Atyid Shrimp Research Articles

Cryptic diversity of stygobiotic shrimp genus Xiphocaridinella Sadowsky, 1930 (Crustacea: Decapoda: Atyidae): the first case of species co-occurrence in the same cave system in the Western Caucasus.

DNA barcoding of stygobiotic shrimps of the genus Xiphocaridinella Sadowsky, 1930 (Crustacea: Decapoda: Atyidae) collected in underground streams flowing inside two neighboring large karst caves (Otap and Abrskil сaves) revealed the presence of two distinct genetic lineages representing the first case of species co-occurrence in the Western Caucasus. The paper presents the complete morphological re-description of stygobiotic atyid shrimp Xiphocaridinella ablaskiri (Birštein, 1939) and the description of a new species using genetic and morphological analysis. Other known cases of co-occurrence of several stygobiotic shrimp species in the same cave system as well as new genetic data (COI mtDNA) on Western Caucasian species of the genus Xiphocaridinella are discussed in the paper.

Freshwater Shrimps from Karst Caves of Southern China, with Descriptions of Seven New Species and the Identity of Typhlocaridina linyunensis Li and Luo, 2001 (Crustacea: Decapoda: Caridea).

Yixiong Cai and Peter Kee Lin Ng (2018) Seven new atyid shrimp species of the genus Caridina H. Milne Edwards, 1837 are described from southern China: C. longshan sp. nov., C. alu sp. nov., C. spinicrus sp. nov., C. beiliu sp. nov., C. jiangkou sp. nov., C. guilin sp. nov. and C. laticarpalis sp. nov. Descriptions and figures for all taxa are provided, and taxa are compared with their closest congeners. An updated list of all cave atyid and palaemonid shrimp species found in China is provided. Caridina semiblepsia Guo, Choy and Gui, 1996 is here regarded as a junior subjective synonym of C. ablepsia Guo, Jiang and Zhang, 1992. One poorly known species, Typhlocaridina linyunensis Li and Luo, 2001, described from a cave in Guangxi is here shown to be a palaemonid instead of an atyid, and is actually the senior synonym of Macrobrachium lingyunense Li, Cai and Clarke, 2006.

COXI based phylogenetic analysis of Caucasian clade of European Troglocaris (Crustacea: Decapoda: Atyidae) with the suggestion of a new taxonomic group structure

New genetic data on Caucasian troglobiotic shrimps collected from the territory of Russia, Abkhazia and Western Georgia are presented. Based on new genetic data on the marker region of subunit I of cytochrome oxidase of mitochondrial DNA (COXI mtDNA) of Caucasian species and other taxa of European cave shrimps (Troglocaris s.l.) from GenBank (NCBI) database, a new generic structure is presented. Based on a significant genetic divergence of COXI mtDNA subgenera of Troglocaris s.l., namely Troglocaris s.s., Xiphocaridinella and Spelaeocaris, should be considered as separate genera while Troglocaris (Troglocaridella) hercegovinensis (Babić, 1922) is suggested to be transferred within Dinaric genus Spelaeocaris as Spealeocaris hercegovinensis (Babić, 1922) comb. nov. Besides, Troglocaris bosnica shows a significant a genetic difference (at the level of the separate genus) from the remaining representatives of the genus Troglocaris s.s. Moreover, p-distances (COXI) of about 17% are supposed for generic separation within European Troglocaris-related atyid shrimps and 5% for separation of cryptic species within Caucasian Xiphocaridinella. A list of all known taxa of Troglocaris-related atyid shrimps of the European part and a discussion of the general distribution of troglocaridid atyid shrimps in the Balkans and the Caucasus are presented. A new version of divergence events between Dinaric–Caucasian Troglocaris lineages (genera) based on new genetic data is suggested.

