Estimating Long-term Trends in Populations of Two Ecosystem Engineering Burrowing Shrimps in Pacific Northwest (USA) Estuaries.

Temporal variation in the density and distribution of the burrowing shrimps, Neotrypaea californiensis and Upogebia pugettensis, were compared in two estuaries along the West coast of the United States (USA) where they are recognized as important ecosystem engineers. Since these shrimp construct deep burrows in the sediment, we quantified the relationship between burrow openings and shrimp density (1.5 and 1.7 burrow openings per shrimp for N. californiensis and U. pugettensis respectively) to permit population abundance estimates to be made over broad landscape scales. Neotrypaea californiensis populations estimated from burrow counts collected using a gridded survey design across representative tide flats declined by 25% between 2008-2010 in Yaquina Bay, Oregon and by 67% in Willapa Bay, Washington from 2006-2011, but increased again in Willapa Bay by 2014. Upogebia pugettensis had mostly disappeared from Willapa Bay by 2006 and declines were observed in Yaquina Bay, but the magnitude and long-term trajectory of U. pugettensis in this estuary was less clear. These species population fluctuations mirrored those observed in density collected at discrete sampling locations over the same period, equate to large changes in secondary production, and have likely resulted in substantial changes to estuarine habitat and food webs.

The complete mitochondrial genome and phylogenetic analysis of Upogebia major (De Haan, 1841).

The complete mitochondrial (mt) genome of Upogebia major (De Haan, 1841) is 16,131 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The nucleotide composition for U. major is 34.3% of A, 36.6% of T, 10.9% of C, and 18.3% of G. All PCGs are initiated by ATN codons, except for the cox1 gene, which was not determined. Nine PCGs use a common stop codon of TAA or TAG, the other four end with an incomplete stop codon (a single stop nucleotide T). Phylogenetic tree analysis showed that U. major had a close relationship with the species from the family Thalassinidae. The study will provide an important theoretical basis for further analysis of mt genome evolution and the phylogenetic relationships of the order Decapoda.

More cautionary tales: family, generic and species synonymies of recently published taxa of ghost and mud shrimps (Decapoda: Axiidea and Gebiidea).

Re-examination of the holotype of Neoaxius nicoyaensis Sakai, 2017 showed that it is conspecific with the axiid Guyanacaris caespitosa Squires, 1979 and thus Neoaxius Sakai, 2017 and Neoaxiidae Sakai, 2017 are respectively subjective junior synonyms of Guyanacaris Sakai, 2011 and Axiidae Huxley, 1879. The types and numerous specimens of the callianassid Trypaea vilavelebita Sakai Türkay, 2012 are juveniles of the common northeastern Atlantic-Mediterranean species, Callianassa subterranea (Montagu, 1808); the name is therefore a subjective junior synonym. The monotypic callianopsid genera Pleurocalliax Sakai, 2011, Neocallianopsis Sakai, 2011 and Phaetoncalliax Sakai, Türkay, Beuck Freiwald, 2015 are found not to differ from Callianopsis de Saint Laurent, 1973, the only alleged differences found to be untrue or trivial. Phaetoncalliax mauritana Sakai, Türkay, Beuck Freiwald, 2015 and Neocallianopsis africana Sakai, Türkay, Beuck Freiwald, 2015 are thereby transferred to Callianopsis, the latter a subjective junior synonym of the former. Contrary to the assertion of its author, the gourretiid Pseudogourretia portsudanensis Sakai, 2005, the only species in its genus, has no pleurobranchs. The genus Pseudogourretia Sakai, 2005 is therefore synonymised with Gourretia de Saint Laurent, 1973. The respective holotypes of Paracalliax stenophthalmus Sakai, Türkay, Beuck Freiwald, 2015 and Paracalliax bollorei de Saint Laurent, 1979 were re-examined. Both are from the Banc d'Arguin, off Mauritania, and are identical at the species level. The upogebiid Kuwaitupogebia nithyanandan Sakai, Türkay Al Aidaroos, 2015 from Kuwait is identical to Upogebia balmaorum Ngoc-Ho, 1990 from the Seychelles, Madagascar and tropical Western Australia. Kuwaitupogebia Sakai, Türkay Al Aidaroos, 2015 is therefore synonymised with Upogebia Leach, 1814 and Kuwaitupogebiidae Sakai, Türkay Al Aidaroos, 2015 with Upogebiidae Borradaile, 1903.

On a New Species of Parasitic Barnacle (Crustacea: Rhizocephala), Sacculina shiinoi sp. nov., Parasitizing Japanese Mud Shrimps Upogebia spp. (Decapoda: Thalassinidea: Upogebiidae), Including a Description of a Novel Morphological Structure in the Rhizocephala.

The rhizocephalan Sacculina shiinoi sp. nov. parasitizes three species of Upogebia in Japan. It is described morphologically and compared with another Upogebia parasite, Sacculina upogebiae Shiino, 1943 from Japan and Korea. These two species are the only sacculinids that parasitize mud shrimps. DNA analyses clearly show the two species to be separate and not closely related. The cuticle differs in being provided with close-set, branched, and spiny excrescences in S. shiinoi, while it lacks excrescences, but forms small scales in S. upogebiae. In S. upogebiae, the bulbous sperm-producing part and the narrow receptacle duct are separated by a compartmentalized mid portion, which is missing in S. shiinoi. A ridge, having a thickened, fluffy cuticle with a U-shaped course, passes across the visceral mass between the two receptacle openings in S. shiinoi. Such a structure has never been described in other rhizocephalans, and its function is uncertain.

Complete mitochondrial genome of Upogebia yokoyai (Decapoda, Crustacea) from Jejudo, Korea.

The complete mitochondrial DNA of an ecologically important crustacean mud shrimp, Upogebia yokoyai (Decapoda, Crustacea) was sequenced. We used next generation sequencing strategy for total genomic DNA and organelle genome pipeline for mitogenome assembly. A newly determined mitogenome was 16,063 bp in total length with 28% of GC content. Thirty-seven genes were identified including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. We found ten case of overlapping between neighboring genes. Based on genome comparison, the mitogenome of U. yokoyai shows general crustacean gene content and identical synteny to the sister species, such as U. major and U. pusilla. Our results will provide useful information for mitochondrial genome diversity and evolution of the Crustacea.

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification.

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79-97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms.