EP4719912A1 - Method and uav for collecting environmental dna - Google Patents

Abstract

A method for collecting environmental DNA from a space (101) within a plant canopy (100) comprises: providing a UAV (1) comprising a propulsion system (2) and a probe (3) hanging from the propulsion system (2); providing the probe (3) with a sampling material (5); flying the UAV 5 (1) with the propulsion system (2) at a height (H) over the plant canopy (100); dipping the probe (3) into the plant canopy (100); brushing the sampling material (5) against a plant surface (102) in the space (101) within the plant canopy (100); and extracting the probe (3) from the plant canopy (100).

Description

Method and UAV for collecting environmental DNA

DESCRIPTION

The present invention relates to a method and an Unmanned Aerial Vehicle (UAV) for collecting environmental DNA, also known as "eDNA".

Environmental DNA is an emerging tool for characterizing biodiversity, establishing diversity thresholds, and monitoring changes in ecological communities resulting from human activities or management decisions.

Environmental DNA refers to DNA which is released by organisms and persists in the environment, see ref. [1] at the end of this description.

More particularly, ref. [2] defines environmental DNA as DNA that can be extracted from environmental samples (such as soil, water or air), without first isolating any target organisms. It is characterized by a complex mixture of genomic DNA from many different organisms and possible degradation (i.e. DNA molecules are cut into small fragments). Total eDNA contains cellular DNA originating from living cells or organisms, and extracellular DNA resulting from natural cell death and subsequent destruction of cell structure.

Ref. [3] shows that the collection of terrestrial eDNA outperforms conventional approaches to detecting invasive pests.

Ref. [4] further shows that eDNA can even be detected for several days when exposed to direct sunlight. eDNA surveys are well established for water bodies because water aggregates and transports DNA released by aquatic organisms, meaning that species are detected from water samples collected well away from the target individuals, see ref. [5,6]. But capturing a general and accurate snapshot of terrestrial biodiversity has proven more complex. The challenge is the local and non-representative nature of the samples because there are fewer mechanisms that facilitate eDNA transport and dispersal across terrestrial landscapes, see ref. [7]. Indeed, the collection of eDNA in terrestrial environments remains challenging because of the many potential surfaces and sources that need to be surveyed and their limited accessibility.

In fact, current sampling approaches are not scalable. Sampling can be done manually using spray aggregation or tree rolling, see ref. [7]. For spray aggregation, deionized water is sprayed on the collection surface, re-collected, and then analyzed. Samples can also be collected by manually rolling the collector material over the tree trunk or branch (tree rolling). These approaches are very time and labor intensive and require direct access to the survey target while providing only localized samples.

Initial approaches using drone technology for terrestrial surface eDNA collection are disclosed in ref. [1], which proposes to survey biodiversity by sampling eDNA on the outer branches of tree canopies with an aerial robot. This known drone combines a force-sensing cage with a hapticbased control strategy to establish and maintain contact with the upper surface of the branches. Surface eDNA is then collected using an adhesive surface integrated in the cage of the drone.

However, the approach from ref. [1] is limited to spatially localized sampling on surfaces directly accessible with a drone. This limitation reduces the variety of species which can be detected. By contrast, it would be desirable to sample eDNA from a wide variety of substrates to offer a solution for broad-scale biodiversity monitoring.

Furthermore, the approach from ref. [1] necessitates physical interaction of the drone with the target surface. Such interaction presents inherent safety concerns and limits the approach to isolated and easily reachable branches. By contrast, it would be desirable to survey even within dense environments without endangering the safety of the drone.

A further drawback is that the approach from ref. [1] can only be partially automated. In fact, a user is still required to align the drone with the tree branch before the autonomous landing procedure can begin. On the contrary, a fully automatable solution would be desirable.

US9984455B1 discloses an organism growth prediction system using drone-captured images.

Therefore, the problem addressed by the present invention is to provide a method and a UAV for collecting environmental DNA, as well as a method for monitoring biodiversity, which are structurally and functionally configured to overcome, at least partially, one or more of the disadvantages set out above with reference to the cited prior art.

It is also an object of the invention to provide a minimally invasive method and UAV to assess the biodiversity present in plant canopies.

A further object of the invention is to provide an automatable method and UAV to assess the biodiversity present in plant canopies.

An object of the invention is also to provide a method and a UAV which improve the known solutions within the scope of a simple, rational and cost-effective solution.

This problem is solved, and these objects are achieved, at least in part, by the invention, in a first aspect, by means of a method for collecting environmental DNA (eDNA) from a space within a plant canopy.