Troglocaris (Xiphocaridinella) kumistavi sp. nov., a new species of stygobiotic atyid shrimp (Crustacea: Decapoda: Atyidae) from Kumistavi Cave, Imereti, Western Georgia, Caucasus

A new species of stygobiotic atyid shrimp genus Troglocaris (Xiphocaridinella) Dormitzer, 1853 from underground stream and lakes of Kumistavi (Prometheus) Cave, Tskaltubo, Imereti region, Western Georgia is described based on morphology and DNA analysis. Troglocaris (Xiphocaridinella) kumistavi sp. nov. clearly differs from all Caucasian congeners by (1) long slender dorsally and ventrally armed rostrum with sting-like tip turned upward, (2) very slender fingers of pereiopod II both in males and females and (3) distally expanded telson with 5–7 pairs of distal spines. These features are rather unique within the known Caucasian Troglocaris (Xiphocaridinella) and show some morphological similarities with Dinaric species of the genus. Neotype of Troglocaris (Xiphocaridinella) kutaissiana (Sadowsky, 1930) is also designated based on the material from Tskaltsitela Cave, Kutaisi, Georgia.

Do upstream migrating, juvenile amphidromous shrimps, provide a marine subsidy to river ecosystems?

Abstract The upstream migration of juvenile amphidromous shrimps has been proposed as a source of marine or estuarine‐derived nutrients into fresh water. Little is known about the size and ecological importance of any such subsidy as there have been few observational or empirical studies on the topic. We investigated the upstream migration of the amphidromous shrimp, Macrobrachium spinipes (Palaemonidae) in the Daly River, of tropical northern Australia, to determine migration phenology, estimate migration biomass and determine whether migrating shrimps transport marine‐derived energy and nutrients upstream. Field observations over 2 years revealed that juvenile M. spinipes migrate upstream en masse during extended periods of declining discharge over a period of 4–6 weeks during the wet season (March–May). In addition, juvenile atyid shrimps from the genus Caridina were also observed migrating upstream during the same period. Fine‐scale sampling using fyke nets over 2 years (2013 and 2014) consistently found discharge to be the strongest predictor of M. spinipes and Caridina spp. biomass, while moon illumination and cloud cover were also important predictors. An estimated 10–20 million shrimps migrated upstream during each wet season, transporting c. 100 kg of carbon and c. 28 kg of nitrogen per year. Muscle sulphur stable isotopes (δ34S) and exoskeleton strontium isotope ratios (87Sr/86Sr) were used to establish if marine carbon was transported upstream by the juvenile M. spinipes. Isotope data from migratory M. spinipes were compared to the non‐migratory freshwater Macrobrachium bullatum. No evidence of a marine signature in body tissue or exoskeleton was found using either technique, suggesting very rapid turnover of body tissues This study provides key insights into the migration phenology of amphidromous shrimps and, importantly, suggests that migrating M. spinipes do not transport significant amounts of marine‐derived energy and nutrients across the marine/freshwater ecotone.

Effects of biocontrol with an atyid shrimp (Caridina denticulata) and a bagrid catfish (Pseudobagrus fulvidraco) on toxic cyanobacteria bloom (Microcystis aeruginosa) in a eutrophic agricultural reservoir

The biocontrol effects of Caridina denticulata, an atyid shrimp, on toxic cyanobacterial bloom (Microcystis aeruginosa) were evaluated in a mesocosm study with stable isotope tracers (13C and 15N) in a eutrophic agricultural reservoir. The accumulated assimilation (at.%) of M. aeruginosa into C. denticulata was increased, causing a significant reduction in the concentration of Chlorophyll-a. The ingestion rate of M. aeruginosa by C. denticulata was influenced by predation pressure exerted by bagrid catfish Pseudobagrus fulvidraco and was dependent on biomass ratio. C. denticulata affected zooplankton density, species composition, and ingestion rate, demonstrating that the number of small-sized cladocerans (Bosmina coregoni and Bosmina longispina) increased because they grazed M. aeruginosa for a food source. This study suggests that C. denticulata and P. fulvidraco can be feasible material to control a nuisance M. aeruginosa bloom in eutrophic agricultural reservoir.

Sexual dimorphism in a freshwater atyid shrimp (Decapoda: Caridea) with direct development: a geometric morphometrics approach.

