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  • Cell Press  (22,463)
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  • 1
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    TurtleCam : a “smart” autonomous underwater vehicle for investigating behaviors and habitats of sea turtles (2018)
    Frontiers Media
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    Publication Date: 2018-05-08
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 90, doi:10.3389/fmars.2018.00090.
    Description: Sea turtles inhabiting coastal environments routinely encounter anthropogenic hazards, including fisheries, vessel traffic, pollution, dredging, and drilling. To support mitigation of potential threats, it is important to understand fine-scale sea turtle behaviors in a variety of habitats. Recent advancements in autonomous underwater vehicles (AUVs) now make it possible to directly observe and study the subsurface behaviors and habitats of marine megafauna, including sea turtles. Here, we describe a “smart” AUV capability developed to study free-swimming marine animals, and demonstrate the utility of this technology in a pilot study investigating the behaviors and habitat of leatherback turtles (Dermochelys coriacea). We used a Remote Environmental Monitoring UnitS (REMUS-100) AUV, designated “TurtleCam,” that was modified to locate, follow and film tagged turtles for up to 8 h while simultaneously collecting environmental data. The TurtleCam system consists of a 100-m depth rated vehicle outfitted with a circular Ultra-Short BaseLine receiver array for omni-directional tracking of a tagged animal via a custom transponder tag that we attached to the turtle with two suction cups. The AUV collects video with six high-definition cameras (five mounted in the vehicle nose and one mounted aft) and we added a camera to the animal-borne transponder tag to record behavior from the turtle's perspective. Since behavior is likely a response to habitat factors, we collected concurrent in situ oceanographic data (bathymetry, temperature, salinity, chlorophyll-a, turbidity, currents) along the turtle's track. We tested the TurtleCam system during 2016 and 2017 in a densely populated coastal region off Cape Cod, Massachusetts, USA, where foraging leatherbacks overlap with fixed fishing gear and concentrated commercial and recreational vessel traffic. Here we present example data from one leatherback turtle to demonstrate the utility of TurtleCam. The concurrent video, localization, depth and environmental data allowed us to characterize leatherback diving behavior, foraging ecology, and habitat use, and to assess how turtle behavior mediates risk to impacts from anthropogenic activities. Our study demonstrates that an AUV can successfully track and image leatherback turtles feeding in a coastal environment, resulting in novel observations of three-dimensional subsurface behaviors and habitat use, with implications for sea turtle management and conservation.
    Description: This research was funded by National Oceanic and Atmospheric Administration Grant #NA16NMF4720074 to the Massachusetts Division of Marine Fisheries under the Species Recovery Grants to States program. Additional funding was provided by Jean Tempel, Hydroid Inc., and over 100 Project WHOI donors.
    Keywords: Autonomous underwater vehicle AUV ; CTD ; Entanglement ; Habitat ; Foraging behavior ; Jellyfish ; Leatherback sea turtle ; Video camera
    Repository Name: Woods Hole Open Access Server
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  • 2
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    High grazing rates on cryptophyte algae in Chesapeake Bay (2018)
    Frontiers Media
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    Publication Date: 2018-07-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 241, doi:10.3389/fmars.2018.00241.
    Description: Cryptophyte algae are globally distributed photosynthetic flagellates found in freshwater, estuarine, and neritic ecosystems. While cryptophytes can be highly abundant and are consumed by a wide variety of protistan predators, few studies have sought to quantify in situ grazing rates on their populations. Here we show that autumnal grazing rates on in situ communities of cryptophyte algae in Chesapeake Bay are high throughout the system, while growth rates, particularly in the lower bay, were low. Analysis of the genetic diversity of cryptophyte populations within dilution experiments suggests that microzooplankton may be selectively grazing the fastest-growing members of the population, which were generally Teleaulax spp. We also demonstrate that potential grazing rates of ciliates and dinoflagellates on fluorescently labeled (FL) Rhodomonas salina, Storeatula major, and Teleaulax amphioxeia can be high (up to 149 prey predator−1 d−1), and that a Gyrodinium sp. and Mesodinium rubrum could be selective grazers. Potential grazing was highest for heterotrophic dinoflagellates, but due to its abundance, M. rubrum also had a high overall impact. This study reveals that cryptophyte algae in Chesapeake Bay can experience extremely high grazing pressure from phagotrophic protists, and that this grazing likely shapes their community diversity.
    Description: The authors thank the National Science Foundation (OCE 1031718 and 1436169) for providing support for this research.
    Keywords: Cryptophytes ; Mixotrophy ; Grazing ; Chesapeake Bay ; Dinoflagellates ; Mesodinium rubrum
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  • 3
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    Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 647, doi:10.3389/fmicb.2014.00647.
    Description: The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.
    Description: This work was supported by the Brazilian National Counsel of Technological and Scientific Development (Polar Canion CNPq 556848/2009-8, ProOasis CNPq 565040/2010-3, Interbiota CNPq 407889/2013-2 and INCT-MAR-COI). Alex Enrich-Prast received a CNPq Productivity fellowship. Camila N. Signori was supported by a WHOI Mary Sears Visitor Award (for the microbial community analyses) and by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) for the “Doctorate Sandwich” scholarship (n. 18835/12-0).
    Keywords: Antarctica ; Pyrosequencing ; Microbial community structure ; Environmental factors ; Microbial oceanography ; Climate change
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  • 4
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    The gut microbiota of rural Papua New Guineans : composition, diversity patterns, and ecological processes (2015)
    Cell Press
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cell Reports 11 (2015): 1-12, doi:10.1016/j.celrep.2015.03.049.
    Description: Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ecological mechanisms have not been elucidated. Here, we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, and bacterial lineages undetectable in US residents. A quantification of the ecological processes that govern community assembly identified bacterial dispersal as the dominant process that shapes the microbiome in PNG but not in the US. These findings suggest that the microbiome alterations detected in industrialized societies might arise from modern lifestyle factors limiting bacterial dispersal, which has implications for human health and the development of strategies aimed to redress the impact of westernization.
    Description: This study was partly funded by BioGaia AB. BioGaia had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. A portion of this research is part of the Microbiomes in Transition Initiative at Pacific Northwest National Laboratory (PNNL). This research was conducted under the Laboratory Directed Research and Development Program at PNNL, a multi-program national laboratory operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Characterizing the duration and severity of fishing gear entanglement on a North Atlantic right whale (Eubalaena glacialis) using stable isotopes, steroid and thyroid hormones in baleen (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 168, doi:10.3389/fmars.2018.00168.
