Copepod Species Diversity Research Articles

Metabarcoding of zooplankton diversity within the Chukchi Borderland, Arctic Ocean: improved resolution from multi-gene markers and region-specific DNA databases

DNA-based analyses have become powerful tools for characterizing the metazoan biodiversity of diverse marine ecosystems. Metabarcoding (i.e., large-scale taxonomic identification of complex samples via high-throughput sequencing of a DNA barcode region) frequently uses hypervariable regions of the nuclear eukaryotic 18S ribosomal RNA (rRNA) gene. However, species-level taxonomic identification is hampered by the conservative nature of the 18S gene in comparison to the mitochondrial cytochrome oxidase I (COI) barcode gene. Additionally, metabarcoding relies on reference DNA sequence databases for classification of millions of unknown sequence reads and molecular operational taxonomic units (OTUs); databases that are at present depauperate for marine zooplankton taxa. Here, we characterized the mesozooplankton community for the Chukchi Borderland (CBL) region, western Arctic Ocean, through metabarcoding analysis of the V4 and V9 hypervariable regions of 18S rRNA and a portion of COI. Characterization of zooplankton diversity for the epipelagic and upper mesopelagic layers (0–500 m) was based upon 17 metazoan taxonomic categories encompassing 24 orders in 14 classes. Taxonomic classification using the V4 and V9 markers was most reliable for orders, with copepods dominating OTU counts. To increase taxonomic resolution and allow detection of species, V4, V9, and COI OTUs were classified against DNA sequence databases for the Arctic Ocean for the subclass Copepoda. The geographic region-specific databases for 18S rRNA and COI resulted in the detection and identification of 6 genera and 49 species of copepods representing 23 families, a marked increase in the taxonomic classification of the 18S rRNA markers. The greatest copepod species diversity was captured with V4 (34 species) followed by COI (28 species) with the least copepod diversity detected by V9 (5 species). Our results demonstrate the power of using multiple gene markers, with DNA reference databases that are specific to the geographic region of interest, providing more accurate metabarcoding biodiversity measures for the copepod assemblages compared to universal metazoan sequence reference databases. Results from this study highlight the need for continued DNA barcode sequencing to increase species representation in the reference sequence databases that are crucial for accurate characterization of mesozooplankton communities.

Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria

BackgroundCopepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic diversity of copepods in Nigeria is unexplored.ResultsUsing a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria.ConclusionsOur findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.

Spatial variability of copepod species distribution in the eastern Arabian Sea in pre-monsoon conditions

This work examines the spatial variability among mesozooplankton abundance and copepod species diversity along the continental margin prior to the onset of southwest monsoon in the eastern Arabian Sea during the year 2011. The eastern Arabian Sea experiences seasonal hypoxia during the receding phase of monsoon that corresponds to low copepod abundance in the slope region. Collectively, fifty copepod species were identified over the continental margin where the diversity index (H′) ranged between 2.59 and 3.73. Bray–Curtis cluster analysis clustered the stations into three groups that corresponded to the continental shelf, slope and break reaches of the eastern Arabian Sea. This spatial variability among the groups is mainly ascribed to changes in the relative contributions of the prevailing species. The distinct genera of the continental shelf were Microsetella spp. and Temora turbinata; at the slope region, Oncaea spp. and at shelf-break, Pleuromamma indica. Overall, herbivorous copepods were numerically abundant at the continental shelf and carnivores at the slope. The discrepancy between the distributions of herbivorous versus carnivorous copepod assemblages may be attributed to environmental factors such as ambient water dissolved oxygen and phytoplankton biomass.