Neocaridina davidi is a caridean shrimp that has gained popularity in recent years as an ornamental species. Using geometric morphometrics, we investigated sexual dimorphism in carapace and second abdominal segment shape of N. davidi. Adult females displayed a more elongated carapace and a longer rostrum than males. However, male carapace shape was similar to that of juvenile females. The second abdominal pleura was more elongated and wider in adult females than in males. Significant differences were found in centroid size for the carapace and the second abdominal segment between sexes, which is consistent with sexual size dimorphism. These results support the hypothesis of a "pure search" mating system in N. davidi, where small males search actively for receptive females, and after insemination they continue searching.

De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water.

BackgroundThe atyid shrimp Paratya australiensis occurs in surface freshwater habitats throughout eastern Australia and has been used to study the ecotoxicology of contaminants such as pesticides and metals. The acidification of surface water that can occur after acid sulfate material in soils and sediments is oxidised and subsequently re-wetted is a serious environmental issue in coastal regions and inland riverine floodplains worldwide. Solubilisation of soil-associated minerals can result in high waterborne concentrations of mineral salts and dissolved metals, which together with low pH represent a potential threat to aquatic ecosystems in affected regions. The aims of the present study were to gain insight into stress responses induced by exposure to acid drainage water (ADW) in P. australiensis by determining changes in the abundance of protein-coding transcripts and to generate a comprehensive transcriptomic resource to facilitate further research into gene regulation or protein structure and function in this species. Adult P. australiensis were exposed for 24 h to undiluted ADW, 50 % ADW diluted in river water, or to river water as control, and high-throughput mRNA sequencing (RNA-Seq) conducted on whole-body tissues. A reference transcriptome was generated using de novo assembly and putative protein-coding regions were identified and annotated. Changes in transcript abundance in response to ADW exposure were determined by aligning reads to the reference transcriptome and quantifying coverage.ResultsA high proportion of arthropod benchmarking universal single-copy orthologues were present in the reference transcriptome. Functions associated with cuticle biosynthesis and oxidative stress were significantly enriched in the lists of transcripts exhibiting differential abundance in either direction after exposure to 50 % or 100 % ADW. Transcripts involved in osmoregulation exhibited decreased abundance following exposure to ADW. The transcriptome contained full-length coding sequences for numerous proteins known to be involved in environmental response pathways, including two putative metallothioneins, four glutathione peroxidases and 19 nuclear receptors.ConclusionsThe results of the present study provide insight into stress response pathways induced in crustaceans by short-term exposure to multiple stressors present in ADW such as low pH, high salinity and dissolved metals, and represent a resource for future toxicogenomics and protein functional studies in P. australiensis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3208-y) contains supplementary material, which is available to authorized users.

First report of the branchiobdellidan Holtodrilus truncatus (Annelida: Clitellata) found on the freshwater atyid shrimp Neocaridina sp. from Korea

The branchiobdellidan species Holtodrilus truncatus (Liang, 1963) is reported for the first time in Korea. The genus Holtodrilus Gelder and Brinkhurst, 1990 is monotypic within the family Xironodrilidae, and the genus and family of this species are also new to the Korean fauna. The branchiobdellidan specimens were collected from the exoskeletons of the freshwater atyid shrimp, Neocaridina sp., sampled from the 'Andeok Valley', Jeju-do Province, South Korea. Holtodrilus truncatus is characterized by its terete body form, 7/7 dental formula (with a large medial tooth and three pairs of smaller lateral teeth), and no trunk appendages. In addition, we determined a partial sequence of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene as a DNA barcode marker for H. truncatus. The present study is the first record of the branchiobdellidan occurrence on a non-crayfish host (shrimp) in Korea. To date, seven species (four genera in three families) of branchiobdellidans have been reported in the Korean fauna.

Developmental Transcriptomics of the Hawaiian Anchialine Shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae).