    Description: North Atlantic right whales (Eubalaena glacialis) are highly endangered and frequently exposed to a myriad of human activities and stressors in their industrialized habitat. Entanglements in fixed fishing gear represent a particularly pervasive and often drawn-out source of anthropogenic morbidity and mortality to the species. To better understand both the physiological response to entanglement, and to determine fundamental parameters such as acquisition, duration, and severity of entanglement, we measured a suite of biogeochemical markers in the baleen of an adult female that died from a well-documented chronic entanglement in 2005 (whale Eg2301). Steroid hormones (cortisol, corticosterone, estradiol, and progesterone), thyroid hormones (triiodothyronine (T3) and thyroxine (T4)), and stable isotopes (δ13C and δ15N) were all measured in a longitudinally sampled baleen plate. This yielded an 8-year profile of foraging and migration behavior, stress response, and reproduction. Stable isotopes cycled in annual patterns that reflect the animal's north-south migration behavior and seasonally abundant zooplankton diet. A progesterone peak, lasting approximately 23 months, was associated with the single known calving event (in 2002) for this female. Estradiol, cortisol, corticosterone, T3, and T4 were also elevated, although variably so, during the progesterone peak. This whale was initially sighted with a fishing gear entanglement in September 2004, but the hormone panel suggests that the animal first interacted with the gear as early as June 2004. Elevated δ15N, T3, and T4 indicate that Eg2301 potentially experienced increased energy expenditure, significant lipid catabolism, and thermal stress approximately 3 months before the initial sighting with fishing gear. All hormones in the panel (except cortisol) were elevated above baseline by September 2004. This novel study illustrates the value of using baleen to reconstruct recent temporal profiles and as a comparative matrix in which key physiological indicators of individual whales can be used to understand the impacts of anthropogenic activity on threatened whale populations.
    Description: The Woods Hole Oceanographic Institution's Ocean Life Institute and Marine Mammal Center funded this study and NL was supported by a Postdoctoral Fellowship from Baylor University.
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  • 6
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    Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Epsilonbacterota ; Evolution
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  • 7
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    Integrating archival tag data and a high-resolution oceanographic model to estimate basking shark (Cetorhinus maximus) movements in the western Atlantic (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 25, doi:10.3389/fmars.2018.00025.
    Description: Basking shark (Cetorhinus maximus) populations are considered “vulnerable” globally and “endangered” in the northeast Atlantic by the International Union for the Conservation of Nature (IUCN). Much of our knowledge of this species comes from surface observations in coastal waters, yet recent evidence suggests the majority of their lives may be spent in the deep ocean. Depth preferences of basking sharks have significantly limited movement studies that used pop-up satellite archival transmitting (PSAT) tags as conventional light-based geolocation is impossible for tagged animals that spend significant time below the photic zone. We tagged 57 basking sharks with PSAT tags in the NW Atlantic from 2004 to 2011. Many individuals spent several months at meso- and bathy-pelagic depths where accurate light-level geolocation was impossible during fall, winter and spring. We applied a newly-developed geolocation approach for the PSAT data by comparing three-dimensional depth-temperature profile data recorded by the tags to modeled in situ oceanographic data from the high-resolution HYbrid Coordinate Ocean Model (HYCOM). Observation-based likelihoods were leveraged within a state-space hidden Markov model (HMM). The combined tracks revealed that basking sharks moved from waters around Cape Cod, MA to as far as the SE coast of Brazil (20°S), a total distance of over 17,000 km. Moreover, 59% of tagged individuals with sufficient deployment durations (〉250 days) demonstrated seasonal fidelity to Cape Cod and the Gulf of Maine, with one individual returning to within 60 km of its tagging location 1 year later. Tagged sharks spent most of their time at epipelagic depths during summer months around Cape Cod and in the Gulf of Maine. During winter months, sharks spent extended periods at depths of at least 600 m while moving south to the Sargasso Sea, the Caribbean Sea, or the western tropical Atlantic. Our work demonstrates the utility of applying advances in oceanographic modeling to understanding habitat use of highly migratory, often meso- and bathy-pelagic, ocean megafauna. The large-scale movement patterns of tagged sharks highlight the need for international cooperation when designing and implementing conservation strategies to ensure that the species recovers from the historical effects of over-fishing throughout the North Atlantic Ocean.
    Description: We gratefully acknowledge funding from the US National Science Foundation (OCE 0825148), the National Aeronautics and Space Administration (NNS06AA96G), the Massachusetts Environmental Trust, and the Federal Aid in Sport Fish Restoration Program. CB was funded by the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Keywords: Movement ecology ; Satellite archival telemetry ; Migration ; Mesopelagic ; Oceanographic modeling ; Site fidelity
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  • 8
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    Identification and removal of contaminant sequences from ribosomal gene databases : lessons from the Census of Deep Life (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 840, doi:10.3389/fmicb.2018.00840.
    Description: Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
    Description: We wish to acknowledge the support of the Sloan Foundation and the Deep Carbon Observatory and the Department of Energy, Office of Fossil Energy (Colwell).
    Keywords: 16S rRNA ; Contamination ; Microbial survey ; Census of Deep Life ; Deep subsurface
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  • 9
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    The eruption of submarine rhyolite lavas and domes in the deep ocean – Havre 2012, Kermadec Arc (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 147, doi:10.3389/feart.2018.00147.
    Description: Silicic effusive eruptions in deep submarine environments have not yet been directly observed and very few modern submarine silicic lavas and domes have been described. The eruption of Havre caldera volcano in the Kermadec arc in 2012 provided an outstanding database for research on deep submarine silicic effusive eruptions because it produced 15 rhyolite (70–72 wt.% SiO2) lavas and domes with a total volume of ∼0.21 km3 from 14 separate seafloor vents. Moreover, in 2015, the seafloor products were observed, mapped and sampled in exceptional detail (1-m resolution) using AUV Sentry and ROV Jason2 deployed from R/V Roger Revelle. Vent positions are strongly aligned, defining NW-SE and E-W trends along the southwestern and southern Havre caldera margin, respectively. The alignment of the vents suggests magma ascent along dykes which probably occupy faults related to the caldera margin. Four vents part way up the steeply sloping southwestern caldera wall at 1,200–1,300 m below sea level (bsl) and one on the caldera rim (1,060 m bsl) produced elongate lavas. On the steep caldera wall, the lavas consist of narrow tongues that have triangular cross-section shapes. Two of the narrow-tongue segments are connected to wide lobes on the flat caldera floor at ∼1,500 m bsl. The lavas are characterized by arcuate surface ridges oriented perpendicular to the propagation direction. Eight domes were erupted onto relatively flat sea floor from vents at ∼1,000 m bsl along the southern and southwestern caldera rim. They are characterized by steep margins and gently convex-up upper surfaces. With one exception, the domes have narrow spines and deep clefts above the inferred vent positions. One dome has a relatively smooth upper surface. The lavas and domes all consist of combinations of coherent rhyolite and monomictic rhyolite breccia. Despite eruption from deep-water vents (most 〉900 m bsl), the Havre 2012 rhyolite lavas and domes are very similar to subaerial rhyolite lavas and domes in terms of dimensions, volumes, aspect ratio, textures and morphology. They show that lava morphology was strongly controlled by the pre-existing seafloor topography: domes and wide lobes formed where the rhyolite was emplaced onto flat sea floor, whereas narrow tongues formed where the rhyolite was emplaced on the steep slopes of the caldera wall.
    Description: This research was funded by an Australian Research Council Postdoctoral fellowship to RJC (DP110102196 and DE150101190), and National Science Foundation grants OCE1357443 and OCE1357216. FI was supported by a Tasmanian Government Postgraduate Award.
    Keywords: Lava ; Dome ; Submarine effusive eruption ; Rhyolite ; Havre
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    Long-term forest soil warming alters microbial communities in temperate forest soils (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 104, doi:10.3389/fmicb.2015.00104.