Keanekaragaman, Kelimpahan, dan Sebaran Kopepoda (Krustasea) di Perairan Bakau Segara Anakan, Cilacap

<strong>Diversity, Abundance, and Distribution of Copepods (Crustacea) in the Mangrove Area of Segara Anakan, Cilacap.</strong> Observations on the diversity of Copepods, its abundance, and its distribution in three mangrove and estuarine locations in Segara Anakan Lagoon, Cilacap, were conducted in May (dry season) and November (rainy season) 2009. This study aims to determine the relationship of diversity and abundance of Copepods with some environmental factors that affect its distribution in the dry and rainy seasons. Copepod samples were taken from Kutawaru waters, Dermaga Sleko, and Ciperet using vertical and horizontal plankton nets, day and night. They were then preserved, deposited, and identified in MZB LIPI. There were 36 species of Copepods from 18 genera and 20 families, including 10 new records. The highest species diversity of Copepods was recorded in November, while the lowest was in May. The average abundance in May was higher than in November. The diversity and abundance in Ciperet in both dry and rainy seasons were always higher than the other two sites. Acartia erythraea, A. sinjiensis and Pseudodiaptomus annandalei were found to dominate the waters especially during the dry season in May. The community composition of Copepods occupying the waters was determined by salinity, while its activity and development were determined by temperature. <br />

Mesozooplankton community structure in the upper 1,000 m along the western Bay of Bengal during the 2002 fall intermonsoon

Stratification, no upwelling, sediment load, and heavy cloud cover are known to limit primary production in the western Bay of Bengal. Studies on primary consumers in this area are few. Recent studies in the Bay have shown the role of cold-core eddies in enhancing the biological production. This study was carried out to provide a detailed account of variation in mesozooplankton biomass, abundance, and copepod assemblages between cold-core eddy and non-eddy regions in the western Bay. In this study carried out in the western Bay during fall 2002 intermonsoon, we observed a very high zooplankton biovolume of 2.2 ml/m3 in the mixed layer at station WB3 located within a shallow cold-core eddy. Zooplankton from 29 groups were observed during this study. Calanoid and poecilostomatoid copepods substantially contributed to the total zooplankton abundance and carbon biomass. Below the 200 m depth, there were fewer groups but higher proportion of copepods. Copepodites of calanoids were more abundant between 500 and 1,000 m at the WB3 eddy station. Invertebrate eggs made up a staggering 65% of the total collection in the 200- to 300-m stratum at WB1, a location in the other cold-core eddy. Copepod species diversity (3.39 to 4.77) and richness (2.32 to 4.84) were lower at WB3. Among 147 copepod species in 69 genera found, Oncaea venusta (17% of the total copepod abundance), Paracalanus indicus (5.4%), Lucicutia flavicornis (5.1%), and Pleuromamma indica (4.5%) were the four most dominant ones. High copepod diversity throughout upper 1,000 m of the western Bay is attributed to the moderate oligotrophy. We reported 93 copepod species for the first time from this region, from which 7 are first records for the Indian Ocean. Cold-core eddies seem to play a pivotal role in sustaining zooplankton in nutrient-limiting regions such as the western Bay of Bengal.

Sediment-mediated effects of lugworms on intertidal meiofauna

Based on a large-scale, long-term lugworm exclusion experiment established on an intertidal sand flat in Königshafen (Sylt, North Sea), the effect of ecosystem engineering by the lugworm Arenicola marina on the meiofaunal community was studied. Samples for sediment and meiofauna analyses were taken from a lugworm exclusion plot three years after lugworms were excluded, a disturbed control plot and a pristine ambient plot. Statistical analyses revealed significantly higher concentrations of total organic matter and chloroplastic pigments at the lugworm exclusion site. The median abundance of total meiofauna was 21–29% higher at the lugworm-free site as compared to the lugworm-inhabited sites. Copepoda and Nematoda were distributed homogeneously over all experimental plots while Ostracoda and copepod nauplii reached their highest abundances in the absence of lugworms. Univariate and multivariate analyses revealed significant differences between the copepod species composition of the experimental sites. While the harpacticoid copepod Arenosetella germanica reacted with a decline in individual numbers to lugworm exclusion, Halectinosoma gothiceps and Asellopsis intermedia benefited from the induced changes in the sediment characteristics. Overall, a higher copepod species diversity and evenness was observed at the lugworm exclusion site. The results of this study indicate that sediment-mediated effects of bioturbating organisms influence the abundance and diversity of surface-living meiofauna.

