LLBN carbon-biodiversity project

KEY DETAILS

PI: Dr. Matthew Rogan
Date; 4 November 2024
Version; v0.4.0
Programme; Rangelands Biodiversity Project (RBP)
Study Site; Lewa-Lolldaiga-Borana-Ngare Ndare (LLBN)
Key partners; Leverhulme Center for Nature Recovery, University of Liverpool
Contact email; mrogan@naturalstate.org

1. PREAMBLE

Natural State’s objectives and activities are detailed by a set of accepted Standard Operating Procedures (SOPs). These documents describe the steps involved in all Natural State projects, from data collection to data processing and storage. Each SOP documents key project details and provides methodological details specific to the project. The objectives and background of the project, features of the study area, and details on survey and sampling design may be found in the project Design Document (DD) which is available in the Related Documents section below.

1.1 SOP PURPOSE

To provide a clear step by step guide to the methods implemented in the project, therefore allowing for consistency in data collection and repeatability of all steps involved in a project’s data collection, processing and storage. This is crucial to Natural State’s mission of facilitating nature restoration at scale by using the latest technology and methods to revolutionise impact monitoring for carbon, biodiversity and human well-being.

1.2 SOP SCOPE

This document details how this project will be implemented. All methodological steps are explained, and the principal team members overseeing the project are listed in case further clarification is required. It also further directs readers to where they can find additional information relevant to the project. This document is intended to be printed out and taken to the field for reference sake.

2. GLOSSARY

BACI: Before-After Control-Impact survey design
Camera-trap: A remote camera with a defined automatic trigger (e.g., motion, time-lapse)
Centroid: A point at the center of a corresponding sampling grid cell denoted by a geohash, a longitude coordinate, and a latitude. Here, the centroid of the CPP.
CPP: Carbon Pool Plot. A 50m X 50m sampling site within which NS measures aboveground and belowground carbon stocks.
Deployment: The period of time a single remote sensor is active within the environment at a single, defined station as part of a survey.
Deployment Group: Temporally distinct sets of geographically or thematically grouped and contemporaneous (e.g., seasonal deployment groups).
Exclosure: A defined area fenced for the purposes of preventing some species of wild animals from accessing the area.
GEM: Global Ecological Monitoring. A global biological research project to measure ecological processes.
A 50m X 50m sampling site within which NS measures aboveground and belowground carbon stocks and rates of carbon cycling.
Project: A concerted, data-driven effort to robustly measure variation in Biodiversity, Carbon, or Human-wellbeing in response to one or more sources of heterogeneity in a designated landscape.
Remote Sensor: An electronic sensor with automated data collecting capabilities that operate independently of a human handler.
S123: Survey123, a field-data collection app from ESRI which NS uses for recording all field observations and survey metadata.
Sampling Protocol: Explicit survey methodology that describes the design, effort, duration, configuration, and operation of a camera-trap survey.
Station: A point location where sampling occurs in space.
Study Area: A defined geographic region of interest within which one or more surveys investigate ecological patterns at one or more sites.
Survey: A set of simultaneous deployments of remote sensors over a defined period of time at a coordinated set of stations for the purposes of collecting data on the environment and its communities.

3. PROJECT OVERVIEW

3.1 PROJECT AIMS

The Rangelands Carbon-Biodiversity project aims to:

Identify correlations between vertebrate diversity and carbon stocks.
Measure the effect of vegetation structure on vertebrate diversity.
Provide robust measures of grazing and browsing activity as predictors of carbon stocks.

3.2 PROJECT BACKGROUND

Natural State’s mission is to restore African landscapes with benefits for carbon, biodiversity and human wellbeing. To maximize outcomes for all three streams, we must understand how the three streams relate to each other. The Rangelands Carbon-Biodiversity Project is designed to robustly investigate the relationship between above- and belowground carbon stocks and biodiversity through intensive sampling of biodiversity where carbon stocks are measured. This research will provide invaluable context for understanding patterns in both carbon and biodiversity. The primary objective of the Rangelands Carbon-Biodiversity survey (hereafter ‘the survey’) is to measure mammal and bird diversity, local (relative) abundance, and relative intensity of use of sites where we have precise information on soil conditions, vegetation structure, invertebrate activity, and above-ground carbon stocks. The data collected will provide insights into the relationship between vertebrate activity and carbon stocks and provide more precise measures of grazing activity to inform long-term monitoring of carbon stocks. Additionally, the data will be used for integrated modeling of plant diversity, soil conditions, and vertebrate populations. The survey can be considered open-ended in the sense that it can be replicated wherever carbon sampling occurs and camera-trap or bioacoustic monitoring is feasible.