As used herein, "environmental DNA" or "eDNA" refers preferably to genetic material obtained directly from environmental samples. This genetic material is preferably characterized by a mixture of intracellular (i.e., from living cells) and extracellular DNA (originating for example from shed skin, hairs, urine, feces, or carcasses).

The term "collecting environmental DNA" may refer to collecting both eDNA and eDNA-containing particles.

The term "collecting" may be used herein as a synonym for sampling.

The term "plant canopy" may refer to the canopy of a single plant or to the canopy of two or more plants that are close to or in contact with each other so as to form a unitary canopy.

The plants may be trees or crops. Accordingly, the term "plant canopy" may refer to a tree canopy or a crop canopy.

The method comprises providing an Unmanned Aerial Vehicle (UAV). Preferably, the UAV comprises a propulsion system and a probe. Further preferably, the probe hangs (i.e., is suspended) from the propulsion system via connection means, more particularly via flexible connection means. In this manner, the probe may swing relative to the propulsion system.

As used herein, the term "flexible connection means" refers preferably to connection means comprising at least a flexible portion. Furthermore, the term "flexible" referred to the connection means preferably means that the connection means are configured to allow the probe to swing relative to the propulsion system.

The probe may be provided with a sampling material advantageously configured to collect eDNA from a surface by brushing the sampling material against the surface. In this context, the term "to brush" may be defined as to pass lightly over or across or to touch gently against in passing. The term "brushing" may be used herein as a synonym for touching and/or swabbing. The probe may thus comprise a sampling material configured to retain eDNA when touching and/or swabbing a surface. In this manner, the probe allows for providing species information from the eDNA acquired from surfaces that come into contact with the sampling material.

Preferably, the method further comprises flying the UAV with the propulsion system at a certain height over the plant canopy. As used herein, the term "height" may refer to the vertical distance between the propulsion system and the upper level of the plant canopy. It is also noted that the terms "vertical", "horizontal", "dipping", "below", "lowering" and "lifting" as used herein may refer to conditions which occur while the UAV is in flight and/or which concern the flight configuration of the UAV.

Preferably, the method comprises dipping the probe into the plant canopy, in particular by reducing the height of the propulsion system over the plant canopy and/or by providing the UAV with an actuator device and extending the connection means away from the propulsion system toward the plant canopy with the actuator device.

If the plant canopy is a tree canopy, the option of extending the connection means is preferred because it allows driving the probe deeper into the foliage notwithstanding the presence of tree branches. This option is further advantageous because it enables deploying the probe while safely hovering the UAV at a fixed height above the upper level of the plant canopy. Conversely, the option of reducing the height of the propulsion system is simpler to be implemented, and it may be advantageous if the plant canopy is a crop canopy, as crops are usually shorter than trees, and therefore there is typically no need to drive the probe deep into crops.

Preferably, the method comprises brushing the sampling material against a plant surface (e.g. leaves, flowers, bark) in a space within the plant canopy so that the sampling material collects eDNA from the plant surface in said space. Advantageously, brushing the sampling material against the plant surface allows the removal and physical transfer of eDNA and eDNA- containing particles from the plant surface without necessarily sampling tissue from the plant itself. In this manner, minimally invasive sampling is obtained.

Further preferably, the method comprises extracting the probe from the plant canopy. In this manner, the probe can be retrieved to extract and analyse the collected eDNA.

It will be appreciated that the method of the invention can automate surface eDNA collection, providing inexpensive, standardized sampling and enabling surveys in normally difficult-to-access environments, such as forest canopies and understorey vegetation.

Compared to known manual solutions for surface eDNA collection, the method of the invention is more scalable, thereby reducing the time, cost, and effort to collect samples over large areas, such as forests and cultivated fields.

Compared to the drone-based solution for surface eDNA collection from ref. [1], the invention is not only more scalable but can also reach densely cluttered environments, greatly expanding the potential application areas for biodiversity monitoring and invasive pest detection. A further advantage of the invention is that it allows for fully automated eDNA collection. In fact, contrary to the approach from ref. [1], there is no need to land the UAV on a tree branch and therefore there is no need to align the UAV with a tree branch by teleoperating the UAV.

The presence of flexible connection means between the propulsion system and the probe, as well as the possibility to extend the probe away from the propulsion system, allows surveying even within dense environments without endangering the safety of the UAV.