    Description: Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
    Description: This work was supported by funding from the University of Massachusetts Amherst to DeAngelis and the National Science Foundation Long-term Ecological Research (LTER) Program.
    Keywords: Climate change ; Microbial ecology ; Ribosomal RNA ; rrn operon copy number ; Trophic strategy
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  • 11
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    Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 90, doi:10.3389/fmicb.2015.00090.
    Description: Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.
    Description: SAW, MA, CN, and CAP were supported by NSF PIRE grant OISE-0968211. GeoChip analysis was supported by the Office of the Vice President for Research at the University of Oklahoma and NSF MacroSystems Biology program EF-1065844 to JZ.
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  • 12
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    Presynaptic nanodomains : a tale of two synapses (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 8 (2015): 455, doi:10.3389/fncel.2014.00455.
    Description: Here we summarize the evidence from two “giant” presynaptic terminals—the squid giant synapse and the mammalian calyx of Held—supporting the involvement of nanodomain calcium signals in triggering of neurotransmitter release. At the squid synapse, there are three main lines of experimental evidence for nanodomain signaling. First, changing the size of the unitary calcium channel current by altering external calcium concentration causes a non-linear change in transmitter release, while changing the number of open channels by broadening the presynaptic action potential causes a linear change in release. Second, low-affinity calcium indicators, calcium chelators, and uncaging of calcium all suggest that presynaptic calcium concentrations are as high as hundreds of micromolar, which is more compatible with a nanodomain type of calcium signal. Finally, neurotransmitter release is much less affected by the slow calcium chelator, ethylene glycol tetraacetic acid (EGTA), in comparison to the rapid chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N’,N’-tetraacetic acid (BAPTA). Similarly, as the calyx of Held synapse matures, EGTA becomes less effective in attenuating transmitter release while the number of calcium channels required to trigger a single fusion event declines. This suggests a developmental transformation of microdomain to nanodomain coupling between calcium channels and transmitter release. Calcium imaging and uncaging experiments, in combination with simulations of calcium diffusion, indicate the peak calcium concentration seen by presynaptic calcium sensors reaches at least tens of micromolar at the calyx of Held. Taken together, data from these provide a compelling argument that nanodomain calcium signaling gates very rapid transmitter release.
    Description: This work was supported by a CRP grant from the National Research Foundation of Singapore and by the World Class Institute (WCI) Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology of Korea (MEST) (NRF Grant Number: WCI 2009-003) (to George J. Augustine), and by Operating Grants from the Canadian Institutes of Health Research (MOP-77610, MOP-81159, MOP-14692, VIH-105441) and Canada Research Chair (to Lu-Yang Wang).
    Keywords: Neurotransmitter release ; Calcium signaling ; Calcium channels ; Presynaptic terminals ; Synaptic vesicle trafficking
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  • 13
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    Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1288, doi:10.3389/fmicb.2015.01288.
    Description: We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.
    Description: This work was supported by grants from the Czech Science Foundation (project GA14-14105S), the Grant Agency of Charles University (project 301711), Charles University Specific Research SVV 260208/2015. VE and MP acknowledge support from NSF OCE-0849578 and OCE-0326175 for DHAB and Cariaco data. Unpublished data from Saanich Inlet were generously provided by Steven Hallam whose long-term research at this site is made possible through funding from the Tula Foundation-funded Centre for Microbial Diversity and Evolution, the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation, and the Canadian Institute for Advanced Research for Saanich Inlet data.
    Keywords: Cryptic species ; Environmental clones ; Marine communities ; Species diversity ; Anaerobic protists
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    Exploring the ecology of deep-sea hydrothermal vents in a metacommunity framework (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 49, doi:10.3389/fmars.2018.00049.
    Description: Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a metacommunity) connected by dispersal of planktonic larvae. The dynamics of the metacommunity are influenced not only by birth rates, death rates and interactions of populations at the local site, but also by regional influences on dispersal from different sites. The connections to other communities provide a mechanism for dynamics at a local site to affect features of the regional biota. In this paper, we explore the challenges and potential benefits of applying metacommunity theory to vent communities, with a particular focus on effects of disturbance. We synthesize field observations to inform models and identify data gaps that need to be addressed to answer key questions including: (1) what is the influence of the magnitude and rate of disturbance on ecological attributes, such as time to extinction or resilience in a metacommunity; (2) what interactions between local and regional processes control species diversity, and (3) which communities are “hot spots” of key ecological significance. We conclude by assessing our ability to evaluate resilience of vent metacommunities to human disturbance (e.g., deep-sea mining). Although the resilience of a few highly disturbed vent systems in the eastern Pacific has been quantified, these values cannot be generalized to remote locales in the western Pacific or mid Atlantic where disturbance rates are different and information on local controls is missing.
    Description: LM was supported by NSF OCE 1356738 and DEB 1558904. SB was supported by the NSF DEB 1558904 and the Investment in Science Fund at Woods Hole Oceanographic Institution. MB was supported by the Austrian Science Fund grants P20190-B17 and P16774-B03. LL was supported by NSF OCE 1634172 and the JM Kaplan Fund. MN was supported by NSF DEB 1558904. Y-JW was supported by a Korean Institute of Ocean Science and Technology (KIOST) grant PM60210.
    Keywords: Metacommunity ; Metapopulation ; Hydrothermal vent ; Connectivity ; Resilience ; Disturbance ; Species diversity ; Dispersal
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    Coincident mass occurrence of gelatinous zooplankton in northern Norway (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.
    Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.
    Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).
    Keywords: Jellyfish bloom ; Genetics ; Acoustics ; Nanomia ; North Norwegian fjords ; Gelatinous zooplankton
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    Microbial community structure and associations during a marine dinoflagellate bloom (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 1201, doi:10.3389/fmicb.2018.01201.
    Description: Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom’s trajectory is also highlighted.
    Description: This work was supported by NSFC (41476092, 41741015), S&T Projects of Shenzhen Science and Technology Innovation Committee (JCYJ20150831192329178, JCYJ20170817160708491, and JCYJ20170412171959157), Key Research and Development Plan of Ministry of Science and Technology of China (2017YFC1403600), as well as by the Woods Hole Center for Oceans and Human Health through the National Science Foundation (Grant OCE-1314642), and National Institute of Environmental Health Sciences (Grant 1-P01-ES021923-01).
    Keywords: Microbial community ; Algal bloom ; Dynamic process ; Network interaction ; Ecological function
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    Modeling tissue and blood gas kinetics in coastal and offshore common bottlenose dolphins, Tursiops truncatus (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 838, doi: 10.3389/fphys.2018.00838.
