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What’s in my Pot? (WIMP), a quantitative analysis tool for real-time species identification

Date: 30th November 2017

WIMP is a quantitative analysis tool for real-time species identification for bacteria, fungi, archaea and viruses. We apply it here to DNA extracted from soil around the roots of a Basmati rice plant

Fig. 1 WIMP report, shown for a sample containing bacteria, viruses and fungi

The WIMP application for bacterial, viral, fungal and archaeal species identification

The WIMP workflow classifies and identifies species in real time: as soon as a strand of DNA passes through the pore it can be basecalled and analysed. WIMP makes use of Centrifuge, which is capable of accurately identifying reads when using databases containing multiple highly similar reference genomes, such as different strains of a bacterial species. Centrifuge works by identifying unique segments of those genomes and building an FM-index that can be used for efficient searches of sequenced reads. WIMP processes Centrifuge results to determine the most reliable placement in the taxonomy tree, assigning a score to each taxonomic placement. WIMP currently supports bacteria, archaea, viruses and fungi (Fig. 1).

Fig. 1 WIMP report, shown for a sample containing bacteria, viruses and fungi

Fig. 2 WIMP species quantification a) vs. qPCR b) on the Zymo microbial community standard

WIMP species counts correlate with qPCR and microbial standard quantification

To demonstrate that the WIMP workflow (including sequencing and library preparation) is quantitative, we took a selection of bacterial genomes, prepared sequencing libraries and pooled them in arbitrary ratios. We then compared the WIMP counts to relative abundance as measured by qPCR. The qPCR counts agreed well with the WIMP data (Fig. 2a). Next, we compared the WIMP counts on a microbial community standard to the manufacturer’s theoretical values and again saw good concordance (Fig. 2b). As a consequence, the limit of sensitivity of the workflow is essentially a question of how many reads are obtained from the sequencing run, which is governed by how long the device is left to generate data.

Fig. 2 WIMP species quantification a) vs. qPCR b) on the Zymo microbial community standard

Fig. 3 Analysis of microbiome from soil around the roots of Basmati rice, shown at genus level

WIMP analysis of complex soil microbial community from Basmati rice roots

To demonstrate the effectiveness of WIMP for the analysis of a highly complex microbial community, we took a sample of soil from around the roots of a Basmati rice plant and extracted total genomic DNA by bead-beating. We prepared and sequenced an LSK-108 library and identified the organisms present with WIMP. The microbial community consisted largely of bacteria, though some fungal species were also identified (Fig. 3). WIMP identified many species of nitrogen-fixing bacteria, such as those belonging to the Bradyrhizobium and Rhizobium genera. Notably, WIMP also revealed the presence of several phytopathogens, including Xanthomonas translucens, which causes leaf streak, and can reduce crop yields substantially.

Fig. 3 Analysis of microbiome from soil around the roots of Basmati rice, shown at genus level

Fig. 4 Analysis of rice soil microbes with 1D and 1D2 reads a) classification b) identified species

Reproducible species identification from 1D and 1D2 reads

We prepared 1D and 1D 2 libraries from the rice soil metagenomic sample, to investigate the effect of using higher-accuracy reads on our ability to classify to species level. The results showed that approximately twice as many 1D 2 reads could be classified by WIMP, compared to 1D reads (Fig. 4a). This is presumably due to a higher proportion of 1D 2 reads passing WIMP’s in-built quality-score filtering. We compared the species identified from several 1D libraries with the 1D 2 results, by exporting CSV files from WIMP, and by generating heat-maps from the data (Fig. 4b). The results from all libraries were in very close agreement, indicating that it is not essential to use the higher-accuracy 1D 2 reads for robust species identification with WIMP.

Fig. 4 Analysis of rice soil microbes with 1D and 1D2 reads a) classification b) identified species

Download the PDF WIMP is a quantitative analysis tool for real-time species identification for bacteria, fungi, archaea and viruses. We apply it here to DNA extracted from soil around the roots of a Basmati rice plant

MyPot Planting Module

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New product

MyPot® PLANTATION MODULE is the main part of the growing system developed by the New Garden System . It is a versatile, easy to use, modular, stackable and efficient structure which you can grow healthy vegetables and / or wonderful floral compositions.

Each MyPot® growing module consists of:

External module structure

Batching tray

Drainage grid

8 lids

4 anti-root filters

* Extended information in “More info”

The module is designed with UNIQUE IN WORLD HYDROPONIC TECHNOLOGY, which makes EASY to any person, with or without gardening experience, plant an urban orchard or vertical flower garden and obtain spectacular results. In each module you can grow up to 8 plants, the same or different to produce your own food or to decorate any home corner with plants growing automatically and in a small space.

It is suitable for practicing 5 types of hydroponics at the same time. It makes the agriculture more efficient of easy form; a same piece combines substrate hydroponics, aeroponics, floating root, bioponics and aquaponics.

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Una pieza única

Yo cultivo mis aromáticas solo con este módulo. Me lo regalaron, lo tengo en el balcon y lo riego a mano

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MORE INFO

The MyPot® Plantation Module is a unique, high tech plantation system. It has been developed after several years of research by the New Garden System team. It is a modular (you can stack it vertically), efficient, clean and highly productive system. It has 8 planting holes where you can easily grow up to 8 plants. The inbuilt hydroponic technology allows you to cultivate all kinds of plants (vegetables, fruit, flowers, herbs . ) that grow in a healthy and spectacular way in the same space that a traditional, medium-sized flower pot would require.