Copepod community structure and abundance in a tropical mangrove estuary, with comparisons to coastal waters

Zooplankton, sampled at five stations from the upper Sangga estuary (7 km upstream) in Matang Mangrove Forest Reserve (MMFR), Malaysia, to 16 km offshore, comprised more than 47% copepod. Copepod abundance was highest at nearshore waters (20,311 ind m−3), but decreased toward both upstream (15,572 ind m−3) and offshore waters (12,330 ind m−3). Copepod abundance was also higher during the wetter NE monsoon period as compared to the drier SW monsoon period, but vice versa for copepod species diversity. Redundancy analysis (RDA) shows that copepod community structure in the upper estuary, nearshore and offshore waters differed, being influenced by spatial and seasonal variations in environmental conditions. The copepods could generally be grouped into estuarine species (dominantly Acartia spinicauda Mori, Acartia sp1, Oithona aruensis Fruchtl, and Oithona dissimilis Lindberg), stenohaline species (Acartia erythraea Giesbrecht, Acrocalanus gibber Giesbrecht, Paracalanus aculateus Giesbrecht, and Corycaeus andrewsi Farran) and euryhaline species (Parvocalanus crassirostris Dahl, Oithona simplex Farran, and Bestiolina similis (Sewell)). Shifts in copepod community structure due to monsoonal effects on water parameters occurred at the lower estuary. Copepod peak abundance in mangrove waters could be associated with the peak chlorophyll a concentration prior to it. Evidence of copepod consumption by many species of young fish and shrimp larvae in the MMFR estuary implies the considerable impact of phytoplankton and microphytobenthos on mangrove trophodynamics.

Potential impact of rising seawater temperature on copepods due to coastal power plants in subtropical areas

The major objective of this study is to understand the upper thermal limits and potential impact of temperature elevation on copepods caused by coastal power plants. Laboratory experiments were designed to evaluate the upper incipient lethal temperature (UILT) and critical thermal maximum (CTMax) of eight coastal copepod species collected from a subtropical bay in spring and summer. The 48h-UILT of copepods acclimatized at 16.0, 20.0, 28.0 °C were 26.4–29.1, 27.3–30.1, 32.9–36.9 °C, respectively. And the CTMax of copepods acclimatized at 28.0 °C was 35.80–41.03 °C. The UILT of copepods increased significantly with rising acclimatization temperatures, but the difference values between UILT and acclimatization temperatures decreased, which indicated that the seawater temperature elevation induced the growing mortalities of copepods with increasing natural seawater temperatures from the thermal addition of power plants. The results also showed that estuarine copepods had more tolerances to the thermal stress than those from other more stable marine environments. As to the calanoid copepod species, there was a significant negative correlation between the CTMax and body length ( p < 0.01). So it seemed that the copepod species with large body size were more sensitive to the thermal addition than the smaller ones. Thus, owing to the temperature increase, the copepod species diversity might reduce and the composition of copepod communities might tend to be small-sized in natural sea areas close to the coastal power plants.

Autumn net copepod abundance and assemblages in relation to water masses on the continental shelf of the Yellow Sea and East China Sea

Copepod species diversity, abundance and assemblages in relation to water masses over the continental shelf of the Yellow Sea (YS) and East China Sea (ECS) were studied extensively based on the net plankton samples in autumn 2000. Multivariate analysis based on copepod assemblage resulted in recognition of five groups (Groups 1−5) corresponding to the water masses. Groups 1 and 2 delineated from inshore stations with low salinity YS Surface Water, and offshore stations with YS Cold Water in the YS. Group 3 located in the joint area of YS and ECS mainly with Mixed Water. Groups 4 and 5 in the ECS delineated two assemblages mainly from inshore and shallow stations with ECS Mixed Water in the southeastern ECS, and offshore stations along the ECS shelf edge controlled by saline Kuroshio Water. Salinity and temperature were more important in characterizing copepod assemblage of the continental shelf than chlorophyll a.

Copepod species diversity and climate variability in the tropical Atlantic Ocean

AbstractA database synthesized from 19 oceanographic expeditions conducted by the former Soviet Union was used to analyse interannual patterns in copepod species diversity in the tropical Atlantic. Mesozooplankton was collected predominately in vertical hauls through the upper 100 m with Juday nets. The samples from 744 oceanographic stations were identified and enumerated to the species level. To assess species diversity, the Shannon diversity index was used. On the interdecadal scale, no statistically confirmed trend was found in species diversity change over the years sampled (1963–89). Multiple regression analysis indicated that interannual fluctuations of the South Atlantic High (pressure and latitude), the Azores High longitude and El Niño–Southern Oscillation (ENSO) index could explain 87% of species diversity fluctuations. Possible mechanisms that drive interannual fluctuations of species diversity are discussed.

