DOI: 10.5061/dryad.x69p8czvd
title: Nematode community dynamics in Johnson Su compost

description: Characterising microscopic communities is important for both ecological
 research and diagnostic applications. In these areas, light microscopy is
 still a fundamental tool due to its accessibility and real-time imaging
 capabilities. However, the higher magnifications required for accurate
 identifications typically necessitates extensive sample preparation.
 Therefore, this study aimed to design and validate a bright field light
 microscopy-based platform with magnification up to 1000x without the need
 for extensive sample preparation. An adapted version of the
 Peter’s slide was developed, which allows the use of specialised
 long-working distance objectives without the need for oil immersion. Image
 quality at higher magnifications were evaluated using nematodes as test
 organisms. Additionally, the use of the adapted Peter’s slide in
 characterising microscopic communities was evaluated by studying the
 temporal dynamics in nematode functional diversity from Johnson Su
 compost. The adapted Peter’s slide facilitated the identification
 and counting of nematodes to genus level, demonstrating sufficient image
 clarity even at 1000x magnification. My results confirmed that this
 platform overcomes the limitations of standard approaches by eliminating
 the need for extensive sample preparation and mounting on microscope
 slides, which are typically required for high-magnification
 observations. This platform reduces sample processing time, while
 also facilitating live viewing under high magnification. These features
 also make it a valuable educational tool in classroom settings. Future
 enhancements could include the integration of AI-based imaging software to
 automate and refine identification and counting processes. However, a
 current limitation is the cost of the long-working objectives, which may
 limit widespread adoption.
description: To validate the adapted Peter’s slide and microscope setup as a
 platform for characterising microscopic communities, the temporal changes
 in nematode functional diversity within Johnson Su composting were
 investigated. This static composting method does not involve any turning
 after startup and aeration is facilitated via vertical shafts in the
 compost reactor. Six Johnson Su compost reactors serving as replicates
 were constructed and maintained following Johnson and DeSimio (2017). The
 feedstock material consisted of 60% dried grass, 30% wood shavings, and
 10% horse manure. Compost samples were collected at three intervals,
 namely the 1<sup>st</sup>, 3<sup>rd</sup>, and
 5<sup>th</sup> months after startup. Using a 20cm stainless
 steel corer (5 cm diameter) attached to a battery drill, five randomly
 located cores were extracted per reactor per interval and homogenised to
 acquire one composite sample. From each composite sample, nematodes were
 extracted from 200 ml of compost using the decanting and sieving followed
 by the sugar centrifugal flotation methods (Marais et al., 2017). The
 nematodes were heat killed and fixed using hot/cold 6% formaldehyde
 solutions (final sample concentration of 4% formaldehyde) (Van Bezooijen,
 2006). Prior to counting, each nematode community
 sample was rinsed with clean water using a 20 µm sieve to remove the
 carcinogenic formaldehyde. The nematodes were transferred to sample
 bottles with a final sample volume of 20 ml. Before counting, each sample
 was vigorously shaken to suspend and homogenise the nematode community.
 Without delay, a 1 ml aliquot was abstracted and transferred to the
 adapted Peter’s slide. All the nematodes in the 1 ml aliquot were
 identified and counted using the described microscope setup. The number of
 nematodes per taxon per 1 ml aliquot were extrapolated to the total volume
 (20 ml) of the original sample.
description: # Nematode community dynamics in Johnson Su compost
 [https://doi.org/10.5061/dryad.x69p8czvd](https://doi.org/10.5061/dryad.x69p8czvd) ## Description of the data and file structure This dataset contains data from an experiment investigating the temporal changes in nematode functional diversity within Johnson Su compost reactors. The compost reactors were constructed and maintained following Johnson and DeSimio (2017), with feedstock comprising dried grass, wood shavings, and horse manure. Sampling occurred at three intervals: the 1st, 3rd, and 5th months after startup. Nematodes were extracted, fixed, and quantified as described in the experimental methods. ### Files and variables #### File: Nematode\_community\_dynamics\_in\_Johnson\_Su\_composting.xlsx **Description:** Temporal dynamics of nematode communities in Johnson Su composting. The dataset includes the following key variables: ##### Variables * **Interval**: Sampling interval (1, 2, or 3). * **Compost reactor**: Identifier for each of the six replicate Johnson Su compost reactors. * **Taxon**: Nematode taxa identified in the aliquots. * **Abundance**: The extrapolated number of nematodes per taxon in the total 20 ml sample volume. ## Code/software Microsoft Excel can be used to view/access the file