Magnitude and predictability of ph fluctuations shape plastic responses to ocean acidification

16 pages, 5 figures, supplemental material https://www.journals.uchicago.edu/doi/suppl/10.1086/712930.-- Data and Code Availability: All raw data and referenced supplemental files in this article have been deposited in the Dryad Digital Repository (https://doi.org/10.5061/dryad.tqjq2bvxc; Bitter et al. 2020). All code associated with statistical analyses and figure generation for this article are publicly available at GitHub (https://github.com/MarkCBitter/pHFluctuation_Plasticity) and Zenodo (https://doi.org/10.5281/zenodo.4306829; Bitter 2020)Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus galloprovincialis. We linked differences in the magnitude and predictability of pH fluctuations in two habitats to population-specific gene expression profiles in ambient and stressful pH treatments. Our results demonstrate population-based differentiation in gene expression plasticity, whereby mussels native to a habitat exhibiting a large magnitude of pH fluctuations with low predictability display reduced phenotypic plasticity between experimentally imposed pH treatments. This work validates recent theoretical findings on evolution in fluctuating environments, suggesting that the predictability of fluctuating selection pressures may play a predominant role in shaping the phenotypic variation observed across natural populationsM.C.B. was supported by a National Science Foundation Graduate Research Fellowship Program grant (1746045) and a Department of Education grant (P200A150101). L.K. was supported by a National Science Foundation grant (OCE-1521597), which provided research support for this work. This research was also supported in part by the University of Chicago’s France and Chicago Collaborating in the Sciences program to C.A.P. and M.C.B.With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)Peer reviewe

A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected South Africans

Author Summary: Human pathogen-specific immune responses are tremendously complex and the techniques to study them ever expanding. There is an urgent need for a quantitative analysis and better understanding of pathogen-specific immune responses. Mycobacterium tuberculosis (Mtb) is one of the leading causes of mortality due to an infectious agent worldwide. Here, we were able to quantify the Mtb-specific response in healthy individuals with Mtb infection from South Africa. The response is highly diverse and 66 epitopes are required to capture 80% of the total reactivity. Our study also show that the majority of the identified epitopes are restricted by multiple HLA alleles. Thus, technical advances are required to capture and characterize the complete pathogen-specific response. This study demonstrates further that the approach combining identified epitopes into "megapools" allows capturing a large fraction of the total reactivity. This suggests that this technique is generally applicable to the characterization of immunity to other complex pathogens. Together, our data provide for the first time a quantitative analysis of the complex pathogen-specific T cell response and provide a new understanding of human infections in a natural infection setting

Standing genetic variation fuels rapid adaptation to ocean acidification

10 pages, 4 figures, supplementary information https://doi.org/10.1038/s41467-019-13767-1Global climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous global change stressor that is affecting marine ecosystems globally. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the Mediterranean mussel, Mytilus galloprovincialis. We reared a genetically diverse larval population in two pH treatments (pH 8.1 and 7.4) and tracked changes in the shell-size distribution and genetic variation through settlement. Additionally, we identified differences in the signatures of selection on shell growth in each pH environment. Both phenotypic and genetic data show that standing variation can facilitate adaptation to declines in seawater pH. This work provides insight into the processes underpinning rapid evolution, and demonstrates the importance of maintaining variation within natural populations to bolster species’ adaptive capacity as global change progressesThis research was supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. 1746045 to M.C.B. and NSF OCE-1521597 to L.K. M.C.B. was supported by Department of Education Grant No. P200A150101. L.K. was also supported by the European Commission Horizon 2020 Marie Sklodowska-Curie Action (No. 747637). Research funding was provided by the France and University of Chicago Center FAACTs award to C.A.P. and M.C.B

Harnessing computational genomics to explore the dynamics of rapid adaptation to ocean acidification