    Description: Bottlenose dolphins (Tursiops truncatus) are highly versatile breath-holding predators that have adapted to a wide range of foraging niches from rivers and coastal ecosystems to deep-water oceanic habitats. Considerable research has been done to understand how bottlenose dolphins manage O2 during diving, but little information exists on other gases or how pressure affects gas exchange. Here we used a dynamic multi-compartment gas exchange model to estimate blood and tissue O2, CO2, and N2 from high-resolution dive records of two different common bottlenose dolphin ecotypes inhabiting shallow (Sarasota Bay) and deep (Bermuda) habitats. The objective was to compare potential physiological strategies used by the two populations to manage shallow and deep diving life styles. We informed the model using species-specific parameters for blood hematocrit, resting metabolic rate, and lung compliance. The model suggested that the known O2 stores were sufficient for Sarasota Bay dolphins to remain within the calculated aerobic dive limit (cADL), but insufficient for Bermuda dolphins that regularly exceeded their cADL. By adjusting the model to reflect the body composition of deep diving Bermuda dolphins, with elevated muscle mass, muscle myoglobin concentration and blood volume, the cADL increased beyond the longest dive duration, thus reflecting the necessary physiological and morphological changes to maintain their deep-diving life-style. The results indicate that cardiac output had to remain elevated during surface intervals for both ecotypes, and suggests that cardiac output has to remain elevated during shallow dives in-between deep dives to allow sufficient restoration of O2 stores for Bermuda dolphins. Our integrated modeling approach contradicts predictions from simple models, emphasizing the complex nature of physiological interactions between circulation, lung compression, and gas exchange.
    Description: AF (N00014-17-1-2756), PT (N000141512553) and FHJ (N00014-14-1-0410) were supported by the Office of Naval Research, and FHJ by an AIASCOFUND fellowship from Aarhus Institute of Advanced Studies, Aarhus University, under EU's FP7 program (Agreement No. 609033). PT received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged.
    Keywords: Diving physiology ; Modeling and simulations ; Gas exchange ; Marine mammals ; Decompression sickness ; Blood gases ; Hypoxia
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    Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 596, doi:10.3389/fmicb.2015.00596.
    Description: Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.
    Description: This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-0644491 awarded to AV.
    Keywords: Mercury ; Metacinnabar ; Sulfur chemosynthesis ; Thiobacillus ; Thiosulfate ; Mercury sulfide dissolution ; Sulfur metabolism ; Sulfur oxidation
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    Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 901, doi:10.3389/fmicb.2015.00901.
    Description: Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
    Description: This work was partly supported by grants from the US National Science Foundation to SS (OCE-0452333, 1136727), to TS (OCE-0117117, 0525907, 0961186, 1043064, 0327261, 1131620), to WS and KD (1434798), as well as a grant by the WHOI Deep Ocean Exploration Institute to SB, TS, and SS.
    Keywords: Hydrothermal vents ; Colonization ; Species sorting ; Settlement ; Volcanic eruption ; 16S rRNA ; Epsilonproteobacteria ; Disturbance
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    Mixotrophic activity and diversity of Antarctic marine protists in austral summer (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 13, doi:10.3389/fmars.2018.00013.
    Description: Identifying putative mixotrophic protist species in the environment is important for understanding their behavior, with the recovery of these species in culture essential for determining the triggers of feeding, grazing rates, and overall impact on bacterial standing stocks. In this project, mixotroph abundances determined using tracer ingestion in water and sea ice samples collected in the Ross Sea, Antarctica during the summer of 2011 were compared with data from the spring (Ross Sea) and fall (Arctic) to examine the impacts of bacterivory/mixotrophy. Mixotrophic nanoplankton (MNAN) were usually less abundant than heterotrophs, but consumed more of the bacterial standing stock per day due to relatively higher ingestion rates (1–7 bacteria mixotroph−1 h−1 vs. 0.1–4 bacteria heterotroph−1 h−1). Yet, even with these high rates observed in the Antarctic summer, mixotrophs appeared to have a smaller contribution to bacterivory than in the Antarctic spring. Additionally, putative mixotroph taxa were identified through incubation experiments accomplished with bromodeoxyuridine-labeled bacteria as food, immunoprecipitation (IP) of labeled DNA, and amplification and high throughput sequencing of the eukaryotic ribosomal V9 region. Putative mixotroph OTUs were identified in the IP samples by taxonomic similarity to known phototroph taxa. OTUs that had increased abundance in IP samples compared to the non-IP samples from both surface and chlorophyll maximum (CM) depths were considered to represent active mixotrophy and include ones taxonomically similar to Dictyocha, Gymnodinium, Pentapharsodinium, and Symbiodinium. These OTUs represent target taxa for isolation and laboratory experiments on triggers for mixotrophy, to be combined with qPCR to estimate their abundance, seasonal distribution and potential impact.
    Description: This work was supported by National Science Foundation Grants OPP-0838955 (RG) and OPP-0838847 (RS).
    Keywords: Protist ; Diversity ; Mixotrophy ; Ross Sea ; Amplicon sequencing
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    Distinct siderophores contribute to iron cycling in the mesopelagic at Station ALOHA (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061.
    Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.
    Description: This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).
    Keywords: Iron ; Siderophores ; Station ALOHA ; Organic ligands ; Iron limitation
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    The origin and role of organic matrix in coral calcification: insights from comparing coral skeleton and abiogenic aragonite (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 170, doi:10.3389/fmars.2018.00170.
    Description: Understanding the mechanisms of coral calcification is critical for accurately projecting coral reef futures under ocean acidification and warming. Recent suggestions that calcification is primarily controlled by organic molecules and the biological activity of the coral polyp imply that ocean acidification may not affect skeletal accretion. The basis for these suggestions relies heavily on correlating the presence of organic matter with the orientation and disorder of aragonite crystals in the skeleton, carrying the assumption that organic matter observed in the skeleton was produced by the polyp to control calcification. Here we use Raman spectroscopy to test whether there are differences in organic matter content between coral skeleton and abiogenic aragonites precipitated from seawater, both before and after thermal annealing (heating). We measured the background fluxorescence and intensity of C-H bonding signals in the Raman spectra, which are commonly attributed to coral polyp-derived skeletal organic matrix (SOM) and have been used to map its distribution. Surprisingly, we found no differences in either fluorescence or C-H bonding between abiogenic aragonite and coral skeleton. Annealing reduced the molecular disorder in coral skeleton, potentially due to removal of organic matter, but the same effect was also observed in the abiogenic aragonites. The presence of organic molecules in the abiogenic aragonites is further supported by measurements of N content and δ15N. Together, our data suggest that some of what has been interpreted in previous studies as polyp-derived SOM may actually be seawater-sourced organic matter or some other signal not unique to biogenic aragonite. Finally, we create a high-resolution Raman map of a Pocillopora skeleton to demonstrate how patterns of fluorescence and elevated calcifying fluid aragonite saturation state (ΩAr) along centers of calcification are consistent with both biological and physico-chemical controls. Our aim is to advance discussion on biological mediation of calcification and the implications for coral resilience in a high-CO2 world.
    Description: This study was supported by an ARC Laureate Fellowship (FL120100049) awarded to Professor Malcolm McCulloch and the ARC Centre of Excellence for Coral Reef Studies (CE140100020).
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    Electrical synapses enhance and accelerate interneuron recruitment in response to coincident and sequential excitation (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 12 (2018): 156, doi:10.3389/fncel.2018.00156.