Plankton communities of the South Atlantic anticyclonic gyre

Data collected during cruises of the Former Soviet Union (in 1963–1989) and the British Atlantic meridional transect program (in 1995–1999) were used to analyse macroscale patterns in phyto- and zooplankton biomass, size structure, species diversity, chlorophyll a, and plankton bioluminescence in the macroscale anticyclonic gyre of the South Atlantic Ocean. The spatial pattern of bioluminescence intensity was in good agreement with that of remotely sensed (CZCS) chlorophyll a, phosphate, salinity, and copepod species diversity index distributions especially in terms of geographic inclinations of the isolines, both associated with the north-westward pattern off the South equatorial current. Among the 416 copepod species recorded in samples, 51 species were noted throughout the whole gyre. On the other hand, there were a number of species found only in one of the currents. The mesozooplankton biomass size spectra (calculated in carbon units), exhibited a fairly stable slope of the curve from the eastern periphery of the gyre to its centre. The British Atlantic meridional transect program meridional transect through the western part of the gyre showed mesozooplankton size spectra in greater detail between the equator and 50° S. Although the spectra change slowly along the transect as far as 36° S, there is a general trend toward increasing slopes from the equatorial region to the oligotrophic central gyre. The calculated phyto-to-zooplankton ratio indicated that for the tropical anticyclonic gyres, the mesozooplankton carbon biomass could be represented as the exponential function of the phytoplankton carbon.

Spills of fuel oil #6 and Orimulsion can have indistinguishable effects on the benthic meiofauna

Fuel oil #6 is used for the production of electrical power in the United States. Orimulsion ® is being considered as an alternative fuel, but its value and risk compared to fuel oil #6 need to be assessed. Our study examined the relative impact of accidental spills of the two hydrocarbons on the meiofaunal community. To do so, we maintained microcosms of the shallow, sandy, subtidal environment for three months. Treatment microcosms received a single application of hydrocarbon-coated sand. As indicators of effect, we used copepod and nematode abundance and copepod species diversity, sex ratio, fecundity, age structure, and neutral-lipid content. A comparison of the hydrocarbon treatments showed no significant differences. The tests had adequate power to detect ecologically significant changes. Our results indicate that a spill of Orimulsion would have approximately the same impact as a spill of fuel oil #6 on the meiofauna.

Meiofaunal Colonization of Artificial Substrates in an Estuarine Embayment

Abstract. Artificial substrates were used to investigate the cryptic meiofauna of a Louisiana estuary. Three types of collectors were used as artificial habitats in colonization studies. Mesh collectors (composed of a plastic thread, approximately 74 m long, woven into a pad) and bottle brushes (with approximately 4400 plastic bristles per brush, each 2.5 mm long) were colonized equally well by meiofauna; Hester‐Dendy plates with less structural complexity were colonized at a slower rate, especially by copepods. Nematodes and harpacticoid copepods were always the two most abundant meiofaunal taxa collected. Mesh collectors were retrieved in July and December after a 2‐week colonization period to examine seasonal trends. Starting in December, a long‐term colonization study was also performed to determine if an equilibrium abundance could be achieved; artificial substrates were collected after 2, 4 and 8 weeks. Meiofauna achieved high abundances (means ranged from 1000 – 20,000 individuals per collector) on artificial substrates regardless of season, and abundance was related to supply, water flow and capture efficiency of the substrates as well as behavior of the meiofauna. Copepod species diversity was low (6 species were observed in July and 11 in December). Diversity and evenness were significantly different between July and December, and among the three collections in the long‐term study. The copepod species assemblage qualitatively differed between July and December. Our data suggest that an abundant and dynamic but understudied meiofaunal assemblage is present in this estuarine embayment. This assemblage is not associated with macroalgae but rather related to presence of hard substrates and seasonally abundant filamentous microalgae.