Furthermore, since a multitude of surfaces can be brushed by the probe during one sampling process, more eDNA material can be recovered compared to ref. [1], providing a more holistic overview of the biodiversity present in the plant canopy.

In a second aspect, the invention relates to a method for monitoring biodiversity comprising collecting eDNA from a space within a plant canopy as described above and sequencing the collected eDNA to identify organisms from said space. The method may further comprise extracting and/or amplifying the collected eDNA and/or subjecting it to bioinformatics analysis.

In a third aspect, the invention refers to a UAV for collecting eDNA from a space within a plant canopy, the UAV comprising a propulsion system, a probe, and flexible connection means for hanging the probe to the propulsion system. More particularly, the connection means are configured to hang the probe in a spaced-out position below the propulsion system, at least when the propulsion system is in flight.

The connection means may connect the probe to the propulsion system movably between a retracted position in which the probe is proximal to the propulsion system and an extended position in which the probe is distal from the propulsion system.

The UAV may further comprise an actuator device. If present, the actuator device is preferably configured to extend/retract the connection means away from/toward the propulsion system so as to preferably move the probe from the retracted position to the extended position and vice versa. The flexible connection means may be configured to allow the probe to swing relative to the propulsion system while the UAV is flying or hovering. The probe may comprise a sampling material configured to collect eDNA from a surface by brushing the sampling material against the surface.

The UAV may further comprise a control unit which may be configured to drive (i.e., to control) the propulsion system and/or the actuator device (if present) so that the UAV performs one or more of the steps of the method according to the first aspect of the invention in a way which may be automated. In fact, even though the UAV may be teleoperated, it is preferred that the control unit is configured to control the propulsion system and/or the actuator device to operate autonomously. This means that the control unit may comprise instructions which, when executed by the control unit, cause the control unit to carry out one or more of the method steps.

For example, the control unit may be configured to drive the propulsion system to fly or hover, preferably autonomously, at a certain height over a plant canopy.

The control unit may be further configured to drive the propulsion system to reduce its height over the plant canopy and/or to drive the actuator device (if present) to extend the connection means away from the propulsion system toward the plant canopy, preferably autonomously, so as to dip the probe into the plant canopy and brush the sampling material against the plant surface in the space within the plant canopy so that the sampling material collects eDNA from the plant surface in said space.

The control unit may be further configured to drive the propulsion system and/or the actuator device to extract the probe from the plant canopy, preferably autonomously. More particularly, the control unit may be configured to drive the propulsion system to increase its height over the plant canopy and/or to drive the actuator device to retract the connection means away from the plant canopy toward the propulsion system, preferably autonomously, so as to extract the probe from the plant canopy. It will be appreciated that the definitions and the advantages mentioned above with reference to the first aspect of the invention also apply to the second and third aspects, mutatis mutandis.

The present invention, in at least one of the above aspects, may also have one or more of the following preferred features in addition to those previously mentioned.

The step of extracting the probe from the plant canopy may be performed by increasing the height of the propulsion system over the plant canopy and/or by retracting the connection means away from the plant canopy toward the propulsion system with the actuator device.

If the plant canopy is a tree canopy, the option of retracting the connection means is preferred because it allows overcoming entanglements of the probe in the tree branches without endangering the safety of the UAV. Conversely, the option of increasing the height of the propulsion system is simpler to be implemented, and it may be advantageous if the plant canopy is a crop canopy, as entanglements are less likely to occur in crops than in tree branches.

Unless expressly stated otherwise, the method steps may be performed in any order.

The brushing may be performed during the steps of dipping and/or extracting the probe. More particularly, the brushing may be obtained as a result of dipping and/or extracting the probe. In fact, the steps of dipping and/or extracting the probe may result in moving (such as lowering/lifting) the probe in the space within the plant canopy such that the probe contacts the plant surface in said space. Depending on the density of the plant canopy, it may be required to dip the probe in a position suitable for contacting the plant surface. However, advantageously, precise positioning of the probe is typically not required, and thus the motion of the probe in the space within the plant canopy may be random.

In embodiments, the brushing may also be performed after the steps of dipping and/or extracting the probe. In fact, the probe may also be moved in the space within the plant canopy by swinging the flexible connection means relative to the propulsion system. In addition, or alternatively, the brushing may be obtained by dragging the probe in a horizontal direction, or a direction having at least a horizontal component, in the space within the plant canopy as explained further below.