    Description: Electrical synapses are ubiquitous in interneuron networks. They form intercellular pathways, allowing electrical currents to leak between coupled interneurons. I explored the impact of electrical coupling on the integration of excitatory signals and on the coincidence detection abilities of electrically-coupled cerebellar basket cells (BCs). In order to do so, I quantified the influence of electrical coupling on the rate, the probability and the latency at which BCs generate action potentials when stimulated. The long-lasting simultaneous suprathreshold depolarization of a coupled cell evoked an increase in firing rate and a shortening of action potential latency in a reference basket cell, compared to its depolarization alone. Likewise, the action potential probability of coupled cells was strongly increased when they were simultaneously stimulated with trains of short-duration near-threshold current pulses (mimicking the activation of presynaptic granule cells) at 10 Hz, and to a lesser extent at 50 Hz, an effect that was absent in non-coupled cells. Moreover, action potential probability was increased and action potential latency was shortened in response to synaptic stimulations in mice lacking the protein that forms gap junctions between BCs, connexin36, relative to wild-type (WT) controls. These results suggest that electrical synapses between BCs decrease the probability and increase the latency of stimulus-triggered action potentials, both effects being reverted upon simultaneous excitation of coupled cells. Interestingly, varying the delay at which coupled cells are stimulated revealed that the probability and the speed of action potential generation are facilitated maximally when a basket cell is stimulated shortly after a coupled cell. These findings suggest that electrically-coupled interneurons behave as coincidence and sequence detectors that dynamically regulate the latency and the strength of inhibition onto postsynaptic targets depending on the degree of input synchrony in the coupled interneuron network.
    Description: This work was supported by the laboratory of Brain Physiology at Paris Descartes University (UMR8118), the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche Grant INterneuron NETwork (INNET), the Laboratory of Cellular and Systemic Neurophysiology, Institute for Physiology I at the University of Freiburg, and the Grass foundation.
    Keywords: Gap junction ; Synaptic integration ; Interneurons ; Inhibition ; Coincidence ; Cerebellum
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    Nitrogen limitation of the summer phytoplankton and heterotrophic prokaryote communities in the Chukchi Sea (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 362, doi:10.3389/fmars.2018.00362.
    Description: Major changes to Arctic marine ecosystems have resulted in longer growing seasons with increased phytoplankton production over larger areas. In the Chukchi Sea, the high productivity fuels intense benthic denitrification creating a nitrogen (N) deficit that is transported through the Arctic to the Atlantic Ocean, where it likely fuels N fixation. Given the rapid pace of environmental change and the potentially globally significant N deficit, we conducted experiments aimed at understanding phytoplankton and microbial N utilization in the Chukchi Sea. Ship-board experiments tested the effect of nitrate (NO3-) additions on both phytoplankton and heterotrophic prokaryote abundance, community composition, photophysiology, carbon fixation and NO3- uptake rates. Results support the critical role of NO3- in limiting summer phytoplankton communities to small cells with low production rates. NO3- additions increased particulate concentrations, abundance of large diatoms, and rates of carbon fixation and NO3- uptake by cells 〉1 μm. Increases in the quantum yield and electron turnover rate of photosystem II in +NO3- treatments suggested that phytoplankton in the ambient dissolved N environment were N starved and unable to build new, or repair damaged, reaction centers. While some increases in heterotrophic prokaryote abundance and production were noted with NO3- amendments, phytoplankton competition or grazers likely dampened these responses. Trends toward a warmer more stratified Chukchi Sea will likely enhance summer oligotrophic conditions and further N starve Chukchi Sea phytoplankton communities.
    Description: Fieldwork and analysis for the ICESCAPE program was supported by Ocean Biology and Biogeochemistry Program of the National Aeronautic and Space Administration under Grant No. NNX10AF42G to KA.
    Keywords: Phytoplankton ; Nitrogen ; Chukchi Sea ; Nitrate ; Nutrient limitation
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    Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 605, doi:10.3389/fmicb.2014.00605.
    Description: Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.
    Description: K. Kormas was partially supported by the University of Thessaly through a sabbatical in 2013. Supported by NSF grants OCE-0849578 to Virginia P. Edgcomb and Joan M. Bernhard and OCE-1061391 to Joan M. Bernhard and Virginia P. Edgcomb.
    Keywords: Eukaryote ; DHABs ; Discovery ; Urania, L’ Atalante ; Diversity ; rRNA
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    Rapid and gradual modes of aerosol trace metal dissolution in seawater (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2015): 794, doi:10.3389/fmicb.2014.00794.
    Description: Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence biota. Dissolution behavior occurs over a continuum ranging from rapid dissolution, in which the majority of soluble metal dissolved immediately upon seawater exposure (Cd and Co in our samples), to gradual dissolution, where metals dissolved slowly over time (Zn, Mn, Cu, and Al in our samples). Additionally, dissolution affected by interactions with particles was observed in which a decline in soluble metal concentration over time occurred (Fe and Pb in our samples). Natural variability in aerosol chemistry between samples can cause metals to display different dissolution kinetics in different samples, and this was particularly evident for Ni, for which samples showed a broad range of dissolution rates. The elemental molar ratio of metals in the bulk aerosols was 23,189Fe: 22,651Al: 445Mn: 348Zn: 71Cu: 48Ni: 23Pb: 9Co: 1Cd, whereas the seawater soluble molar ratio after 7 days of leaching was 11Fe: 620Al: 205Mn: 240Zn: 20Cu: 14Ni: 9Pb: 2Co: 1Cd. The different kinetics and ratios of aerosol metal dissolution have implications for phytoplankton nutrition, and highlight the need for unified extraction protocols that simulate aerosol metal dissolution in the surface ocean.
    Description: This work was supported by NSF-OCE grant 0850467 to Adina Paytan, NSF-OCE grant 1233261 to Mak A. Saito, and NATO Science for Peace Grant to Adina Paytan and Anton F. Post (SfP 982161). Katherine R. M. Mackey was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology (Grant No. NSF 1103575) and Chia-Te Chien by an international graduate student fellowship from the ministry of education, Taiwan.
    Keywords: Aerosols ; Atmospheric deposition ; Phytoplankton ; Trace metals ; Ligands
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    The transcriptional response of microbial communities in thawing Alaskan permafrost soils (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 197, doi:10.3389/fmicb.2015.00197.
    Description: Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.
    Description: This work was fostered by grants from WHOI's Arctic Research Initiative to MJLC and AS, as well as a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to WDO.
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    Oxidative formation and removal of complexed Mn(III) by Pseudomonas species (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 560, doi:10.3389/fmicb.2018.00560.
    Description: The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.
    Description: This work was funded by grants from the Chemical Oceanography program of the National Science Foundation (OCE-1558738 and OCE-1558692).
    Keywords: Manganese(III) ; Mn(III)-DFOB ; Mn(III)-citrate ; Mn(III)-L ; Pseudomonas ; Bacterial manganese oxidation
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    Resting metabolic rate and lung function in wild offshore common bottlenose dolphins, Tursiops truncatus, near Bermuda (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 886, doi:10.3389/fphys.2018.00886.
