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Biology subjects

Seymour, J. R.

Publications and source records attributed to Seymour, J. R..

3 recordsLinked to original sources

Rhometa: Population recombination rate estimation from metagenomic read datasets

Bacterial evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a bacterial population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes.It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. In simulated datasets, the deviation from the expected value decreased as the number of genomes increased and we show that 80 genomes are sufficient to reduce these variations below 30%. Testing on an S. pneumoniae transformation experiment dataset we show that Rhometa accurately estimate the expected levels of recombination in a real world dataset.

bioinformatics↗

Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions

Bacterioplankton communities play major roles in governing marine productivity and biogeochemical cycling, yet what drives the relative influence of the types of deterministic ecological processes which result in diversity patterns remains unclear. Here we examine how differing deterministic processes (environmental factors and biotic interactions) drive temporal dynamics of bacterioplankton diversity at three different oceanographic time-series locations, spanning 15 degrees of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples, collected over a period of 5.5 years, were analyzed using 16S rRNA amplicon sequencing. The high and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity respectively, with both alpha (local) diversity (72 % and 24 % of total variation) and beta diversity (32 % and 30 %) patterns within bacterioplankton assemblages primarily explained by environmental determinants, including day length, ammonium, and mixed layer depth. In contrast, at North Stradbroke Island, a sub-tropical location where environmental conditions are less seasonally variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha diversity: 33 %; beta diversity: 26 %) with environment only contributing 11 and 13 % to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity. ImportanceMarine bacterioplankton drives important biological processes, including the cycling of key nutrients or fixing atmospheric carbon. Therefore, to predict future climate scenarios its critical to model these communities accurately. Processes that drive bacterioplankton diversity patterns in the oceans however remain unresolved, with most studies focusing on deterministic environmental drivers, ie temperature or available inorganic nutrients. Biotic deterministic processes including interactions among individuals are also important for structuring diversity patterns, however, this is rarely included to predict bacterioplankton communities. We develop an approach for determining the relative contribution of environmental and potential biotic interactions that structure marine bacterioplankton at three series at different latitudes. Environmental factors best predicted temporal trends in bacterioplankton diversity at the two high latitude time series, while biotic influence was most apparent at the low latitude time series. Our results suggest environmental heterogeneity is an important attribute driving the contribution of varying deterministic influence of bacterioplankton diversity.

ecology↗

Synergy of turbulence and fishing reduce aquatic biomass

A universal scaling relationship exists between organism abundance and body size1,2. Within ocean habitats this relationship deviates from that generally observed in terrestrial systems2-4, where marine macro-fauna display steeper size-abundance scaling than expected. This is indicative of a fundamental shift in food-web organization, yet a conclusive mechanism for this pattern has remained elusive. We demonstrate that while fishing has partially contributed to the reduced abundance of larger organisms, a larger effect comes from ocean turbulence: the energetic cost of movement within a turbulent environment induces additional biomass losses among the nekton. These results identify turbulence as a novel mechanism governing the marine size-abundance distribution, highlighting the complex interplay of biophysical forces that must be considered alongside anthropogenic impacts in processes governing marine ecosystems.

ecology↗