Nigel Keeley

Bio: Nigel Keeley is an academic researcher from Cawthron Institute. The author has contributed to research in topics: Benthic zone & Environmental DNA. The author has an hindex of 13, co-authored 28 publications receiving 752 citations. Previous affiliations of Nigel Keeley include University of Tasmania.

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

Abstract: A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.

The Answer Is 17 Years, What Is the Question

Abstract: This study aimed to review the literature describing and quantifying time lags in the health research translation process. Papers were included in the review if they quantified time lags in the development of health interventions. The study identified 23 papers. Few were comparable as different studies use different measures, of different things, at different time points. We concluded that the current state of knowledge of time lags is of limited use to those responsible for R&D and knowledge transfer who face difficulties in knowing what they should or can do to reduce time lags. This effectively ‘blindfolds’ investment decisions and risks wasting effort. The study concludes that understanding lags first requires agreeing models, definitions and measures, which can be applied in practice. A second task would be to develop a process by which to gather these data.

What is bioturbation? The need for a precise definition for fauna in aquatic sciences

Abstract: The term 'bioturbation' is frequently used to describe how living organisms affect the substratum in which they live. A closer look at the aquatic science literature reveals, however, an inconsistent usage of the term with increasing perplexity in recent years. Faunal disturbance has often been referred to as particle reworking, while water movement (if considered) is re ferred to as bioirrigation in many cases. For consistency, we therefore propose that, for contemporary aquatic scientific disciplines, faunal bioturbation in aquatic environments includes all transport processes carried out by animals that directly or indirectly affect sediment matrices. These pro- cesses include both particle reworking and burrow ventilation. With this definition, bioturbation acts as an 'umbrella' term that covers all transport processes and their physical effects on the sub- stratum. Particle reworking occurs through burrow construction and maintenance, as well as ingestion and defecation, and causes biomixing of the substratum. Organic matter and microor- ganisms are thus displaced vertically and laterally within the sediment matrix. Particle reworking animals can be categorized as biodiffusors, upward conveyors, downward conveyors and regen- erators depending on their behaviour, life style and feeding type. Burrow ventilation occurs when animals flush their open- or blind-ended burrows with overlying water for respiratory and feeding purposes, and it causes advective or diffusive bioirrigation ex change of solutes between the sedi- ment pore water and the overlying water body. Many bioturbating species perform reworking and ventilation simultaneously. We also propose that the effects of bioturbation on other organisms and associated processes (e.g. microbial driven biogeochemical transformations) are considered within the conceptual framework of ecosystem engineering.

Marine urbanization: an ecological framework for designing multifunctional artificial structures

Abstract: Underwater cities have long been the subject of science fiction novels and movies, but the “urban sprawl” of artificial structures being developed in marine environments has widespread ecological consequences. The practice of combining ecological principles with the planning, design, and operation of marine artificial structures is gaining in popularity, and examples of successful engineering applications are accumulating. Here we use case studies to explore marine ecological engineering in practice, and introduce a conceptual framework for designing artificial structures with multiple functions. The rate of marine urbanization will almost certainly escalate as “aquatourism” drives the development of underwater accommodations. We show that current and future marine developments could be designed to reduce negative ecological impacts while promoting ecosystem services.