    Description: Diving mammals have evolved a suite of physiological adaptations to manage respiratory gases during extended breath-hold dives. To test the hypothesis that offshore bottlenose dolphins have evolved physiological adaptations to improve their ability for extended deep dives and as protection for lung barotrauma, we investigated the lung function and respiratory physiology of four wild common bottlenose dolphins (Tursiops truncatus) near the island of Bermuda. We measured blood hematocrit (Hct, %), resting metabolic rate (RMR, l O2 ⋅ min-1), tidal volume (VT, l), respiratory frequency (fR, breaths ⋅ min-1), respiratory flow (l ⋅ min-1), and dynamic lung compliance (CL, l ⋅ cmH2O-1) in air and in water, and compared measurements with published results from coastal, shallow-diving dolphins. We found that offshore dolphins had greater Hct (56 ± 2%) compared to shallow-diving bottlenose dolphins (range: 30–49%), thus resulting in a greater O2 storage capacity and longer aerobic diving duration. Contrary to our hypothesis, the specific CL (sCL, 0.30 ± 0.12 cmH2O-1) was not different between populations. Neither the mass-specific RMR (3.0 ± 1.7 ml O2 ⋅ min-1 ⋅ kg-1) nor VT (23.0 ± 3.7 ml ⋅ kg-1) were different from coastal ecotype bottlenose dolphins, both in the wild and under managed care, suggesting that deep-diving dolphins do not have metabolic or respiratory adaptations that differ from the shallow-diving ecotypes. The lack of respiratory adaptations for deep diving further support the recently developed hypothesis that gas management in cetaceans is not entirely passive but governed by alteration in the ventilation-perfusion matching, which allows for selective gas exchange to protect against diving related problems such as decompression sickness.
    Description: Funding for this project was provided by the Office of Naval Research (ONR YIP Award No. N000141410563, and Dolphin Quest, Inc. FHJ was supported by the Office of Naval Research (Award No. N00014-1410410) and an AIAS-COFUND fellowship from Aarhus Institute of Advanced Studies under the FP7 program of the EU (Agreement No. 609033).
    Keywords: Lung mechanics ; Total lung capacity ; Field metabolic rate ; Energetics ; Minimum air volume ; Diving physiology ; Marine mammals ; Spirometry
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    Neural control of dynamic 3-dimensional skin papillae for cuttlefish camouflage (2018)
    Cell Press
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in iScience 1 (2018): 24-34, doi:10.1016/j.isci.2018.01.001.
    Description: The color and pattern changing abilities of octopus, squid, and cuttlefish via chromatophore neuro-muscular organs are unparalleled. Cuttlefish and octopuses also have a unique muscular hydrostat system in their skin. When this system is expressed, dermal bumps called papillae disrupt body shape and imitate the fine texture of surrounding objects, yet the control system is unknown. Here we report for papillae: (1) the motoneurons and the neurotransmitters that control activation and relaxation, (2) a physiologically fast expression and retraction system, and (3) a complex of smooth and striated muscles that enables long-term expression of papillae through sustained tension in the absence of neural input. The neural circuits controlling acute shape-shifting skin papillae in cuttlefish show homology to the iridescence circuits in squids. The sustained tension in papillary muscles for long-term camouflage utilizes muscle heterogeneity and points toward the existence of a “catch-like” mechanism that would reduce the necessary energy expenditure.
    Description: This work was funded by an AFOSR grant no. FA9550-14-1-0134, Isaac Newton Trust/Wellcome Trust ISSF/University of Cambridge Joint Research Grant (097814/Z/11/Z) to P.T.G-B., and a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (BBSRC, BB/L024667/1) to T.J.W.
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    Evaluation of mixotrophy-associated gene expression in two species of polar marine algae (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 273, doi:10.3389/fmars.2018.00273.
    Description: Mixotrophic flagellates can comprise significant proportions of plankton biomass in marine ecosystems. Despite the growing recognition of the importance of this ecological strategy, and the identification of major environmental factors controlling phagotrophic behavior (light and nutrients), the physiological and molecular mechanisms underlying mixotrophic behavior are still unclear. In this study, we performed RNA-Seq transcriptomic analysis for two mixotrophic prasinophytes, Micromonas polaris and Pyramimonas tychotreta, under dissolved nutrient regimes that altered their ingestion of bacteria prey. Though the strains examined were polar isolates, both belong to genera with widespread distribution. Our aim was to characterize the transcriptomes of these two non-model phytoflagellates, identify transcripts consistent with phagotrophic activity and assess their differential expression in response to nutrient stress. De novo assembly of the transcriptomes yielded large numbers of novel coding transcripts with no known match within public databases. A summary of the transcripts by Gene Ontology terms showed many expected expression patterns, including genes involved in photosynthetic pathways and enzymes implicated in nutrient uptake pathways. Searches of KEGG databases identified several genes associated with intra-cellular digestive pathways actively transcribed in both prasinophytes. Differential expression analysis showed a larger response in P. tychotreta, where 23,373 genes were up-regulated and 1,752 were down-regulated in the low nutrient treatment when phagotrophy was enhanced. In contrast, in M. polaris, low nutrient treatments resulted in up-regulation of 314 transcripts while down-regulating 371. With respect to phagotrophic-related expression, 37 genes were co-expressed in both P. tychotreta and M. polaris, and although the response was less pronounced in M. polaris, it is consistent with differences in observed ingestion behavior. This study presents the first genomic data for Pyramimonas tychotreta, and also contributes to the limited available data for Micromonas polaris. Furthermore, it provides insight into the presence of genes associated with phagocytosis within the Prasinophyceae and contributes to the understanding of potential target genes required for the construction of a complete model of gene regulation of phagocytic behavior in algae.
    Description: The Owlsnest Super-Computing Cluster at Temple University is funded by a National Science Foundation Grant CNS-09-58854. The CUNY HPCC is operated by the College of Staten Island and funded, in part, by grants from the City of New York, State of New York, CUNY Research Foundation, and National Science Foundation Grants CNS-0958379, CNS-0855217, and ACI 1126113. Support for this work was also supplied by National Science Foundation grants PLR-1341362 (RG), PLR-1603538 (RS), and PLR-1603833 (RG).
    Keywords: Mixotrophy ; Pyramimonas ; Micromonas ; RNA-Seq ; Transcriptomics ; Phagotrophy
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    Using maximum entropy production to describe microbial biogeochemistry over time and space in a meromictic pond (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Environmental Science 6 (2018): 100, doi:10.3389/fenvs.2018.00100.
    Description: Determining how microbial communities organize and function at the ecosystem level is essential to understanding and predicting how they will respond to environmental change. Mathematical models can be used to describe these communities, but properly representing all the biological interactions in extremely diverse natural microbial ecosystems in a mathematical model is challenging. We examine a complementary approach based on the maximum entropy production (MEP) principle, which proposes that systems with many degrees of freedom will likely organize to maximize the rate of free energy dissipation. In this study, we develop an MEP model to describe biogeochemistry observed in Siders Pond, a phosphate limited meromictic system located in Falmouth, MA that exhibits steep chemical gradients due to density-driven stratification that supports anaerobic photosynthesis as well as microbial communities that catalyze redox cycles involving O, N, S, Fe, and Mn. The MEP model uses a metabolic network to represent microbial redox reactions, where biomass allocation and reaction rates are determined by solving an optimization problem that maximizes entropy production over time, and a 1D vertical profile constrained by an advection-dispersion-reaction model. We introduce a new approach for modeling phototrophy and explicitly represent oxygenic photoautotrophs, photoheterotrophs and anoxygenic photoautotrophs. The metabolic network also includes reactions for aerobic organoheterotrophic bacteria, sulfate reducing bacteria, sulfide oxidizing bacteria and aerobic and anaerobic grazers. Model results were compared to observations of biogeochemical constituents collected over a 24 h period at 8 depths at a single 15 m deep station in Siders Pond. Maximizing entropy production over long (3 day) intervals produced results more similar to field observations than short (0.25 day) interval optimizations, which support the importance of temporal strategies for maximizing entropy production over time. Furthermore, we found that entropy production must be maximized locally instead of globally where energy potentials are degraded quickly by abiotic processes, such as light absorption by water. This combination of field observations and modeling results indicate that natural microbial systems can be modeled by using the maximum entropy production principle applied over time and space using many fewer parameters than conventional models.