3.3 STUDY AREA

The Carbon-Biodiversity Survey will be conducted across Lewa, Borana, and Ngare-Ndare forest conservancies with an emphasis on sampling the full range of management conditions within the three properties. This includes sampling inside and outside mammal exclosures, within intact and degraded forest patches, and across the full range of livestock management practices (no livestock, sparse livestock, intensive livestock, and regenerative grazing).

3.4 DEPLOYMENT GROUPS

Due to the large number of CPPs and limited equipment and logistical, sampling for the Carbon-Biodiversity Survey will be split into 8-12 deployment groups. Four deployment groups will be defined as seasonal sampling (2 X wet season and 2 X long dry season) at GEM plots. The remaining 4-8 will consist of geographical clusters by property and by CPP phase. Each deployment group consists of ~20 CPPs.

Deployment groups in Ngare-Ndare and Makurian will consist of audiomoths only. No cameras will be deployed. In Makurian, deployments should only occur at sites where a community member can be hired to safeguard the device.

3.5 PROJECT TIMELINE

Approximate timeline for deployment groups:

Q1 2024

Lolldaiga Phase I CPP sites
Borana Phase I CPP sites
BACI CPP sites

Q2 2024

Lewa Phase I CPP Sites

Q3-Q4 2024

GEM continuous sampling

2025

GEM continuous sampling
Ngare-Ndare (unconfirmed)

4. SAMPLING PREPARATION

The equipment mentioned in the list below needs to be gathered, checked and packed before fieldwork begins. If any sensors need to be configured prior to commencing fieldwork this will be documented below the equipment list.

4.1 EQUIPMENT LIST

Camera traps - Browning Elite HP5. Cameras must be up-to-date with the latest firmware. Each camera must be tagged with a QR code for scanning into S123.
Audiomoths up-to-date with the latest firmware and tagged with a QR code.
Fully charged Eneloop Pro Rechargeable batteries (for Browning cameras, audiomoths, and GPS)
Audiomoth Cases
Handheld GPS with coordinates of prospective sites
SD cards (minimum 64 GB) for Browning Cameras. Each SD card must be tagged with a QR code for scanning into S123.
MicroSD cards (minimum 32 GB, preferably 64 GB) for Audiomoths. Each MicroSD card must be tagged with a QR code for scanning into S123.
Straps and cables for securing cameras.
Straps for securing audiomoths.
Tablet with S123
Charging cable for tablet
Powerbank
Poles for attaching camera traps to
Slashers for clearing vegetation
A mallet.
Spare cameras, batteries, SD cards, and MicroSD cards.
Water and a medical kit in the vehicle.

4.2 DEVICE CONFIGURATION

All devices must be programmed to have their date and time in UTC.

Browning Elite HP5 Configuration Settings Only Browning cameras will be used for the Carbon-Biodviersity Survey. Cameras should be programmed in the field.

Setting	Selection
Operation Mode	Trail Cam
Photo Quality	Low (4 MP)
Photo Delay	5 Secs
Multishot Mode	Off
HDR	On
Temp Units	Celsius
Image data strip	Off
Motion Detection	Normal Range (60 ft)
Battery Type	NIMH
Trigger Speed	Normal (0.7 Seconds)
IR Flash Power	Blur Reduction

AudioMoth Configuration Settings

See the AudioMoth Standard Operating Procedures for all configuration settings.

5. SAMPLING PROCEDURES

Each site (i.e., CPP) in the Carbon-Biodiversity Survey will be sampled with two camera-traps and one AudioMoth, unless the site is within a community area (Ngare Ndare or Makurian) in which case sites will be sampled with one AudioMoth only.

Sampling for each sub-survey should generally follow standard NS protocols for passive recorders. All recorders should operate for a minimum of 28 days but at GEM plots, sampling will extend beyond the 28-day window to provide richer datasets. In particular, the duration of rainy season sampling will depend heavily on rainfall patterns.