Many crustacean species progress through a series of metamorphoses during the developmental transition from embryo to adult. The molecular genetic basis of this transition, however, is not well characterized for a large number of crustaceans. Here, we employ multiple RNA-Seq methodologies to identify differentially expressed genes (DEGs) between "early" (i.e., Z1 - Z2) as well as "late" (i.e., Z3 - Z4) larval and adult developmental stages of Halocaridina rubra Holthuis (1963), an atyid shrimp endemic to the environmentally variable anchialine ecosystem of the Hawaiian Islands. Given the differences in salinity tolerance (narrow vs. wide range), energy acquisition (maternal yolk-bearing vs. microphagous grazing), and behavior (positively phototactic vs. not) between larvae and adults, respectively, of this species, we hypothesized the recovery of numerous DEGs belonging to functional categories relating to these characteristics. Consistent with this and regardless of methodology, hundreds of DEGs were identified, including upregulation of opsins and other light/stimulus detection genes and downregulation of genes related to ion transport, digestion, and reproduction in larvae relative to adults. Furthermore, isoform-switching, which has been largely unexplored in crustacean development, appears to be pervasive between H. rubra larvae and adults, especially among structural and oxygen-transport genes. Finally, by comparing RNA-Seq methodologies, we provide recommendations for future crustacean transcriptomic studies, including a demonstration of the pitfalls associated with identifying DEGs from single replicate samples as well as the utility of leveraging "prepackaged" bioinformatics pipelines.

Distribution of Holtodrilus truncatus, a Branchiobdellidan Ectosymbiotic on Atyid Shrimps in the Kii Peninsula, Western Japan, with Reference to Salinity Tolerance and Host Preference.

The distribution of the branchiobdellidan Holtodrilus truncatus (Liang, 1963), which is symbiotic on atyid shrimps, was surveyed in 26 river catchments, covering almost all of the Kii Peninsula, western Japan. Holtodrilus truncatus has been recorded in 10 rivers located from the southwest to northeast regions of the peninsula. Paratya compressa was the dominant host species in all rivers, with a lower prevalence on Caridina leucosticta, C. multidentata, C. typus, and Neocaridina denticulata. The longitudinal distribution of H. truncatus was limited to the middle and upper reaches, while its main host P. compressa occurred widely from the lower to the upper reaches. The numbers of H. truncatus and their cocoons per host increased in summer and decreased in winter, in accordance with the abundance of the host P. compressa. The body size of P. compressa was larger in individuals with H. truncatus than those without H. truncatus in some rivers, while in another river, sizes of the two groups were not different. A salinity tolerance experiment revealed that the threshold of salinity tolerance of H. truncatus occurred between 0-0.5%. A choice experiment between two host species showed that H. truncatus preferred C. leucosticta to C. multidentata, P. compressa to C. multidentata, and P. compressa to C. leucosticta.

Functional morphology of the feeding and associated appendages of the detritivore-collector atyid shrimps, Caridina cantonensis and Caridina trifasciata — a scanning electron microscopy study

The present study used Scanning Electron Microscopy (SEM) to examine the functional morphology of the feeding and associated appendages of the detritivore-collector atyid shrimps Caridina cantonensis Yu, 1938 and C. trifasciata Yam & Cai, 2003. The third maxillipedes of both species are equipped with serrate setae ending in a terminal pore, which setae may thus serve both as mechano- and chemo-receptors. Pereiopods 1 and 2 have dense, long, simple setae and single-rowed serrate setae for effective brushing fine-particulate organic matter and scraping periphyton from the substratum. Pereiopods 3 and 4 are heavily armed with large cuspidate setae and with simple type setae, which can be used for food collection or providing strong anchorage. The dactylus of pereiopod 5 is oval, flattened, and equipped with serrate setae on the ventral margin. In contrast to the suspension-feeding Atya innocuous (Herbst, 1792), Caridina spp. show a lower setal diversity, while all setal types on the pereiopods are mechano-receptors, being specialized for collecting food.