    Description: Primary funding for this project was from NSF GG grant EAR-1451356 to JV and JH, with additional support from Gordon and Betty Moore Foundation grant GBMF 3297. JV also received support from NSF Grants OCE-1637630 and OCE-1558710 and Simons Foundation grant 549941. The NSF Center for Dark Energy Biosphere Investigations (C-DEBI; OCE-0939564) also supported the participation of JH.
    Keywords: Maximum entropy production ; Microbial biogeochemistry ; Metabolic networks ; Phototrophy ; Community function ; Meromictic
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    Grxcr1 promotes hair bundle development by destabilizing the physical interaction between Harmonin and Sans usher syndrome proteins (2018)
    Cell Press
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cell Reports 25 (2018): 1281–1291, doi:10.1016/j.celrep.2018.10.005.
    Description: Morphogenesis and mechanoelectrical transduction of the hair cell mechanoreceptor depend on the correct assembly of Usher syndrome (USH) proteins into highly organized macromolecular complexes. Defects in these proteins lead to deafness and vestibular areflexia in USH patients. Mutations in a non-USH protein, glutaredoxin domain-containing cysteine-rich 1 (GRXCR1), cause non-syndromic sensorineural deafness. To understand the deglutathionylating enzyme function of GRXCR1 in deafness, we generated two grxcr1 zebrafish mutant alleles. We found that hair bundles are thinner in homozygous grxcr1 mutants, similar to the USH1 mutants ush1c (Harmonin) and ush1ga (Sans). In vitro assays showed that glutathionylation promotes the interaction between Ush1c and Ush1ga and that Grxcr1 regulates mechanoreceptor development by preventing physical interaction between these proteins without affecting the assembly of another USH1 protein complex, the Ush1c- Cadherin23-Myosin7aa tripartite complex. By elucidating the molecular mechanism through which Grxcr1 functions, we also identify a mechanism that dynamically regulates the formation of Usher protein complexes.
    Description: This work was supported by grants from the NIH (DC004186, OD011195, and HD22486).
    Keywords: Grxcr1 ; Usher syndrome ; Hair cell ; Stereocilia ; Glutathionylation ; Harmonin ; Sans
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    Identification of erosional terraces on seamounts : implications for interisland connectivity and subsidence in the Galápagos Archipelago (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 88, doi:10.3389/feart.2018.00088.
    Description: Shallow seamounts at ocean island hotspots and in other settings may record emergence histories in the form of submarine erosional terraces. Exposure histories are valuable for constraining paleo-elevations and sea levels in the absence of more traditional markers, such as drowned coral reefs. However, similar features can also be produced through primary volcanic processes, which complicate the use of terraced seamounts as an indicator of paleo-shorelines. In the western Galápagos Archipelago, we utilize newly collected bathymetry along with seafloor observations from human-occupied submersibles to document the location and depth of erosional terraces on seamounts near the islands of Santiago, Santa Cruz, Floreana, Isabela, and Fernandina. We directly observed erosional features on 22 seamounts with terraces. We use these observations and bathymetric analysis to develop a framework to identify terrace-like morphologic features and classify them as either erosional or volcanic in origin. From this framework we identify 79 erosional terraces on 30 seamounts that are presently found at depths of 30 to 300 m. Although intermittent subaerial connectivity between the islands has been hypothesized, the depths of these erosional terraces in the Santiago region are the first direct evidence of paleo-connectivity in the modern archipelago. Collectively, the terraces have non-randomly distributed depths. We suggest that peaks in the distribution of terrace depths likely represent long durations of exposure (i.e., sea-level still or lowstands). By comparing these peaks to those of subsidence adjusted sea-level curves, we identify the average subsidence rate that best reproduces the observed terrace distributions. These rates are 0.2–0.4 m/ka for this portion of the central Galápagos, since the formation of the seamounts, consistent with previous independent estimates. Using these subsidence rates and evidence for erosional terraces at depths up to 300 m, we conclude that all islands in the central archipelago have been intermittently connected starting between 435 and 900 ka. Individual island pairs have likely been repeatedly subaerially connected for short intervals since that time.
    Description: This project was carried out with financial support from the NSF (OCE-1634685 to SS and OCE-1634952 to VW) and the Dalio Explore Fund.
    Keywords: Erosional terraces ; Paleogeography ; Hotspot ; Ocean island ; Multibeam bathymetry ; Wave erosion
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    Two forms of electrical transmission between neurons (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Molecular Neuroscience 11 (2018): 427, doi:10.3389/fnmol.2018.00427.
    Description: Electrical signaling is a cardinal feature of the nervous system and endows it with the capability of quickly reacting to changes in the environment. Although synaptic communication between nerve cells is perceived to be mainly chemically mediated, electrical synaptic interactions also occur. Two different strategies are responsible for electrical communication between neurons. One is the consequence of low resistance intercellular pathways, called “gap junctions”, for the spread of electrical currents between the interior of two cells. The second occurs in the absence of cell-to-cell contacts and is a consequence of the extracellular electrical fields generated by the electrical activity of neurons. Here, we place present notions about electrical transmission in a historical perspective and contrast the contributions of the two different forms of electrical communication to brain function.
    Description: This research was supported by National Institutes of Health grants DC03186, DC011099, NS055726, NS085772 and NS0552827 to AP.
    Keywords: Synaptic communication ; Electrical synapse ; Gap junction ; Electric field ; Ephapsis
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    Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 358, doi:10.3389/fmicb.2015.00358.
    Description: Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (〈0.0001%) to relatively abundant (〉0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
    Description: This research was supported by the French National Research Agency (Agence National de Recherche) project Metasoil (Projet ANR-08-GENM-025). TOD was funded by the Rhone-Alpes Région. LM was supported with a PhD fellowship from the Région Rhône-Alpes.
    Keywords: Rare biosphere ; Soil ; Metagenomics ; Environmental genomics ; Plasmids ; Phages
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    Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 646, doi:10.3389/fmicb.2014.00646.