The method may comprise moving the propulsion system and/or the control unit may be configured to move the propulsion system in a direction having at least a horizontal component such that the probe is dragged through the plant canopy by the propulsion system moving in said direction. In this manner, the brushing occurs as a result of the dragging, and the sampling material touches as many plant or crop surfaces as possible such that eDNA is aggregated over larger areas. This is particularly advantageous if the plant canopy is a crop canopy. In fact, crops are typically of limited height and cover a large area. Thus, dragging the probe through the crop canopy is a scalable and efficient solution for invasive pest detection in agricultural fields.

As mentioned above, the control unit may be configured to autonomously operate the UAV during eDNA collection. To facilitate this task, the control unit may comprise a sensor system configured to localize the plant canopy. Preferably, the sensor system comprises a GPS module configured to store a waypoint corresponding to the location of the plant canopy. In addition, or alternatively, the sensor system may comprise one or more range sensors configured to optimize the positioning of the UAV with respect to the plant canopy. In this manner, the autonomous operation of the UAV is facilitated.

Preferably, the connection means comprise a cable or, in other words, a tether. In this manner, the probe can be flexibly connected to and spaced out below the propulsion system with minimal weight and complexity.

In addition, or alternatively, the connection means may comprise a beam. The beam is preferably flexible and/or connected to the propulsion system with a flexible joint. In this manner, the flexible joint can accommodate oscillations of the probe due to contact with the plant.

The actuator device may be mounted to a supporting surface of the propulsion system, such as a lower supporting surface or a downwardfacing supporting surface of the propulsion system.

Preferably, the actuator device is a winch and, further preferably, the method comprises and/or the control unit is configured for lowering/lifting the probe relative to the propulsion system by winding/unwinding the cable with the winch. In this manner, the distance of the probe from the propulsion system can be controlled with a high degree of precision.

In embodiments, the UAV comprises a load cell configured to measure the load on the cable and/or the method comprises providing the UAV with a load cell and, preferably, measuring the load on the cable with the load cell. Measuring the load on the cable allows for improving the penetration of the probe into the plant canopy and overcoming entanglements while retracting the probe, as explained further below.

When dipping the probe into the plant canopy, depending on the density of the plant canopy, the probe may happen to rest on some vegetation, thereby reducing the load experienced by the load cell. Preferably, the method comprises and/or the control unit is configured for lifting the probe for a certain distance and lowering it again, if the load measured during the dipping is less than the weight of the probe or less than a first (predefined) threshold. The probe can be lifted and lowered again multiple times to eventually penetrate into the plant canopy. In fact, the lifting and lowering will result in the probe slightly changing its position with respect to the vegetation, thereby increasing the probability of overcoming the obstacle.

If no obstacles are encountered during the descent of the probe into the plant canopy, the weight force acting on the probe is typically sufficient to make the probe penetrate the foliage autonomously, i.e. without the need to actively push the probe.

When extracting the probe from the plant canopy, the probe may become entangled in the vegetation, thereby increasing the load experienced by the load cell. Preferably, the method comprises and/or the control unit is configured for lowering the probe for a certain distance and lifting it again, if the load measured during the extracting exceeds a second (predefined) threshold. The probe can be lowered and lifted multiple times. In fact, as explained above, the lowering and lifting will result in the probe slightly changing its position with respect to the vegetation, thereby increasing the probability of overcoming the obstacle.

In addition, or alternatively, the UAV may comprise cutting means configured to cut the cable and/or the method may comprise providing the UAV with cutting means and cutting the cable with the cutting means if the probe becomes entangled in the plant, e.g., despite the previously described procedure. The cutting means may comprise a metal coil arranged around the cable and configured to melt the cable when current is applied.

Preferably, the probe is provided with a central body hanging from the propulsion system via the connection means, and the sampling material is arranged around the central body. In this manner, the sampling material is optimally exposed to contact with the vegetation.

Preferably, the sampling material is a flexible material. Further preferably, the sampling material is configured to deform and/or the method comprises deforming the sampling material upon contact with the plant surface in the space within the plant canopy. In this manner, the probability of entanglement is reduced, while also increasing the collection area as the sampling material may at least partially wrap around the plant surface.

In embodiments, the arrangement of the flexible sampling material around the central body of the probe is particularly advantageous in preventing entanglement because it allows the sampling material to adhere to the central body when the probe penetrates dense and cluttered environments. Preferably, the sampling material is a flexible sheet material, and preferably stiffening means are provided for reinforcing the sampling material with the stiffening means so that the stiffening means push the sampling material against the plant surface during said brushing. In this manner, brushing the sampling material against leaves and branches exerts a noticeable force to peel off eDNA particles from the environment and retain them on the sampling material.

