Nanopore metatranscriptomics reveals cryptic catfish species as potential Shigella flexneri vectors in Kenya.

Bacteria in the Shigella genus remain a major cause of dysentery in sub-Saharan Africa, and annually cause an estimated 600,000 deaths worldwide. Being spread by contaminated food and water, this study highlights how wild caught food, in the form of freshwater catfish, can act as vectors for Shigella flexneri in Southern Kenya. A metatranscriptomic approach was used to identify the presence of Shigella flexneri in the catfish which had been caught for consumption from the Galana river. The use of nanopore sequencing was shown to be a simple and effective method to highlight the presence of Shigella flexneri and could represent a potential new tool in the detection and prevention of this deadly pathogen. Rather than the presence/absence results of more traditional testing methods, the use of metatranscriptomics highlighted how primarily one SOS response gene was being transcribed, suggesting the bacteria may be dormant in the catfish. Additionally, COI sequencing of the vector catfish revealed they likely represent a cryptic species. Morphological assignment suggested the fish were widehead catfish Clarotes laticeps, which range across Africa, but the COI sequences from the Kenyan fish are distinctly different from C. laticeps sequenced in West Africa.

The ecological importance of habitat complexity to the Caribbean coral reef herbivore Diadema antillarum: three lines of evidence.

When Caribbean long-spined sea urchins, Diadema antillarum, are stable at high population densities, their grazing facilitates scleractinian coral dominance. Today, populations remain suppressed after a mass mortality in 1983-1984 caused a loss of their ecosystem functions, and led to widespread declines in ecosystem health. This study provides three lines of evidence to support the assertion that a lack of habitat complexity on Caribbean coral reefs contributes to their recovery failure. Firstly, we extracted fractal dimension (D) measurements, used as a proxy for habitat complexity, from 3D models to demonstrate that urchins preferentially inhabit areas of above average complexity at ecologically relevant spatial scales. Secondly, controlled behaviour experiments showed that an energetically expensive predator avoidance behaviour is reduced by 52% in complex habitats, potentially enabling increased resource allocation to reproduction. Thirdly, we deployed a network of simple and cost-effective artificial structures on a heavily degraded reef system in Honduras. Over a 24-month period the adult D. antillarum population around the artificial reefs increased by 320% from 0.05 ± 0.01 to 0.21 ± 0.04 m-2 and the juvenile D. antillarum population increased by 750% from 0.08 ± 0.02 to 0.68 ± 0.07 m-2. This study emphasises the important role of habitat structure in the ecology of D. antillarum and as a barrier to its widespread recovery.