Microbiome analyses and presence of cable bacteria in the burrow sediment of Upogebia pugettensis

We utilized methods of sediment cultivation, catalyzed reporter deposition-fluorescence in situ hybridization, scanning electron microscopy, and 16s rRNA gene sequencing to investigate the presence of novel filamentous cable bacteria (CB) in estuarine sediments bioturbated by the mud shrimp Upogebia pugettensis Dana and also to test for trophic connections between the shrimp, a commensal bivalve (Neaeromya rugifera), and the sediment. Agglutinated sediments from the linings of shrimp burrows exhibited higher abundances of CB compared to surrounding suboxic and anoxic sediments. Furthermore, CB abundance and activity increased in these sediments when they were incubated under oxygenated seawater. Through core microbiome analysis, we found that the microbiomes of the shrimp and bivalve shared 181 taxa with the sediment bacterial community, and that these shared taxa represented 17.9% of all reads. Therefore, bacterial biomass in the burrow sediment lining is likely a major food source for both the shrimp and the bivalve. The biogeochemical conditions created by shrimp burrows and other irrigators may help promote the growth of CB and select for other dominant members of the bacterial community, particularly a variety of members of the Proteobacteria. These associations give new understanding to the ecology of a burrowing crustacean that is common, but in decline, throughout intertidal mudflats of Northeastern Pacific estuaries.

Physiological consequences of parasite infection in the burrowing mud shrimp, Upogebia pugettensis, a widespread ecosystem engineer

The burrowing mud shrimp, Upogebia pugettensis, is an important ecosystem engineer throughout bays and estuaries along the Pacific coast of North America. Populations of U. pugettensis have recently declined throughout its range. A likely reason for this decline is the arrival of an invasive bopyrid isopod parasite, Orthione griffenis, which has colonised the system and increased in prevalence. We tested the following three hypotheses regarding this host–parasite system: (1) parasite infection is correlated with the volume of water processed by the host; (2) infection negatively affects host’s energetic state; and (3) infection causes feminisation in male hosts. We used several physiological and morphological measures to quantify the effects of this parasite infection on U. pugettensis. The parasite appears to have different physiological effects on male and female hosts. Our study provides mixed support for the previous theory that predicted the mechanistic interactions between this host and its new parasite. Recent examples from other systems have demonstrated that invasive parasites can have far-reaching influences when they infect ecosystem engineers. Given the negative effects of O. griffenis on U. pugettensis, this invasive parasite may have similarly large impacts on Pacific North-west estuaries throughout its invaded range.

Ecological periodic tables for nekton usage of four US Pacific Northwest estuarine habitats

We compared the species composition and abundance of the total nekton community, using the Bray–Curtis similarity coefficient, and mean total nekton, fish and crab species richness, abundance and biomass, and shrimp abundance across four intertidal habitats in a US Pacific Northwest estuary: (i) eelgrass ( Zostera marina ); (ii) burrowing mud shrimp ( Upogebia pugettensis ); (iii) burrowing ghost shrimp ( Neotrypaea californiensis ); and (iv) unvegetated sand. Field sampling was conducted during daytime high tides, and was quantitative, stratified-by-habitat, randomized, and estuary-wide. More than 10 000 nekton specimens belonging to 64 taxa were collected in 454 samples during 10 sampling periods, each approximately one-month-long (from June to November), over 3 years (1998–2000). Non-metric multidimensional scaling analyses revealed annually recurring across-habitat patterns in total nekton Bray–Curtis similarity. Two-way (habitat, year) analyses of variance revealed annually recurring across-habitat patterns on 10 indicators of nekton-habitat quality and preference. Total nekton species richness, abundance, and biomass were, respectively, on average, 8 ×, 25 ×, and 25× greater in eelgrass, 4 ×, 6 ×, and 5× greater in mud shrimp, and 2 ×, 3 ×, and 2× greater in ghost shrimp, than in sand habitat. Our findings validate the ecological relevance of our habitats to nekton, and suggest they can serve as elements in ecological periodic tables of nekton habitat usage.