Preferably, the sampling material is hydrophilic, and the method preferably comprises moistening the sampling material before the brushing. In this manner, the collection of eDNA material during the brushing is increased. The sampling material may be provided with chemically and/or electrically adhesive means so that the eDNA adheres to the sampling material by chemical and/or electrical adhesion during the brushing. These properties enhance the transfer of eDNA and eDNA-containing particles from the surface of the vegetation to the sampling material.

The features and advantages of the invention will be better appreciated from the detailed description of a preferred embodiment thereof, which is illustrated by way of non-limiting example with reference to the appended drawings, in which:

- Figure 1 is a schematic illustration of a UAV dipping a probe into a plant canopy according to the method of the invention;

- Figure 2 is a perspective view of the UAV and probe of Figure 1 according to an embodiment of the invention;

- Figure 3 is a sectional view of a detail of the embodiment of Figure 2;

- Figures 4 and 5 are a perspective view and a side view of the probe of the embodiment of Figure 2 contacting the surface of a plant;

- Figure 6 is a schematic illustration of a UAV dipping a probe into a plant canopy according to a further embodiment of the invention;

- Figure 7 is a perspective view of an embodiment of the UAV and probe of Figure 6 contacting a plant surface;

- Figure 8 is an enlarged view of the probe of Figure 7.

In the Figures, the numeral 1 generally indicates an Unmanned Aerial Vehicle (UAV) for collecting environmental DNA (eDNA) from a space 101 within a plant canopy 100 according to the invention.

The UAV 1 preferably comprises a propulsion system 2, a probe 3, and connection means 4 for hanging the probe 3 to the propulsion system 2.

The propulsion system 2 may comprise one or more propellers driven by electric motors controlled by a control unit 15 and powered by one or more batteries according to various configurations that are per se known in the art. Within the scope of the invention, the propulsion system may however be driven by other types of motors, for instance combustion motors and the energy source provided in the form for instance of liquid fuel. In preferred embodiments, the propulsion system may comprise four propellers, for instance in a rectangular configuration, the propellers being individually controlled, or controlled in pairs, to adjust the roll, yaw, and pitch angles of the UAV for flight and hovering of the UAV.

Preferably the probe 3 hangs from the propulsion system 2 via the connection means 4 so that the probe 3 is arranged in a position below the propulsion system 2. The position of the probe 3 is preferably spaced out from the propulsion system by a vertical distance D. The length of the connection means 4 may be fixed or may be adjustable. Accordingly, the distance D may be fixed, or it may be adjustable.

The connection means 4 may connect the probe 3 to the propulsion system 2 movably between a retracted position in which the probe 3 is proximal to the propulsion system 2 and an extended position in which the probe 3 is distal from the propulsion system 2.

As shown in the example of Figure 1, the UAV 1 may comprise an actuator device 9 configured to selectively extend/ retract the connection means 4 away from and toward the propulsion system 2 so as to advantageously adjust the vertical distance D of the probe 3 from the propulsion system. Preferably, the probe 3 is provided with a sampling material 5 advantageously configured to collect eDNA from a surface by brushing the sampling material 5 against the surface.

Preferably, the method comprises flying the UAV 1 and/or the UAV is configured to fly with the propulsion system 2 at a height H over the plant canopy 100 so that the probe 3 is preferably suspended above the upper level of the plant canopy 100.

The probe 3 is then dipped into the plant canopy 100, in particular by reducing the height H of the propulsion system over the plant canopy and/or by extending the connection means 4 away from the propulsion system 2 into the plant canopy 100 with the actuator device 9 (if present). As a result of dipping the probe 3 into the plant canopy 100, the sampling material 5 is advantageously brushed against a plant surface 102 in the space 101 within the plant canopy 100 so that the sampling material 5 collects eDNA from the plant surface 102 in said space 101, as shown in the examples of Figures 4 or 8. The plant surface 102 may include, for instance, the surface of a crop stem or a tree trunk, a piece of bark, a branch, a flower or a leaf.

The method and/or UAV configuration may further include extracting the probe 3 from the plant canopy 100, in particular by increasing the height H of the propulsion system over the plant canopy and/or by retracting the connection means 4 away from the plant canopy toward the propulsion system 2 with the actuator device 9. Extracting the probe 3 from the plant canopy may result in further brushing of the probe 3 against the plant surface and therefore further collection of eDNA. The UAV 1 with the propulsion system 2 may hover over the plant canopy 100 while dipping/extracting the probe 3 and/or brushing the sampling material 5. In this manner, the propulsion system 2 maintains a safe distance from the plant canopy.