All recorders (cameras and audiomoths) should be powered by rechargeable eneloop batteries. Batteries should be replaced, devices checked, and data downloaded from all three recorders every two weeks.

Below is a figure illustrating the layout of a carbon pool plot with reference point labels.

5.1 CAMERA-TRAPPING

Camera Placement

One camera will be deployed at or near the northern midpoint (F1M304) and another at the southern midpoint (F1M1-2). Cameras at the northern midpoint (F1M3-4) should face south and cameras at the southern midpoint (F1M1-2) should face north such that both cameras are facing the cell centroid.

At GEM plots, the cameras should be placed at least one meter inside the plot so that they are not affected by the 1m X 1m quadrats within the woody debris transect.

If the field of view at either midpoint is obstructed, the field team should move the camera to the closest location inside the carbon plot where the field of view towards the interior of the plot is clear. Cameras at GEM plots should be set above the height of the grass up to 2m above the ground. At sites where the grass is more than 60 cm tall, the cameras may be angled slightly downward to facilitate detection of small animals. In such cases, the maximum detection distance should be adjusted to reflect the reduced detection range of the camera.

Cameras at non-GEM plots should be placed on trees or poles driven into the ground at a height of 45-55 cm between the ground and the motion sensor and angled parallel to the slope of the terrain. Vegetation may be cleared after vegetation surveys are completed at a distance of up to 15 m from the camera.

Camera Setup

Once a tree is selected or a pole is driven into the ground, select a camera and scan the barcode into S123. Choose and SD card and scan its barcode before inserting into the camera. Insert a full complement of 8 fully charged Eneloop Pro batteries.

The person recording the camera metadata in S123 is responsible for ensuring the configuation settings are correct. First navigate to camera setup mode and then ensure that the date is correct and that the time is set to UTC (i.e., 3 hrs prior to EAT). Then delete all images (if using a Solaris camera, choose the format option). Ensure that each of the settings listed above are correct. Video settings do not need to be checked or changed. The camera name should be edited to the station label as designated in the GPX file of prospective sites.

Record details of the camera deployment in S123. The recorder must be standing within 1 m of the camera to ensure that he location is recorded accurately. Run the test setting on the camera to ensure the camera is functioning properly and angled to maximize detections. In S123, detection distance should be specified as the lesser distance of i) the maximum detection distance determined during device testing (e.g., 18 m for Browning cameras on normal detection) and ii) the maximum feasible detection distance given the angle of the camera and the configuration of the site. Cameras should be recorded as type ‘fixed’.

Set the camera to its normal operating setting and, when the site setup is complete and all metadata have been collected, turn the camera on and record a photo of the white board with the station label, date and time info.

After setting a camera, confirm all steps in the camera deployment checklist have been followed:

Confirm the camera’s ssettings were checked.
Confirm the camera’s date and time were correct and recorded in UTC.
Confirm the empty SD card was inserted into the camera after its barcode was scanned.
Confirm a full complement of batteries.
Check all appropriate fields have been filled in Survey123
Confirm the recorded settings in S123 match the settings programmed in the camera.
Confirm the station is correctly recorded as type ‘fixed’ or ‘float’.
Confirm all features the camera is covering have been recorded.
Confirm the camera was set at the correct height and at a suitable angle and orientation.
Confirm the camera has been turned on.
Confirm the camera’s detector has been tested at a distance up to 5 m.
Confirm all necessary vegetation has been cleared without interfering with carbon sampling.
Confirm the camera is secure.
Confirm the camera recorded a photo of the white board with the sampling point ID and the date and time.
Confirm all equipment and other items have been collected.

When returning to the office, one team member is responsible for checking the deployments in S123 to ensure that the locations were captured correctly.

Report any challenges or issues to the PI or project officer.

Camera Check

Check the deployment coordinates on S123 prior to departing the office and ensure the exact station coordinates are loaded into a handheld GPS (do not rely on the coordinates of the prospective sites from the survey design). Ensure that all equipment including spare cameras and a full set of replacement batteries and SD cards is in the vehicle.

When approaching a camera, first allow it to take a picture to determine if it was still operational then check the battery and turn the camera off and scan the camera into S123. Next, check the number of photos recorded on the camera. If the camera recorded very few photos or more than 2000 photos, try to determine why so few or so many photos were recorded. Scan at least a few of the triggers to ensure data quality was sufficient and the field of view was appropriate for maximizing detections. If the camera was knocked down or interfered with by animals such that it was no longer collecting valid data, look through the photos to determine when the camera stopped operating properly. If the camera was operational for less than one week, make a note that the site needs additional sampling to meet minimum data requirements.

As a team, determine what, if any steps need to be conducted to maintain data quality. Trim any vegetation as necessary and record the activity in S123. Move the camera if its previous position appears unconducive to recording high quality data. Replace batteries and SD card and scan the new SD card. Place the old SD card in a clearly marked bag. Record other details in S123 or redeploy the camera as needed. Recheck the date, time, and camera configuration settings are correct.

Set the camera to its normal operating setting and record a photo of the white board with the station label, date and time info.

After checking a camera, confirm all steps in the camera check checklist have been followed:

Confirm batteries were replaced and the camera has a proper charge.
Confirm the SD card was replaced and the new card was scanned.
Confirm vegetation was trimmed as needed.
Confirm all metadata has been captured in S123.
Confirm the camera is secure.
Confirm the camera is at the correct height and parallel to the ground.
Confirm he camera recorded a photo of the white board with the sampling point ID and the date and time.
Confirm all equipment and other items have been collected.

Camera Retrieval

Check the deployment coordinates on S123 prior to departing the office and ensure the exact station coordinates are loaded into a handheld GPS.

When approaching a camera, first allow it to take a picture to determine if it was still operational then check the battery and turn the camera off and scan the camera into S123. Check the number of photos recorded on the camera. If the camera recorded very few photos or more than 2000 photos, try to determine why so few or so many photos were recorded. Scan at least a few of the triggers to ensure data quality was sufficient and the field of view was appropriate for maximizing detections. If that was not the case, or if the camera was knocked down or otherwise interfered with such that it recorded less than one week of valid data, record the activity as a camera check and follow the protocols outlined above. If the site has recorded at least 21 days of valid data, capture all metadata in S123, collect all equipment and check the site for any equipment or other items that may be left behind.

5.2 BIOACOUSTIC RECORDING

Acoustic Monitor Placement

In general, AudioMoths must be placed within the CP plot as far from any sources of ambient noise as possible. If no ambient noise is present, then the AM should be placed in whatever vegetation seems most appropriate. All else being equal, it is better to put AudioMoths nearer the centroid of the plot than the edge. AudioMoths should be recorded in S123 as type ‘Fixed’. At Ngare-Ndare Forest carbon pool plots, AudioMoths should be positioned so that they are as inconspicuous and hidden as possible without inhibiting data collection.

AudioMoths should be firmly attached to the tree or pole with their velcro strap such that the device is 1.5-2 m above the ground and the microphone hole is angled parallel to the slope of the terrain. When placing AudioMoths along tourist roads, emphasis should be put on using trees.

Record details of the AudioMoth deployment in S123. Ensure the location is recorded within 2 m of the AudioMoth.

Speak clearly near the AudioMoth to record the date, time, and grid ID (preferably use the geohash ID and not the label).

After setting up an AudioMoth, confirm all steps in the AudioMoth deployment checklist have been followed:

Confirm the AudioMoth is deployed within the carbon plot as far as possible from any sources of ambient noise and otherwise as close to the centroid as is feasible.
Confirm all appropriate fields in Survey123 have been filled.
Confirm the AudioMoth has a fresh battery (hint. Check the battery level on the configure AudioMoth app).
Confirm the AudioMoth has an empty SD card.
Ensure the AudioMoth has been programmed to sample for 20 hrs per day at a sampling rate of 32 khz and medium-low gain.
Confirm the recorded settings in Survey123 match the settings programmed in the camera.
Confirm AudioMoth sampling periods were set using the correct timezone.
Confirm the recording duration is less than 3600.
Confirm the AudioMoth ID was recorded correctly.
Confirm the microSD card ID was recorded correctly.
Confirm the AudioMoth is secure.
Confirm all features the AudioMoth is covering have been recorded.
Confirm the AudioMoth is on.
Speak near the AudioMoth to record the date, time, and CPP ID (preferably use the geohash ID and not the label).