Aquarium hitchhikers: attached commensals imported with freshwater shrimps via the pet trade

The keeping of home aquaria is one of the most popular hobbies globally. In contrast to the ornamental fish trade, decapod crustaceans such as shrimps, crayfish and crabs are relatively new to the pet trade. Nevertheless, the popularity of ornamental shrimp in freshwater aquaria has rapidly increased in recent years. Indonesia is one of the leading producers and exporters of ornamental aquatic animals globally and the Czech Republic is a gateway for these animals into the European Union territory. The pathway for introductions of organisms unintentionally moved in association with ornamental shrimps via the international trade has to date not been evaluated. We examined a small number of shrimps imported from Indonesia into the Czech Republic in May 2015 and found large numbers of the protozoan Vorticella sp., one species of scutariellid temnocephalidan (Caridinicola sp.), and one species of bdelloid rotifer, associated with two species of atyid shrimps, indicating an invasion risk from fauna carried unintentionally by this vector. Although our observations were limited in scale, we estimate the total number of commensal fauna imported into the Czech Republic with ornamental shrimps via the pet trade to be in the order of hundreds of thousands per month. As attached organisms can directly or indirectly cause diseases in certain species of decapod crustaceans, we recommend five steps to reduce risks of introduction of “hitchhikers” to aquaria and wildlife.

Morphological and molecular data for three species of the Microphallidae (Trematoda: Digenea) in Australia, including the first descriptions of the cercariae of Maritrema brevisacciferum Shimazu et Pearson, 1991 and Microphallus minutus Johnston, 1948.

Cercariae and metacercariae of three species of the Microphallidae Travassos, 1920 were found in snails and crustaceans from tributaries of the Brisbane River, Queensland, Australia. Specimens of Maritrema brevisacciferum Shimazu et Pearson, 1991 and Microphallus minutus Johnston, 1948, which have previously been reported in Queensland, were found as cercariae in the tateid gastropod Posticobia brazieri (Smith) and as metacercariae of M. brevisacciferum in the atyid shrimp Caridina indistincta Calman and of M. minutus in the parastacid crayfish Cherax dispar Reik. Combined analysis of morphological and molecular data, based on newly generated ITS2 and partial 28S rDNA data, linked cercariae and metacercariae for both species. This is the first report of the first intermediate hosts of M. brevisacciferum and M. minutus. Infections of another unidentified microphallid metacercariae, Microphallidae gen. sp., were found in P. brazieri and C. indistincta. The sequences of metacercarial isolates from both hosts were identical. The data on the Microphallidae from Australia and species that develop in freshwater invertebrates were examined in detail.

The atyid shrimps from Lake Lindu, Central Sulawesi, Indonesia with description of two new species (Crustacea: Decapoda: Caridea).

The atyid shrimp Caridina linduensis Roux, 1904, has not been reported since its description more than a century ago. We here redescribe and figure this poorly known species based on new material from its type locality, Lake Lindu, Central Sulawesi, Indonesia. Two new species, C. dali sp. nov. and C. kaili sp. nov. are also found in this lake and they are described and illustrated. Compared to C. linduensis, C. dali sp. nov. is distinguished by its relatively shorter rostrum which only overreaches the end of basal segment of antennular peduncle and the fewer teeth on the incisor process of the mandible. Caridina kaili sp. nov. can be separated from C. linduensis by its extremely short rostrum, which reaches almost or just reaches the end of the basal segment of the antennular peduncle, proportionately stouter second pereiopod and larger egg size. The two new species also prefer different habitats; C. linduensis is a true lake inhabitant, C. dali sp. nov. can be found both in the lake itself and associated streams while C. kaili sp. nov. is an obligate stream species.

The complete mitogenome of the Australian freshwater shrimp Paratya australiensis Kemp, 1917 (Crustacea: Decapoda: Atyidae)

The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.

New records of anchialine fauna from the Yucatan Peninsula, Mexico

New records for 17 species of crustaceans from anchialine systems in the Yucatan Peninsula, Mexico, are presented. The records come from explorations in Dzilam de Bravo, Yucatan, and from Puerto Aventuras and the Nohoch Nah Chich and Ox Bel Ha cave systems near Tulum in Quintana Roo, Mexico. For five of the 17 species dealt with here, the records presented constitute the second time those species are reported after their original descriptions. For the alpheid shrimp Yagerocaris cozumel, we present the first record of the species for continental Yucatan and for the atyid shrimp Jonga serrei, the second record from Mexico. Depth data are provided for all species.