In embodiments, the method and/or UAV configuration may also comprise moving the propulsion system 2 in a forward direction F over the plant canopy 100 such that the probe 3 is dragged through the plant canopy by the propulsion system 2 moving in the forward direction F, as shown in the example of Figure 6. The forward direction F may be horizontal or have at least a horizontal component. The step of dragging is preferred if the plant canopy 100 is a crop canopy and can be particularly advantageous for detecting invasive pest insects within an agricultural ecosystem.

The eDNA collection may be performed by teleoperating the UAV 1 or, preferably, it may be performed autonomously by the UAV 1, thereby providing a scalable solution. To this effect, the UAV 1 is structurally and functionally configured as follows.

The UAV may comprise a control unit 15 configured to control the propulsion system 2 so that the UAV flies with the propulsion system at a height H over the plant canopy, reduces its height H over the plant canopy so as to dip the probe 3 into the plant canopy and brush the sampling material 5 against a plant surface in the space within the plant canopy so that the sampling material 5 collects eDNA from the plant surface in said space.

In embodiments, the UAV may comprise an actuator device 9 for extending the connection means 4 away from the propulsion system 2. In such case, the control unit 15 may be further configured to control the actuator device 9 so that the actuator device 9 extends the connection means 4 away from the propulsion system 2 toward the plant canopy, so as to dip the probe 3 into the plant canopy and brush the sampling material 5 against a plant surface in the space within the plant canopy so that the sampling material 5 collects eDNA from the plant surface in said space.

The control unit 15 may be further configured to control the propulsion system 2 and/or the actuator device 9 (if present) to extract the probe 3 from the plant canopy.

Advantageously, the control unit 15 is configured to perform the aforementioned operations in an autonomous manner. To facilitate this task, the control unit 15 may comprise a sensor system. Preferably, the sensor system comprises a GPS module by which the control unit 15 can control the propulsion system 2 so as to reach a certain waypoint. The control unit 15 may be further configured to control the propulsion system 2 and/or the actuator device 9 (if present) to lower the probe 3 once the waypoint has been reached.

Further sensors can be used to optimize the positioning of the UAV with respect to the plant canopy. For example, the sensor system may comprise a downward-facing camera and/or a LIDAR, to detect the plant canopy and thus assist the control unit 15 to align the UAV with respect to the plant canopy. In addition, or alternatively, the sensor system may comprise one or more range sensors (e.g., ultrasonic sensors, stereo cameras, LIDAR) configured to detect the height H of the propulsion system 2 over the plant canopy and assist the control unit 15 to adjust said height. The connection means 4 are preferably connected below the propulsion system 2. Further preferably, the connection means 4 are flexible, i.e., they comprise at least a flexible portion. In embodiments, the connection means 4 may comprise a cable 6 as shown in the example of Figure 2 and/or a beam 7 as shown in the example of Figure 7. Preferably, the beam 7 is flexible and/or connected to the propulsion system 2 with a flexible joint 8.

The actuator device 9, if present, is preferably attached below the propulsion system 2 and may comprise a winch 14, as shown in examples of Figures 2 and 3. The winch 14 may be configured to wind/unwind the cable 6 so as to lower/lift the probe 3 relative to the propulsion system 2. The UAV 1 may be further provided with the control unit 15 configured to drive the actuator device 9, more particularly the winch 14, to selectively lift/lower the probe 3.

In embodiments, the UAV 1 comprises a load cell 10 configured to measure the load on the cable 6. The load cell 10 may be operatively coupled to the control unit 15. The control unit 15 may be configured to lift the probe 3 for a certain distance and lower it again, if the load measured while lowering the probe is less than the weight of the probe 6 or less than a first threshold. In addition, or alternatively, the control unit 15 may be configured to lower the probe 3 for a certain distance and lift it again, if the load measured while lifting the probe exceeds a second threshold. Lifting/lowering the probe 3 is preferably performed by driving the actuator device 9, more particularly the winch 14, with the control unit 15.

In embodiments, the UAV 1 is provided with cutting means 11 configured to cut the cable 6 if the probe 3 becomes entangled in the plant canopy or if the load measured by the load cell 10 exceeds a certain threshold.

The cutting means 11 may comprise a wire configured to contact the cable 6 and means for supplying electric current to the wire so that the wire heats up to melt the cable 6.

