Reduction of Salmonella Shedding by Sows during Gestation in Relation to Its Fecal Microbiome

International audiencePork meat is estimated to be responsible for 10-20% of human salmonellosis cases in Europe. Control strategies at the farm could reduce contamination at the slaughterhouse. One of the targeted sectors of production is maternity, where sows could be Salmonella reservoirs. The aim of this study was to assess the dynamics of shedding of Salmonella in terms of variation in both shedding prevalence and strains excreted during gestation in Quebec's maternity sector. The evolution of the fecal microbiota of these sows during gestation was also assessed to detect bacterial populations associated with these variations. A total of 73 sows both at the beginning and the end of the gestation were randomly selected and their fecal matter was analyzed. Salmonella detection was conducted using a method that includes two selective enrichment media (MSRV and TBG). Nine isolates per positive samples were collected. Among the 73 sows tested, 27 were shedding Salmonella. Sows in the first third of their gestation shed Salmonella significantly more frequently (21/27) than those in the last third (6/46) (χ2P < 0.05). The shedding status of 19 of the sows that were previously sampled in the first third of their gestation was followed, this time in the last third of their gestation, which confirmed reduction of shedding. Using 16S rRNA gene sequencing and qPCR, significant differences between the fecal flora of sows at the beginning and the end of the gestation, shedding Salmonella or not and with different parity number were detected. Using MaAsLin, multiple OTUs were found to be associated with the time of gestation, the status of Salmonella excretion and parity number. Some of the identified taxa could be linked to the reduction of the shedding of Salmonella at the end of gestation. In this study, we showed that the level of Salmonella shedding was variable during gestation with significantly higher shedding at the beginning rather than at the end of gestation. We also observed for the first time a significant change in the microbiota during sow gestation and identified interesting taxa which could be linked to a reduced Salmonella shedding

Bacterial Subspecies Variation and Nematode Grazing Change P Dynamics in the Wheat Rhizosphere

Low phosphorus soils are thought to constitute the majority of soils worldwide and cannot support intensive agriculture without high fertilizer inputs. Rhizobacteria are well-known to modify P dynamics and an increased bacterial diversity normally has a positive impact on various process rates. However, it is not known how variation in bacterial diversity at the subspecies level could influence trophic interactions in the rhizosphere and its consequences on plant P nutrition. We therefore hypothesized that the interactions between closely related P solubilizing bacteria and their grazing nematodes could improve plant P dynamics from an unavailable P source. We isolated four Pseudomonas poae strains and extracted nematodes from a Saskatchewan wheat field soil sample. The potential of all bacterial isolates with and without nematodes for increasing P availability in the wheat rhizosphere was tested in controlled microcosms with Ca3(PO4)2 as sole P source. Liberated P, phosphatase activity, plant P and bacterial abundance based on phnX gene copies were determined. Phosphorus solubilization efficiency of isolates varied between isolates whereas phosphatase enzyme activity was only detected under nematodes grazing and during the first 15 days of the experiment. Nematodes grazing upon individual Pseudomonas poae increased phosphatase enzyme activity, bacterial abundance, but decreased plant P concentration compared to non-grazed system. In contrast, the treatment combining all Pseudomonas poae isolates together with nematodes resulted in significant increases in P availability and plant P concentration. Diverse P-solubilizing efficiency and interaction with nematodes within the same bacterial “species” suggest that P dynamics might be linked to micro variation in soil diversity that would not accurately be picked up using common tools such as 16S rRNA gene sequencing

The willow microbiome is influenced by soil petroleum-hydrocarbon concentration with plant compartment-specific effects

International audienceThe interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

The fate of the carbon stocked in permafrost following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but no comprehensive study has yet addressed their composition and functional potential in permafrost. Here, a 2-m deep permafrost sample and its overlying active layer soil were subjected to metagenomic sequencing, quantitative PCR (qPCR) and microarray analyses

Funding structures for Build-to-Suit developments in Brazil: advantages and risks

