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ArticleChallenges associated with modeling low-oxygen waters in Chesapeake Bay : a multiple model comparison(Copernicus Publications on behalf of the European Geosciences Union, 2016-04-06) Irby, Isaac D. ; Friedrichs, Marjorie A. M. ; Friedrichs, Carl T. ; Bever, Aaron J. ; Hood, Raleigh R. ; Lanerolle, Lyon W. J. ; Li, Ming ; Linker, Lewis ; Scully, Malcolm E. ; Sellner, Kevin G. ; Shen, Jian ; Testa, Jeremy M. ; Wang, Hao ; Wang, Ping ; Xia, MengAs three-dimensional (3-D) aquatic ecosystem models are used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, 2-year simulations of the Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically compared to each other and to historical monitoring data. Results show that although models have difficulty resolving the variables typically thought to be the main drivers of dissolved oxygen variability (stratification, nutrients, and chlorophyll), all eight models have significant skill in reproducing the mean and seasonal variability of dissolved oxygen. In addition, models with constant net respiration rates independent of nutrient supply and temperature reproduced observed dissolved oxygen concentrations about as well as much more complex, nutrient-dependent biogeochemical models. This finding has significant ramifications for short-term hypoxia forecasts in the Chesapeake Bay, which may be possible with very simple oxygen parameterizations, in contrast to the more complex full biogeochemical models required for scenario-based forecasting. However, models have difficulty simulating correct density and oxygen mixed layer depths, which are important ecologically in terms of habitat compression. Observations indicate a much stronger correlation between the depths of the top of the pycnocline and oxycline than between their maximum vertical gradients, highlighting the importance of the mixing depth in defining the region of aerobic habitat in the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in hypoxia simulations will thus depend more on the ability of models to reproduce the correct mean and variability of the depth of the physically driven surface mixed layer than the precise magnitude of the vertical density gradient.
ArticleToward an understanding of the molecular mechanisms of barnacle larval settlement : a comparative transcriptomic approach(Public Library of Science, 2011-07-29) Chen, Zhang-Fan ; Matsumura, Kiyotaka ; Wang, Hao ; Arellano, Shawn M. ; Yan, Xingcheng ; Alam, Intikhab ; Archer, John A. C. ; Bajic, Vladimir B. ; Qian, Pei-YuanThe barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.