Regional variability in the trophic requirements of shelf sea fisheries in the Northeast Atlantic, 1973-2000

Hydrographic, plankton, benthos, fisheries landings, and fish diet data from shelf sea areas in the Northeast Atlantic have been combined into an analysis of the foodweb structure and secondary production requirements of regional fisheries. Fish landings from the Baltic and North Sea are shown to be taken from a lower trophic level and are shown to be overall more planktivorous than those from shelf edge regions. The secondary production required per unit of landed fish from the North Sea was approximately half that for landings from the southwest approaches to the UK, referred to as the Celtic Seas, where zooplankton production accounted for only a small fraction of the secondary production demands of the fisheries. In the North Sea, variability in zooplankton production seems to have exerted a bottom-up effect on fish production, which in turn has exerted a top-down effect on the benthos. Conversely, Celtic Seas benthos production has been a bottom-up driver of fish production, which seems to have been independent of variability in plankton production.Thus, climate and fishing pressures can be expected to influence these regional fisheries in very different ways. Overall, the results indicate very strong spatial patterns in the fish foodweb structure and function, which will be important considerations in the establishment of regional management plans for fisheries

The Role of Cod in the Ecosystem

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Analysis of the transcriptional pathways associated with the induction of quiescent embryonic arrest in the calanoid copepod <i>Acartia tonsa</i>

The copepod species Acartia tonsa (Dana)(Crustacea) have the unique ability to induce quiescent embryonic dormancy if adverse environmental conditions occur; a characteristic shared by 41 other species belonging to the superfamily Centropagoida in the Calanoida order. However, the transcriptional changes characterizing this process are not known. Here, we compare the transcriptome of embryos in arrested quiescence with the normal development to identify pathways and differentially regulated transcripts involved in quiescent embryogenesis. Quiescence was induced by incubating eggs at 4 °C with anoxia for 26 h(hr), while eggs undergoing normal immediate development were incubated at 16.9 °C in normoxia for 7 h (where gastrulation occurs) or 14 h (where organogenesis occurs) before collecting for RNA extraction and analysis by RNA-sequencing. Results indicate that the expression profile of the quiescent embryo is not as different from the normal embryonic gastrulation as initially expected: None of the mapped transcripts is uniquely expressed in quiescence. Moreover, in quiescence a large proportion of the annotated transcripts display expression values halfway in-between the normal, immediate developmental stages of gastrulation and organogenesis. In depth comparison between the organogenesis stage and quiescent samples, reveal a high degree of divergence, confirming that a developmental arrest has been induced through quiescence. Specifically: Stress response transcripts are prominent in the quiescent phase with a transcript like the mammalian autophagy gene Sequestosome-1/p62 (SQSTM) being upregulated. The present analysis provides a better understanding of the molecular mechanisms characterizing the quiescent embryonic state of A. tonsa.</p

Current strategies for mobilome research

Mobile genetic elements (MGE) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of MGEs is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery

The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi. Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available

Changes in the structure and functionof the North Sea fish foodweb, 1973-2000, and the impacts of fishing and climate

North Sea environmental and biological data were analysed to examine 30-year changes in production and consumption in the fish food web. The analysis revealed that the demand for secondary production placed on the ecosystem by fish declined from approximately 20 g Cm-2 y-1 in the 1970s to 16 g C m-2 y-1 in the 1990s. Over the same period, the proportion of demand provided by zooplankton production increased from around 70% to 75%. The overall decrease was mainly due to a reduction in piscivorous demersal fish. Average secondary production by omnivorous zooplankton was estimated to be 35 g Cm-2 y-1, and annual fluctuations were positively correlated with the gross production of planktivorous fish. The results suggest a ''bottom-up'' control of the pelagic foodweb. Individual planktivore species have been impacted by fishing, but the populations of other functionally similar species have expanded to fill the vacant niches, thus maintaining the planktivore role in the system. In contrast, the results indicate that benthos production was more "top-down" controlled. Overall, demersal fish species have been depleted by fishing, with no obvious species expansions to fill the vacant niche, releasing the benthos from predation pressure, and leading to an increase in benthic production and fisheries for invertebrates