Ocean Sciences Meeting (OSM), 16-21 February 2020, San Diego, CA, USAAccurately forecasting biological responses to global ocean change hinges upon understanding the capacity for marine species to adapt in response to the shifting abiotic environment. Emerging methods from computational genomics provide a promising, and increasingly affordable, means to quantify levels of adaptive genetic variation within natural populations, thereby providing a proxy for this adaptive capacity. By linking the phenotypic and physiological traits affected by global change stressors to their underlying genetic basis, it is possible to probe the extent to which these traits may evolve under an ocean global change scenario. I will discuss a cross-disciplinary study that combined an extensive lab-based experiment with high-throughput sequencing to determine the capacity of the marine mussel, Mytilus galloprovincialis, to adapt to extreme and abrupt changes in seawater pH. Specifically, we tracked the shell size distribution and frequency of 30,000 single nucleotide polymorphisms of a single, and genetically diverse, larval population of M. galloprovincialis in ambient (pHT = 8.1) and extreme low pH conditions (pHT = 7.4) from the embryo stage through settlement. Additionally, we separated larvae by size to link a fitness-related trait to its underlying genetic background in each treatment. Our phenotypic and genetic data illuminate a reservoir of standing variation within the species to adapt to reductions in seawater pH. We further demonstrate that unique genotypic groups are associated with accelerated shell growth in the ambient and low pH treatments. Lastly, we report a resulting list of candidate genes that will be putatively under selection as ocean acidification progresses, as well as ongoing functional validations (utilizing qPCR and in situ hybridizations) to affirm these candidatesPeer reviewe

Ocean pH fluctuations affect mussel larvae at key developmental transitions

10 pages, 4 figures, supplementary material https://dx.doi.org/10.6084/m9.figshare.c.4325828.-- Data are archived on BCO-DMO, https://www.bco-dmo.org/project/720349Coastal marine ecosystems experience dynamic fluctuations in seawater carbonate chemistry. The importance of this variation in the context of ocean acidification requires knowing what aspect of variability biological processes respond to. We conducted four experiments (ranging from 3 to 22 days) with different variability regimes (pHT 7.4–8.1) assessing the impact of diel fluctuations in carbonate chemistry on the early development of the mussel Mytilus galloprovincialis. Larval shell growth was consistently correlated to mean exposures, regardless of variability regimes, indicating that calcification responds instantaneously to seawater chemistry. Larval development was impacted by timing of exposure, revealing sensitivity of two developmental processes: development of the shell field, and transition from the first to the second larval shell. Fluorescent staining revealed developmental delay of the shell field at low pH, and abnormal development thereof was correlated with hinge defects in D-veligers. This study shows, for the first time, that ocean acidification affects larval soft-tissue development, independent from calcification. Multiple developmental processes additively underpin the teratogenic effect of ocean acidification on bivalve larvae. These results explain why trochophores are the most sensitive life-history stage in marine bivalves and suggest that short-term variability in carbonate chemistry can impact earlyThis research was funded by the US National Science Foundation (NSF; OCE-1521597 to L.K.). L.K. was also supported by the European Commission Horizon 2020 Marie Skłodowska-Curie Action (No. 747637). M.C.B. was supported by US Department of Education (Grant No. 200A150101) and NSF Graduate Research Fellowship (No. 1000198423). A.M. was supported by an Erasmus+ traineeship scholarship (University of Genova) and by the Observatoire Océanologique de Villefranch

Molecular basis of ocean acidification sensitivity and adaptation in <i>Mytilus galloprovincialis</i>

Predicting the potential for species adaption to climate change is challenged by the need to identify the physiological mechanisms that underpin species vulnerability. Here, we investigated the sensitivity to ocean acidification in marine mussels during early development, and specifically the trochophore stage. Using RNA and DNA sequencing and in situ RNA hybridization, we identified developmental processes associated with abnormal development and rapid adaptation to low pH. Trochophores exposed to low pH seawater exhibited 43 differentially expressed genes. Gene annotation and in situ hybridization of differentially expressed genes point to pH sensitivity of (1) shell field development and (2) cellular stress response. Five genes within these two processes exhibited shifts in allele frequencies indicative of a potential for rapid adaptation. This case study contributes direct evidence that protecting species’ existing genetic diversity is a critical management action to facilitate species resilience to climate change