Empreendimentos build-to-suit são aqueles em que o locador desenvolve um imóvel sob medida para o locatário, que o ocupará pelo prazo previsto em contrato. Dadas as peculiaridades desse tipo de contrato no contexto do real estate, o objetivo deste artigo é analisar as diferentes origens de recursos (fontes de funding) e a forma como eles são empregados (estruturas de funding) para desenvolver os empreendimentos, e discutir as vantagens e riscos dessas estruturas de funding do ponto de vista do empreendedor, que também é o locador. De forma a desenvolver este estudo e formatar as estruturas de funding apresentadas, parte-se de uma revisão das\ud práticas atuais do mercado imobiliário brasileiro (através de notícias veiculadas\ud na mídia e de prospectos de negócios realizados), da literatura brasileira sobre o tema e do conhecimento gerado no Grupo de Real Estate da Escola Politécnica da USP. De maneira a verificar a validade legal das soluções, é realizada uma checagem com\ud base na legislação brasileira e nas normas da Comissão de Valores Mobiliários.\ud Considera-se fontes de funding aquelas tratadas (1) como equity: capital próprio do empreendedor, capital de parceiros (e sócios) no empreendimento na forma de dinheiro ou imóveis (notadamente, o terreno onde será construído o empreendimento), ou investimento de Fundo de Investimento Imobiliário (FII); e (2) como dívida: financiamento bancário, securitização dos recebíveis de aluguéis com CRI ou debêntures. As estruturas de funding apresentadas serão combinações dessas fontes. A análise evidencia que estruturas com financiamento por securitização e emissão de CRI são as mais adequadas de forma geral para os negócios, assim como o investimento completo por FII para negócios de maior porte e nos quais o FII é proprietário direto do empreendimento. \ud Palavras-chave: real estate, build-to-suit, locação, funding, project financeBuild-to-suit real estate assets are tailor made developments for the tenant purposes, who occupies and operates the property for the duration agreed. Given the peculiarities of these contracts and the specificities of the property, this article aims at analyzing the sources of capital and how these funds are mixed and structured for the developments. The article discusses the risks and benefits of each of these funding\ud structures assuming the role of developer. In order to do this study and establish the funding structures shown, the research starts with a review of the current practices in Brazilian real estate market (based on press releases and prospects of deals), of local research papers, and will use the knowledge created at the Real Estate Research Group at Escola Politécnica at Universidade de São Paulo. Since it’s necessary to validate\ud the solutions proposed, Brazilian laws and Comissão de Valores Mobiliários (CVM) norms\ud are reviewed. Funding sources considered will be treated as (1) equity: developers own funds, partnership (via capital or real state – mainly land – investment), or Fundo de Investimento Imobiliário (Brazilian investment structure comparable to REITs); or as (2) debt: banks traditional credit lines, securitization of receivables with CRI emissions\ud , and debt bond emissions. The funding structures presented are mixes of these sources. The analysis shows that the structures best suited for this purpose are those with debt by securitization with CRI emissions, along with the complete investment by a FII but only with large emissions and having the FII as the sole owner of the real estate. \ud Keywords: real estate, build-to-suit, rent, funding, project financ

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons

Fell-field soil microbiology

Only 0.33 % of the Antarctic land surface area is free of ice, with much of this area representing fell-field environments. Antarctic fell-fields are a type of tundra ecosystem that are generally nutrient-limited (especially N) and have a sparse cover of vegetation that is dominated by lichen or bryophytes, although dense vegetative cover and even vascular plants can be present in moister fell-field habitats. Environmental conditions are generally unfavourable in fell-field Antarctic environments, but these soils are spectacular in terms of the diversity of conditions that they offer for microbial life. This is reflected in the variety of microbial taxa and functions that can be found in these environments. Several factors were identified as having strong influences on the microbial communities inhabiting Antarctic fell-field soils, including water, temperature, plants, birds and pH. This chapter reviews microbiological studies that have been carried out in Antarctic fell-field soils.Peer reviewed: YesNRC publication: Ye

Climate change and microbial populations

By 2100, the mean air temperature at the Earth\u2019s surface is predicted to increase by 1.4 \ub0C to 5.8 \ub0C, with a disproportionate effect at high altitudes and latitudes. This chapter reviews the currently available information regarding the responses of key microbial parameters, including diversity, community composition, abundance and functions, to climate change in Antarctic soils. For microorganisms inhabiting Antarctic soils, some insight has been gained by comparing microbial communities across latitudinal gradients, or through short-term laboratory incubations and field studies. Rapid responses of mosses, nematodes, soil algae, cyanobacteria, fungi, and bacteria have been observed in some Antarctic soils. Despite these interesting findings, it is difficult to specifically predict the effects of warming on Antarctic soil microorganisms. One reason is the extreme heterogeneity of soil habitats in this region, as they vary from moist eutrophic ornithogenic soils to nutrient- and water-limited Dry Valley soils. Climate change might have rapid and direct effects on soil microbes that are not otherwise limited, but the release of other limitations (e.g., water, nutrients) could be more important in several environments.Peer reviewed: YesNRC publication: Ye

À la découverte d'une possible révolution végétale !

Les découvertes qui viennent révolutionner notre façon de comprendre le monde sont rares en science. C’est néanmoins ce que les recherches sur le microbiote nous forcent à faire, en remettant en question le concept même d’individu

Bacterial Subspecies Variation and Nematode Grazing Change P Dynamics in the Wheat Rhizosphere

International audienceLow phosphorus soils are thought to constitute the majority of soils worldwide and cannot support intensive agriculture without high fertilizer inputs. Rhizobacteria are well-known to modify P dynamics and an increased bacterial diversity normally has a positive impact on various process rates. However, it is not known how variation in bacterial diversity at the subspecies level could influence trophic interactions in the rhizosphere and its consequences on plant P nutrition. We therefore hypothesized that the interactions between closely related P solubilizing bacteria and their grazing nematodes could improve plant P dynamics from an unavailable P source. We isolated four Pseudomonas poae strains and extracted nematodes from a Saskatchewan wheat field soil sample. The potential of all bacterial isolates with and without nematodes for increasing P availability in the wheat rhizosphere was tested in controlled microcosms with Ca3(PO4)2 as sole P source. Liberated P, phosphatase activity, plant P and bacterial abundance based on phnX gene copies were determined. Phosphorus solubilization efficiency of isolates varied between isolates whereas phosphatase enzyme activity was only detected under nematodes grazing and during the first 15 days of the experiment. Nematodes grazing upon individual Pseudomonas poae increased phosphatase enzyme activity, bacterial abundance, but decreased plant P concentration compared to non-grazed system. In contrast, the treatment combining all Pseudomonas poae isolates together with nematodes resulted in significant increases in P availability and plant P concentration. Diverse P-solubilizing efficiency and interaction with nematodes within the same bacterial "species" suggest that P dynamics might be linked to micro variation in soil diversity that would not accurately be picked up using common tools such as 16S rRNA gene sequencing