Swart, E. | Search bioRxiv

bioRxiv2021

Assessing the efficacy of antibiotic treatment for the creation of axenic earthworms

Earthworms are an integral part of soil ecosystems, especially for their role in soil functions such as organic matter (OM) decomposition and nutrient cycling. Earthworms and microorganisms are interdependent, and a considerable portion of the contribution earthworms make to influencing OM fate is through interactions with microorganisms. However, the importance of the earthworm-associated microbiome is not fully understood, because it is difficult to separate the direct influence of the earthworms from the indirect influence of their microbiome. Here, we evaluated an antibiotic-based procedure for producing axenic ecologically-contrasting earthworm species (E. fetida, L. terrestris, A. chlorotica) as the first step towards soil studies aimed at understanding the importance of the earthworm microbiome for host health and function. Individual earthworms were exposed to antibiotics: cycloheximide (150 g ml-1), ampicillin (100 g ml-1), ciprofloxacin (50 g ml-1), nalidixic acid (50 g ml-1), and gentamicin (50 g ml-1) either singly or in a cocktail via culture (96 h) in a semi-solid agar carrier. Compared to the non-antibiotic treated control, the cocktail (for all three species) and ciprofloxacin (for E. fetida and A. chlorotica) treatments significantly reduced (P<0.05) culturable microbial abundance on nutrient agar and potato dextrose agar. The microbial counts were reduced to below detection (<50 CFU individual-1) for E. fetida and A. chlorotica receiving the cocktail. Illumina 16S rDNA amplicon sequence analysis of culturable L. terrestris -associated bacteria showed that antibiotic treatment influenced community composition revealing putative sensitive (Comomonas, Kosakonia and Sphingobacterium) and insensitive (Aeromonas, Pseudochrobactrum) taxa. Overall, we report a rapid, with minimal earthworm-handling, process of creating axenic E. fetida and A. chlorotica individuals or L. terrestris with a suppressed microbiome as a tool to be used in future ecological studies of earthworm microbial interactions affecting host health and function.

ecology↗

bioRxiv2020

Limitations of DNA barcoding in determining the origin of smuggled seahorses and pipefishes

Seahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM markets in East Asia, but the usefulness of this approach in determining the region of origin remains poorly explored. Here, we generated DNA barcodes of dried seahorses and pipefishes destined for TCM that were confiscated at South Africas largest airport because they lacked the export permits required for the CITES-listed seahorses. These were compared with published sequences and new sequences generated for Mozambican seahorses, with the aim of determining whether it is possible to identify their country of origin. All pipefishes were identified as Syngnathoides biaculeatus, a widespread Indo-Pacific species, but the published sequence data did not provide sufficient resolution to identify the region of origin. The same was true of the majority of seahorses, which could not even be identified to species level because they clustered among an unresolved species complex whose sequences were published under the names Hippocampus kuda, H. fuscus and H. capensis. The presence of a few specimens of a second seahorse, H. camelopardalis, suggests that the shipment originated from East Africa because the range of this seahorse is centred around this region, but again, it was not possible to determine their country of origin. Even though seahorses and pipefishes have high levels of genetic population structure because of their low dispersal potential, DNA barcoding was only suitable to tentatively identify species, but not their region of origin. DNA barcoding is increasingly used to identify illegally traded wildlife, but our results show that more sophisticated methods are needed to monitor and police the trade in seahorses and pipefishes.

genetics↗