Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Is the Russell Cycle a true cycle? Multidecadal zooplankton and climate trends in the western English Channel

The Russell Cycle is one of the classical examples of climate influence on biological oceanography, represented as shifts in the marine plankton over several decades with warm and cool conditions. While the time-series data associated with the phenomenon indicate cyclical patterns, the question remains whether or not the Russell Cycle should be considered a “true cycle”. Zooplankton time-series data from 1924 to 2011 from the western English Channel were analysed with principal component (PC), correlation and spectral analyses to determine the dominant trends, and cyclic frequencies of the Russell Cycle indicators in relation to long-term hydroclimatic indices. PC1 accounted for 37.4% of the variability in the zooplankton data with the main contributions from non-clupeid fish larvae, southwestern zooplankton, and overall zooplankton biovolume. For PC2 (14.6% of data variance), the dominant groups were northern fish larvae, non-sardine eggs, and southern fish larvae. Sardine eggs were the major contributors to PC3 (representing 12.1% of data variance). No significant correlations were observed between the above three components and climate indices: Atlantic Multidecadal Oscillation, North Atlantic Oscillation, and local seawater temperature. Significant 44- and 29-year frequencies were observed for PC3, but the physical mechanisms driving the cycles are unclear. Harmonic analysis did not reveal any significant frequencies in the physical variables or in PCs 1 and 2. To a large extent, this is due to the dominant cycles in all datasets generally being long term (>50 years or so) and not readily resolved in the examined time frame of 88 years, hence restricting the ability to draw firm conclusions on the multidecadal relationship between zooplankton community dynamics in the western English Channel and environmental indices. Thus, the zooplankton time-series often associated and represented as the Russell Cycle cannot be concluded as being truly cyclical.

Is the Russell Cycle a true cycle? Multidecadal zooplankton and climate trends in the western English Channel

The Russell Cycle is one of the classical examples of climate influence on biological oceanography, represented as shifts in the marine plankton over several decades with warm and cool conditions. While the time-series data associated with the phenomenon indicate cyclical patterns, the question remains whether or not the Russell Cycle should be considered a “true cycle”. Zooplankton time-series data from 1924 to 2011 from the western English Channel were analysed with principal component (PC), correlation and spectral analyses to determine the dominant trends, and cyclic frequencies of the Russell Cycle indicators in relation to long-term hydroclimatic indices. PC1 accounted for 37.4% of the variability in the zooplankton data with the main contributions from non-clupeid fish larvae, southwestern zooplankton, and overall zooplankton biovolume. For PC2 (14.6% of data variance), the dominant groups were northern fish larvae, non-sardine eggs, and southern fish larvae. Sardine eggs were the major contributors to PC3 (representing 12.1% of data variance). No significant correlations were observed between the above three components and climate indices: Atlantic Multidecadal Oscillation, North Atlantic Oscillation, and local seawater temperature. Significant 44- and 29-year frequencies were observed for PC3, but the physical mechanisms driving the cycles are unclear. Harmonic analysis did not reveal any significant frequencies in the physical variables or in PCs 1 and 2. To a large extent, this is due to the dominant cycles in all datasets generally being long term (>50 years or so) and not readily resolved in the examined time frame of 88 years, hence restricting the ability to draw firm conclusions on the multidecadal relationship between zooplankton community dynamics in the western English Channel and environmental indices. Thus, the zooplankton time-series often associated and represented as the Russell Cycle cannot be concluded as being truly cyclical.

Progressive changes in the Western English Channel foster a reorganization in the plankton food web

Growing evidence has shown a profound modification of plankton communities of the North East Atlantic and adjacent seas over the past decades. This drastic change has been attributed to a modification of the environmental conditions that regulate the dynamics and the spatial distribution of ectothermic species in the ocean. Recently, several studies have highlighted modifications of the regional climate station L4 (50° 15.00′N, 4° 13.02′W) in the Western English Channel. We here focus on the modification of the plankton community by studying the long-term, annual and seasonal changes of five zooplankton groups and eight copepod genera. We detail the main composition and the phenology of the plankton communities during four climatic periods identified at the L4 station: 1988–1994, 1995–2000, 2001–2007 and 2008–2012. Our results show that long-term environmental changes underlined by Molinero et al. (2013) drive a profound restructuration of the plankton community modifying the phenology and the dominance of key planktonic groups including fish larvae. Consequently, the slow but deep modifications detected in the plankton community highlight a climate driven ecosystem shift in the Western English Channel.