When returning to the office, one team member is responsible for checking the deployments in S123 to ensure that the locations were captured correctly.

Report any challenges or issues to the PI or project officer.

Acoustic Monitor Check

Check the deployment coordinates on S123 prior to departing the office and ensure the exact station coordinates are loaded into a handheld GPS. Ensure that all equipment including spare AudioMoths and a full set of replacement batteries and SD cards are in the vehicle.

Approach the AudioMoth, undo to velcro to remove it from the tree of pole on which it was deployed and open the plastic casing. Check to see if there is a green light flashing on the side where you inserted the microSD card. If it is flashing both green and red, there is an error, and you will have to go back to your computer to reprogram. If there are no lights shining then the AudioMoth has run out of battery power. Scan the AudioMoth into S123. As a team, determine what, if any steps need to be conducted. Switch the AudioMoth off. Replace batteries and SD card and scan the new SD card. Place the old SD card in a clearly marked bag. Record details in S123 and redeploy the AudioMoth.

Set the AudioMoth to to its normal operating setting by switching the mode from USB/Off to Custom. Speak clearly near the AudioMoth to record the date, time, and grid ID (preferably use the geohash ID and not the label).

After checking an AudioMoth, confirm all steps in the AudioMoth check checklist have been followed:

Confirm batteries were replaced and the AudioMoth has proper charge.
Confirm the SD card was replaced and the new card was scanned.
Confirm all metadata has been captured in S123.
Confirm the AudioMoth is at the correct height and parallel to the ground.
Confirm the AudioMoth is secure.
Confirm someone spoke near the AudioMoth to record the date, time, and grid ID (preferably use the geohash ID and not the label).
Confirm all equipment and other items have been collected.

Acoustic Monitor Retrieval

Check the deployment coordinates on S123 prior to departing the office and ensure the exact station coordinates are loaded into a handheld GPS.

Undo velcro to remove the AudioMoth from the tree. Turn the AudioMoth off and scan the Audiomoth into S123. Capture all metadata in S123 and check the site for any equipment or other items that may be left behind.

6. POST PROCESSING

==XXX==

6.1 SAMPLE PROCESSING AND STORAGE

The Carbon-Biodiversity survey does not involve collecting any samples.

6.2 DATA ENTRY AND UPLOADS

Data should be uploaded to Azure Cloud Storage and backed up to a local harddrive within 48 hours of collection. The airtable field schedule should be updated to reflect the progress in the field work schedule.

In the case of camera trap data, one person from the field team should be designated to scan through images from each camera and ensure that the collected data exceed minimum data quality standards of at least 7 days. Minimum data quality standards are defined as i) the camera was opertional, ii) the camera was positioned such that it had a reasonable chance of detecting animals within at least 5 m, and iii) the camera yielded sufficiently clear images to allow species identification. Examples of sub-standard data include cameras that were operational for less than one week, cameras that were so obscured by grass or other vegetation that they could not detect animals, cameras that were positioned such that they had a detection distance of less than 5 m, or cases where dirt or moisture obscured the camera lens or flash resulting in more quality, unidentifiable images.

If the data quality was minimum standards, the field team lead should be notified and the airtable field schedule should be updated to reflect the need for additional monitoring at the site.

7.1 DESIGN DOCUMENT

7.2 OTHER RELEVANT SOPS

Passive Acoustic Monitoring Camera Trapping

7.3 DATA ELEMENTS

Survey Design

Data Collection

8. REVISION AND VERSION HISTORY AND DESCRIPTION

v0.1.0 Initial operating procedure.

v0.1.1 Minor updates for clarity. Protocol used for Lolldaiga Phase I CPP deployments. Specified time set in local timezone (UTC+3), not UTC.

v0.2.0 Updates to camera and audiomoth configuration settings including switching to programming sensors in UTC. Effective from date of SOP revision.

v0.3.0 Updated to ensure more rigorous quality control and to necessesitate additional monitoring at sites with poor quality data. Additional edits for clarity.

v0.4.0 Updated 2025 sampling plan and referenced all audiomoth configurations to Passive Acoustic Monitoring SOP.

9. SIGNATURES OF CONFIRMATION

Principal Investigator: ______________ Date: ___________

Director of Impact Insights: ____________ Date: ___________

10. APPENDICES

None currently available