The module is watertight; this ensures that the water and fertilizer only leave the system through the plants’ leaves (evapotranspiration) making the most of these resources. The sun or wind will not make the water evaporate or volatilize the fertilizer. Inside the module, a water-saturated atmosphere, that distributes the humidity homogeneously throughout the interior of the module, is created. In addition, the lower part consists of a security system that reserves 4L. of water that prevents the plants from wilting at any time.

This module integrates five hydroponic techniques, used by professional farmers, never before combined in the same cultivation system: Substrate Hydroponics, Aeroponics, Floating Root and Bioponics in the same hydroponic growing system.

SUBSTRATE HYDROPONICS: The module comes filled with natural substrate called PERLITA. This substrate is inert and has highly desirable characteristics for root development. It provides optimum oxygenation and water retention.

AEROPONICS: Thanks to the humidity chamber inside, the roots develop outside of the substrate, in the upper area of the planting module; there they receive the water and nutrients as a soft rain. This ensures that the plant roots always have oxygen.

FLOATING ROOT: Once the plant is developed, the roots will colonize the lower area of the module, where they make contact with the water directly. The water in this internal reservoir is renewed in each recirculation cycle, providing fresh water, nutrients and oxygen. This reservoir guarantees that the plants always have enough water.

BIOPONICS: This is live hydroponics; the planting module’s substrate is biologically activated with beneficial microorganisms that are naturally present in the most fertile soils. These microorganisms, harmless to humans and pets, create “liquid soil” and provide organic compounds that act as natural fortifiers for buds, stems, flowers and fruits.

AQUAPONICS: In addition, MyPot® planting modules can be used as biological filters in an Acuaponic System. Aquaponics is a hydroponic growing system that combines plant cultivation with fish farming. The MyPot® planting module is ideal for filtering ponds and small lakes, you can plant and grow vegetables while purifying the water in your systems. The plants’ roots will absorb the castings produced by the fish and the vegetables (or flowers) will grow in a completely eco-friendly way in this closed cycle. The perlite will filter the larger particles of organic matter, returning high quality, filtered water to the fish tank. It can be used with ornamental or edible fish such as tilapia.

All our MyPot® modules are manufactured in Spain with high quality, toxin-free (no hormone disruptors, e.g. bisphenol). plastics (polypropylene). They are treated with UV protection which guarantees that they do not deteriorate and can be used for both indoor and outdoor grows. Both polypropylene and perlite are materials authorized for organic growing.

The MyPot® plantation module is composed of several parts that are detailed below:

EXTERNAL STRUCTURE: This is the main structure of the MyPot® plantation module; it is cylindrical and consists of 4 lateral plantation holes. It is a sturdy, high quality and light-weight piece. The other module parts fit perfectly into this, as do the other modules of the MyPot® system (reservoir and spacer).

DOSING DEVICE : It is the “lid” module that is placed at the top and has four planting holes that allow cultivation in the MyPot® system. It has holes for placing guides for the plants. It acts as a water flow regulator and creates a fine shower of water and nutrients inside the module.

DRAINAGE GRID : It is an internal part that has the function of separating the substrate from the internal, 4L. reservoir. It has several functions, such as helping to drain the substrate, promote nutrient solution capillarity, root control and oxygenate the water.

ANTI-ROT FILTER : It is a set of 4 sponges that are placed in special holes in the drainage grid that prevent excessive root colonization inside the internal nutrient solution reservoir.

INTERNAL RESERVOIR TANK: It is an internal, 4L. Safety tank, where the roots of adult plants fluctuate. Through the perlite, it provides the correct moisture to the entire Mypot® module.

MyPot® planting module offers great versatility in its use, for example, you can use it as a self-irrigating planter, in which you can place up to 8 different ornamental plants or herbs. When combined with other similar modules, you can create a wonderful autonomous vertical flower column and, if you include the tank module and the recirculation pumps, you will get an automatic growing table for an urban vertical kitchen garden or a magnificent vertical garden, specially designed for urban cultivation. In addition, it is a suitable for creating bio-constructions, with which you can erect floral and/or edible columns to decorate your space or build bio-arbours/bio-pergolas.

MyPot® PLANTATION MODULE is the main part of the growing system developed by the New Garden System. It is a versatile, easy to use, modular, stackable and efficient structure which you can grow healthy vegetables and / or wonderful floral compositions. Each MyPot® growing module consists of: – External module structure – Batching tray – Drainage grid – 8 lids – 4 anti-root filters * Extended information in "More info" The module is designed with UNIQUE IN WORLD HYDROPONIC TECHNOLOGY, which makes EASY to any person, with or without gardening experience, plant an urban orchard or vertical flower garden and obtain spectacular results. In each module you can grow up to 8 plants, the same or different to produce your own food or to decorate any home corner with plants growing automatically and in a small space. It is suitable for practicing 5 types of hydroponics at the same time. It makes the agriculture more efficient of easy form; a same piece combines substrate hydroponics, aeroponics, floating root, bioponics and aquaponics.