In embodiments, the probe 3 may comprise a central body 12 around which the sampling material 5 is arranged so as to be optimally exposed to contact with the vegetation. The connection means 4 may be attached to the central body 12.

Preferably, the shape of the central body 12 is elongated or streamlined along an axis X so as to reduce entanglement in the vegetation. Such a shape may define two opposite longitudinal ends 12a, 12b between which the central body 12 is elongated or streamlined. The connection means 4 may be attached to one of the longitudinal ends 12a, 12b so that the central body 12 is vertically arranged when hanging from the connection means 4, thereby facilitating the penetration of the probe 3 into the vegetation.

As shown in the example of Figure 4, the sampling material 5 may be shaped as a disc. The disc-shaped sampling material 5 may extend radially from the axis X of central body and may be arranged on a plane which is transverse to the central body 12. This design facilitates penetration into tree canopies and eDNA sampling from tree branches.

As shown in the example of Figure 6, the sampling material 5 may comprise a plurality of bristles 51 extending away from the central body 12 and preferably surrounding the central body 12. As shown in the example of Figure 8, the sampling material 5 may comprise a plurality of separate portions 50 arranged at a certain angular distance from each other around the axis X of the central body. The separate portions 50 may be arranged on planes passing through the axis X of the central body. In this manner, vertical stems of vegetation can be received in the space available between the separate portions 50.

The central body 12 may be made of a material heavier than the sampling material 5 so that the sampling material 5 is dragged vertically through the vegetation by the weight of the central body 12. As shown in the example of Figure 5, the weight distribution in the probe 3 may be such that the centre of gravity G of the probe is located between the longitudinal end 12a or 12b to which the connection means 4 are attached and the portion of the central body 12 to which the sampling material 5 is attached. This weight distribution further reduces entanglement in the vegetation. Preferably, the sampling material 5 is a flexible material, more particularly a flexible sheet material, such as synthetic fleece or cotton gauze. The method may comprise deforming the sampling material 5 upon contact with the plant surface 102 so that the sampling material 5 at least partially conforms to the plant surface 102. Such deformation is shown for example in Figures 4 and 5 where the surface 102 may be the bark of a tree branch, and in Figure 8 where the surface 102 may be the stem of a crop. The flexibility contributes to avoiding entanglement. In addition, the collection area may be increased by at least partially wrapping the flexible sampling material 5 around tree branches or crops.

As shown in the example of Figure 4, the probe 3 may further comprise stiffening means 13 for reinforcing the sampling material 5. The stiffening means 13 may be configured to push the sampling material 5 against the plant surface 102 during the brushing to increase the swabbing action thus facilitating the collection of eDNA.

Before deployment of the probe 3, the sampling material 5 is preferably sterile or DNA-free. To this effect, the method may comprise sterilizing the sampling material 5 before deployment of the probe 3.

The sampling material 5 may be provided with chemically and/or electrically adhesive means so that the eDNA adheres to the sampling material 5 by chemical and/or electrical adhesion during the brushing. For this purpose, the sampling material 5 may comprise an adhesive tape and/or may be electrostatically charged.

In embodiments, the sampling material 5 may be hydrophilic and moistened. This increases the collection of eDNA material. The moistening can be done with water, more particularly deionized water (DNA-free), or with a solution of water and DNA-free sugar. In fact, water facilitates the transfer of eDNA from dry substrates, whereas sugar adds an adhesive action to the sampling material 5.

Possible applications of the invention include biodiversity monitoring in (rain)forests and invasive species detection in agriculture. To this effect, the eDNA collected from the space within the plant canopy may advantageously be extracted and sequenced so as to identify any relevant species. The invention thus solves the proposed problem, achieving numerous advantages, such as allowing for autonomous, scalable eDNA sampling even in challenging environments, and allowing for biodiversity monitoring or invasive species detection in previously inaccessible locations and at industrially applicable temporal and spatial scales.

