restored soils.

Results

Concentrations of Pt and most Hedley fractions changed with restoration period, declined with depth and were strongly positively correlated with C and N concentrations. Biological P dominated the Labile and Intermediate P fractions while Long-term P was dominantly inorganic. Organic P concentrations in NaOH-EDTA extracts and their chemical natures were similar in restored and unburned native forest sites. Phosphomonoesters were the dominant class of organic P.

Conclusions

Surprisingly rapid P accretion and fractional changes occurred over 26 years, largely in the surface soils and closely associated with organic matter status. Alkaline hydrolysis products of phosphodiesters and pyrophosphate indicated the importance of microbial P cycling. The important consequences for long-term ecosystem development and biological diversity require further study.

     

Production of caffeoylmalic acid from glucose in engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

Objectives

To achieve biosynthesis of caffeoylmalic acid from glucose in engineered Escherichia coli.

Results

We constructed the biosynthetic pathway of caffeoylmalic acid in E. coli by co-expression of heterologous genes RgTAL, HpaBC, At4CL2 and HCT2. To enhance the production of caffeoylmalic acid, we optimized the tyrosine metabolic pathway of E. coli to increase the supply of the substrate caffeic acid. Consequently, an E. coli–E. coli co-culture system was used for the efficient production of caffeoylmalic acid. The final titer of caffeoylmalic acid reached 570.1 mg/L.

Conclusions

Microbial production of caffeoylmalic acid using glucose has application potential. In addition, microbial co-culture is an efficient tool for producing caffeic acid esters.

     

Involvement of reactive oxygen species and Ca<Superscript>2+</Superscript> in the differential responses to low-boron in rapeseed genotypes

Background and aims

Invasive weeds may exert negative impact on other plant species and soil processes. The observed negative impact of an invasive weed species may be driven by allelopathy or nutrient availability.

Methodology

Sorghum halepense is one of the worst invasive weeds in crop fields. We quantified the species richness in the S. halepense-invaded communities and communities not yet invaded by the weed. Sorghum soil and no-sorghum soil were analysed for total phenolics, microbial activity, available nitrogen (N) and organic carbon. Manipulative experiments were carried out to understand the interference potential of S. halepense. Soil was amended with root or shoot leachate of S. halepense, and its impact on plant growth and soil properties was studied.

Results

Out of four S. halepense-sites, lower plant species richness was observed in one site compared to uninvaded sites. S. halepense-invaded soil had higher levels of total phenolics and lower levels of available N. Higher inhibition in the root growth of Brassica juncea or Bidens pilosa was observed in root leachate-amended soil than shoot leachate-amended soil. Shoot leachate-amended soil had higher levels of total phenolics and available N than root leachate-amended soils. Significant reduction in the available N was observed in soil amended with root leachate. Significant decline in the total phenolics over a period of time was observed in soil amended with root leachate or shoot leachate of S. halepense. Higher CO₂ release was observed 24 h after amending soil with root leachate or shoot leachate of S. halepense.

Conclusions

Sorghum halepense interference potential in its soil is likely due to lower levels of available N. Greater reduction in root dry weight of assay species in root leachate amended soil compared to shoot leachate amended soil was likely due to lower levels of available N in root leachate-amended soil. Relative interference potential of both root and shoot leachates or extracts should be evaluated in allelopathy bioassays and further experiments should be designed to distinguish the role of allelochemicals and nutrient availability in plant growth inhibition.

     

<Emphasis Type="Italic">massPix</Emphasis>: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics

Introduction

Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.

Objectives

We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.

Methods

massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.

Results

Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.

Conclusion

massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.