Progressive changes in the Western English Channel foster a reorganization in the plankton food web

Growing evidence has shown a profound modification of plankton communities of the North East Atlantic and adjacent seas over the past decades. This drastic change has been attributed to a modification of the environmental conditions that regulate the dynamics and the spatial distribution of ectothermic species in the ocean. Recently, several studies have highlighted modifications of the regional climate station L4 (50° 15.00′N, 4° 13.02′W) in the Western English Channel. We here focus on the modification of the plankton community by studying the long-term, annual and seasonal changes of five zooplankton groups and eight copepod genera. We detail the main composition and the phenology of the plankton communities during four climatic periods identified at the L4 station: 1988–1994, 1995–2000, 2001–2007 and 2008–2012. Our results show that long-term environmental changes underlined by Molinero et al. (2013) drive a profound restructuration of the plankton community modifying the phenology and the dominance of key planktonic groups including fish larvae. Consequently, the slow but deep modifications detected in the plankton community highlight a climate driven ecosystem shift in the Western English Channel.

Notes on recent experiments relating to the growth and rearing of food-fish at the laboratory

The rearing of lobster larvae and larval fish.

Severe tissue damage in Atlantic cod larvae under increasing ocean acidification

Ocean acidification, caused by increasing atmospheric concentrations of CO2 (refs 1-3), is one of the most critical anthropogenic threats to marine life. Changes in seawater carbonate chemistry have the potential to disturb calcification, acid-base regulation, blood circulation and respiration, as well as the nervous system of marine organisms, leading to long-term effects such as reduced growth rates and reproduction(4,5). In teleost fishes, early life-history stages are particularly vulnerable as they lack specialized internal pH regulatory mechanisms(6,7). So far, impacts of relevant CO2 concentrations on larval fish have been found in behaviour(8,9) and otolith size(10,11), mainly in tropical, non-commercial species. Here we show detrimental effects of ocean acidification on the development of a mass-spawning fish species of high. commercial importance. We reared Atlantic cod larvae at three levels of CO2, (1) present day, (2) end of next century and (3) an extreme, coastal upwelling scenario, in a long-term (2; months) mesocosm experiment. Exposure to CO2 resulted in severe to lethal tissue damage in many internal organs, with the degree of damage increasing with CO2 concentration. As larval survival is the bottleneck to recruitment, ocean acidification has the potential to act as an additional source of natural mortality, affecting populations of already exploited fish stocks.

Organ damage in Atlantic herring larvae as a result of ocean acidification

The dissolution of anthropogenically emitted excess carbon dioxide lowers the pH of the world's ocean water. The larvae of mass spawning marine fishes may be particularly vulnerable to such ocean acidification (OA), yet the generality of earlier results is unclear. Here we show the detrimental effects of OA on the development of a commercially important fish species, the Atlantic herring (Clupea harengus). Larvae were reared at three levels of CO2: today (0.0385 kPa), end of next century (0.183 kPa), and a coastal upwelling scenario (0.426 kPa), under near-natural conditions in large outdoor tanks. Exposure to elevated CO2 levels resulted in stunted growth and development, decreased condition, and severe tissue damage in many organs, with the degree of damage increasing with CO2 concentration. This complements earlier studies of OA on Atlantic cod larvae that revealed similar organ damage but at increased growth rates and no effect on condition.

Ecological Investigations with the Continuous Plankton Recorder: The Zooplankton (other than Copepoda and Young Fish) in the Southern North Sea, 1932-37.

I. The report describes the main monthly changes in the distribution and abundance of the zooplankton, other than Copepoda and young fish (dealt with in separate reports), over the southern part of the North Sea from 1932 to 1937. The work is part of the survey carried out by Continuous Plankton Recorders towed at a depth of 10 metres on regular steamship lines between England and the Continent. 2. The limitations to the sampling method are discussed, and it is shown to be unsuitable for recording Mysidacea and Euphausiacea on account of their marked diurnal variation due presumably to vertical migration; they are omitted from the report. 3. The changing distribution of Sagitta, Limacina, Clione, Lamellibranch larvae, Cladocera, Caprellid Amphipoda, Decapod larvae, Echinoderm larvae and Oikopleura are shown in a series of monthly charts while their seasonal fluctuations are compared in time-chart histograms. 4. The Alima larvae of Squilla are recorded on a few occasions in the regions where the Channel opens into the North Sea. 5. The distributional characteristics of the different forms, i.e. their tendencies to even or " patchy " production, are compared.