To "bee" or not to be-on some ornamental shrimp from Guangdong Province, Southern China and Hong Kong SAR, with descriptions of three new species.

Several atyid specimens were collected from hill streams in Guangdong Province, Southern China and Hong Kong during fieldtrips between 2004 and 2013. Some of these species, most of them also sold as ornamental pet shrimp in the international aquarium trade, proved to be new to science by morphological observation and analysis of mtDNA sequences. Three new species, Caridina logemanni n. sp., Caridina mariae n. sp. and Caridina conghuensis n. sp., all of them members of the so called Caridina serrata species group (Cai & Ng 1999) are described in detail below. Caridina tumida Wang, Liang & Li, 2008 is synonymised with Caridina venusta Wang, Liang & Li, 2008. Caridina meridionalis Wang, Liang & Li, 2008 is moved to the genus Paracaridina Liang, Guo & Tang, 1999 and synonymised with Paracaridina zijinica Liang, 2002. New records for Caridina trifasciata Yam & Cai, 2003 and Caridina serrata Stimpson, 1860 are recorded. All species are compared to their morphologically closest congeners and the phylogenetic relationships between atyid shrimps from Southern China are shown.

How might sea level change affect arthropod biodiversity in anchialine caves: a comparison of Remipedia and Atyidae taxa (Arthropoda: Altocrustacea)

Sea level change influences biodiversity of endemic cave fauna to varying degrees. In anchialine systems, a marine layer flows under less saline layers, each with differing associated fauna. We assess the role of present and historic (last glacial maximum – 18,000 years ago) distance from the ocean in determining species richness and phylogenetic diversity patterns for two groups of anchialine crustaceans: the marine-restricted Remipedia and a subset of groundwater-inhabiting atyid shrimp with greater tolerance for salinity variation. We calculated species richness and phylogenetic diversity per cave based on records of remipede and atyid diversity at 137 locations in the Yucatan Peninsula, Caribbean, Australia, and the Canary Islands. After calculating the distance of each cave’s surface opening from the past and present shoreline, we evaluated how species richness and phylogenetic diversity change with distance from the present and historic ocean. Remipede species richness and phylogenetic diversity declined rapidly with distance from the ocean. Ninety-five percent of the remipedes surveyed were located within 7 km of the present ocean and 18 km of the historic ocean. Atyid species richness and phylogenetic diversity declined more slowly with distance from the ocean than that of remipedes. Atyid shrimp were also distributed over a broader range: 95 % were located within 100 km of the present ocean and 240 km of the historic ocean. Our findings indicate that coastal geomorphology and salinity tolerance influence a clade’s distribution with respect to its distance from the ocean. We also report a possible latent response to sea level change.

Redescription of the stygobitic shrimp Troglocaris (Xiphocaridinella) jusbaschjani Birštein, 1948 (Decapoda: Caridea: Atyidae) from Agura River, Sochi, Russia, with remarks on other representatives of the genus from Caucasus.

The complete re-description of Caucasian local endemic stygobitic atyid shrimp Troglocaris (Xiphocaridinella) jusbaschjani Birštein, 1948 is firstly presented after its original description given by Dr. Ya. A. Birštein (1948) under the name Troglocaris schmidti jusbaschjani. The species is still known exclusively from the type locality, hydrogen sulfide bathes of the small Agura River, Sochi area, Russian Federation. Remarks on morphology, coloration of both females and males and data on ecology of Troglocaris (Xiphocaridinella) jusbaschjani Birštein, 1948 as well as remarks on morphology of relative congeneric species from Caucassus, Troglocaris (Xiphocaridinella) kutaissiana (Sadowsky, 1930) (type species of the subgenus) and Troglocaris (Xiphocaridinella) fagei Birštein, 1939, are provided. Discussion on the validity of some subgenera within the genus Troglocaris s. str. Dormitzer, 1853 are also presented.