References:

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Claims

1. Method for collecting environmental DNA from a space (101) within a plant canopy (100), the method comprising:

- providing a UAV (1) comprising a propulsion system (2) and a probe (3) hanging from the propulsion system (2) via flexible connection means (4);

- providing the probe (3) with a sampling material (5) configured to collect environmental DNA from a surface by brushing the sampling material (5) against the surface;

- flying the UAV (1) with the propulsion system (2) at a height (H) over the plant canopy (100);

- dipping the probe (3) into the plant canopy (100) by reducing the height (H) of the propulsion system (2) over the plant canopy and/or by providing the UAV (1) with an actuator device (9) and extending the connection means (4) away from the propulsion system (2) toward the plant canopy with the actuator device (9);

- moving the propulsion system (2) in a direction (F) having at least a horizontal component such that the probe (3) is dragged through the plant canopy by the propulsion system (2) moving in said direction (F) and, as a result of the dragging, brushing the sampling material (5) against a plant surface (102) in the space (101) within the plant canopy (100) so that the sampling material (5) collects environmental DNA from the plant surface (102) in said space (101);

- extracting the probe (3) from the plant canopy (100).

2. Method according to claim 1, wherein extracting the probe (3) from the plant canopy (100) is performed by increasing the height (H) of the propulsion system (2) over the plant canopy and/or by retracting the connection means (4) away from the plant canopy toward the propulsion system (2) with the actuator device (9).

3. Method according to claim 1 or 2, wherein the plant canopy (100) is a crop canopy.

4. Method according to any one of the preceding claims, wherein the flexible connection means (4) comprise a cable (6) and/or a beam (7), wherein the beam (7) is flexible and/or connected to the propulsion system (2) with a flexible joint (8).

5. Method according to claim 4, wherein the actuator device (9) comprises a winch (14), the method comprising lowering/lifting the probe (3) relative to the propulsion system (2) by winding/unwinding the cable (6) with the winch (14).

6. Method according to claim 5, comprising providing the UAV (1) with a load cell (10), measuring the load on the cable (6) with the load cell (10), lifting the probe (3) for a certain distance and lowering it again if the load measured during the dipping is less than the weight of the probe (6) or less than a first threshold, and/or lowering the probe (3) for a certain distance and lifting it again if the load measured during the extracting exceeds a second threshold.

7. Method according to any one of claims 4 to 6, comprising providing the UAV (1) with cutting means (11) and cutting the cable (6) with the cutting means (11) if the probe (3) becomes entangled in the plant canopy (100).

8. Method according to any one of the previous claims, comprising providing the probe (3) with a central body (12), hanging the central body (12) to the propulsion system (2) via the flexible connection means (4), and arranging the sampling material (5) around the central body (12).

9. Method according to any one of the previous claims, wherein the sampling material (5) is a flexible material, and the method comprises deforming the sampling material (5) upon contact with the plant surface (102) in the space (101) within the plant canopy.

10. Method according to claim 9, wherein the sampling material (5) is a flexible sheet material, and the method comprises providing stiffening means (13) and reinforcing the sampling material (5) with the stiffening means (13) so that the stiffening means push the sampling material (5) against the plant surface (102) during said brushing.

11. Method according to any one of the previous claims, wherein the sampling material (5) is hydrophilic, and the method comprises moistening the sampling material (5) before said brushing.

12. Method according to any one of the previous claims, comprising providing the sampling material (5) with chemically and/or electrically adhesive means so that the environmental DNA adheres to the sampling material (5) by chemical and/or electrical adhesion during said brushing.

13. Method for monitoring biodiversity comprising collecting environmental DNA from a space (101) within a plant canopy (100) according to the method of any one of the previous claims and sequencing the collected environmental DNA to identify organisms from said space (101).

14. UAV (1) for collecting environmental DNA from a space (101) within a plant canopy (100), the UAV comprising:

- a propulsion system (2);

- a probe (3) comprising a sampling material (5) configured to collect environmental DNA from a surface by brushing the sampling material (5) against the surface;

- flexible connection means (4) by which the probe (3) hangs from the propulsion system (2);

- a control unit (15) configured to control the propulsion system (2) so that the UAV flies with the propulsion system at a height (H) over the plant canopy (100), the control unit (15) being further configured to control the propulsion system (2) so that the propulsion system reduces its height (H) over the plant canopy and/or to control an actuator device (9) of the UAV so that the actuator device (9) extends the connection means (4) away from the propulsion system (2) toward the plant canopy, so as to dip the probe (3) into the plant canopy, the control unit (15) being further configured to move the propulsion system (2) in a direction (F) having at least a horizontal component such that the probe (3) is dragged through the plant canopy by the propulsion system (2) moving in said direction (F), so as to brush the sampling material (5) against a plant surface (102) in the space within the plant canopy so that the sampling material (5) collects environmental DNA from the plant surface (102) in said space (101), the control unit (15) being further configured to control the propulsion system (2) and/or the actuator device (9) to extract the probe (3) from the plant canopy.