    Description: Rising temperatures and changing winds drive the expansion of the highly productive polynyas (open water areas surrounded by sea ice) abutting the Antarctic continent. Phytoplankton blooms in polynyas are often dominated by the haptophyte Phaeocystis antarctica, and they generate the organic carbon that enters the resident microbial food web. Yet, little is known about how Phaeocystis blooms shape bacterial community structures and carbon fluxes in these systems. We identified the bacterial communities that accompanied a Phaeocystis bloom in the Amundsen Sea polynya during the austral summers of 2007–2008 and 2010–2011. These communities are distinct from those determined for the Antarctic Circumpolar Current (ACC) and off the Palmer Peninsula. Diversity patterns for most microbial taxa in the Amundsen Sea depended on location (e.g., waters abutting the pack ice near the shelf break and at the edge of the Dotson glacier) and depth, reflecting different niche adaptations within the confines of this isolated ecosystem. Inside the polynya, P. antarctica coexisted with the bacterial taxa Polaribacter sensu lato, a cryptic Oceanospirillum, SAR92 and Pelagibacter. These taxa were dominated by a single oligotype (genotypes partitioned by Shannon entropy analysis) and together contributed up to 73% of the bacterial community. Size fractionation of the bacterial community [〈3 μm (free-living bacteria) vs. 〉3 μm (particle-associated bacteria)] identified several taxa (especially SAR92) that were preferentially associated with Phaeocystis colonies, indicative of a distinct role in Phaeocystis bloom ecology. In contrast, particle-associated bacteria at 250 m depth were enriched in Colwellia and members of the Cryomorphaceae suggesting that they play important roles in the decay of Phaeocystis blooms.
    Description: This work received financial support from NSF Antarctic Sciences awards ANT-1142095 (Anton F. Post), ANT-0839069 and ANT-0741409 (Patricia L. Yager), and ANT-0839012 (Hugh W. Ducklow). We further acknowledge the support by “Oden Southern Ocean,” SWEDARP 2010/2011, a project organized by the Swedish Polar Research Secretariat and National Science Foundation Office of Polar Programs.
    Keywords: Amundsen Sea polynya ; Phytoplankton bloom ; Phaeocystis antarctica ; Microbial community structure ; Mutualism
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    Microbes in the coral holobiont : partners through evolution, development, and ecological interactions (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular and Infection Microbiology 4 (2015): 176, doi:10.3389/fcimb.2014.00176.
    Description: In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.
    Description: Support for this work was provided to Janelle R. Thompson by the National Research Foundation of Singapore through the Center for Environmental Sensing and Modeling (CENSAM) and by the MIT Civil and Environmental Engineering Department; to Hanny E. Rivera by the MIT Presidential Fellowship; to Collin J. Closek by the National Geographic Society; and to Mónica Medina by NSF projects IOS 1146880 and IOS 0926906.
    Keywords: Coral ; Holobiont ; Metamorphosis ; Biological ; Symbiosis ; Pollution and global change ; Ecosystem ; Bacterial interactions
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    Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1090, doi:10.3389/fmicb.2015.01090.
    Description: Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
    Description: This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095 to AP.
    Keywords: Southern Ocean ; Amundsen Sea Polynya ; Phytoplankton bloom ; Phaeocystis ; Micromonas ; Microbial communities ; Metagenomics ; Genome reconstruction
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    Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 189, doi:10.3389/fmicb.2018.00189.
    Description: Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that 〉95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.
    Description: This work was funded by NSF research grants OCE-1260233, OCE-1260490, OCE-1657757, and OCE-143566.
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    Marine virus-like particles and microbes : a linear interpretation (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 358, doi:10.3389/fmicb.2018.00358.
    Description: Viruses are key players in ocean ecology and biogeochemistry, not only because of their functional roles but also partially due to their sheer abundance (Fuhrman, 1999; Wilhelm and Suttle, 1999). Because viruses cannot replicate without their hosts' machinery, their abundance is inextricably related to that of their (mostly microbial) hosts. The relationship between viral and microbial abundances is thus of great interest.
    Keywords: Marine viruses ; Virus ; Virioplankton ; Viral abundance ; Virus-like particles ; Virus to microbe ratio ; Virus to bacterium ratio ; Virus-microbe relationship
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    Leaf-FISH : microscale imaging of bacterial taxa on phyllosphere (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2018): 2669, doi:10.3389/fmicb.2017.02669.
    Description: Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.
    Description: Funding was provided by the J. Unger Vetleson Foundation to SS.
    Keywords: Arabidopsis thaliana ; Combinatorial labeling ; Fluorescence in situ hybridization ; Leaf microenvironments ; Methylobacterium ; Phyllosphere ; Preferential colonization ; Zostera marina
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    Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping (2015)
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    Publication Date: 2022-05-26
    Description: .© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 568, doi:10.3389/fmicb.2014.00568.
    Description: The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. Our previous work established that many of these oligotypes had dramatically different distributions between individuals and across oral habitats, suggesting that they represented functionally different organisms. Here we demonstrate the presence of a consistent tongue microbiome but with rapidly fluctuating proportions of the characteristic taxa. In some cases closely related oligotypes representing strains or variants within a single species displayed fluctuating relative abundances over time, while in other cases an initially dominant oligotype was replaced by another oligotype of the same species. We use this high temporal and taxonomic level of resolution to detect correlated changes in oligotype abundance that could indicate which taxa likely interact synergistically or occupy similar habitats, and which likely interact antagonistically or prefer distinct habitats. For example, we found a strong correlation in abundance over time between two oligotypes from different families of Gamma Proteobacteria, suggesting a close functional or ecological relationship between them. In summary, the tongue is colonized by a microbial community of moderate complexity whose proportional abundance fluctuates widely on time scales of days. The drivers and functional consequences of these community dynamics are not known, but we expect they will prove tractable to future, targeted studies employing taxonomically resolved analysis of high-throughput sequencing data sampled at appropriate temporal intervals and spatial scales.
    Description: Supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to Gary G. Borisy). Daniel R. Utter was supported by the Woods Hole Partnership Education Program; A. Murat Eren was supported by a G. Unger Vetlesen Foundation grant to the Marine Biological Laboratory; David B. Mark Welch was supported by NSF DBI-1262592
    Keywords: Human microbiome ; Oral microbiota ; 16S ribosomal RNA ; Haemophilus ; Neisseria ; Streptococcus ; Veillonella
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    Oligotyping reveals community level habitat selection within the genus Vibrio (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 563, doi:10.3389/fmicb.2014.00563.
    Description: The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including the causative agents of human cholera and fish vibriosis. Vibrios display a wide variety of known life histories, from opportunistic pathogens to long-standing symbionts with individual host species. Studying Vibrio ecology has been challenging as individual species often display a wide range of habitat preferences, and groups of vibrios can act as socially cohesive groups. Although strong associations with salinity, temperature and other environmental variables have been established, the degree of habitat or host specificity at both the individual and community levels is unknown. Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats. Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments. Our analyses show that Vibrio communities share considerable overlap between two distinct hosts (i.e., sponge and fish), yet are distinct from the abiotic plastic substrates. Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others. In addition to providing insights into Vibrio ecology across a broad range of habitats, our study shows the utility of oligotyping as a facile, high-throughput and unbiased method for large-scale analyses of publically available sequence data repositories and suggests its wide application could greatly extend the range of possibilities to explore microbial ecology.
    Description: This work was supported by an NSF Collaborative grant to Erik Zettler (OCE-1155379), Tracy J. Mincer (OCE-1155671) and Linda A. Amaral-Zettler (OCE-1155571), NSF TUES grant to Erik Zettler and Linda A. Amaral-Zettler (DUE-1043468). Additional support came from the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J: Linda A. Amaral-Zettler and Leslie Murphy) and an NSF/OCE-1128039 award (Linda A. Amaral-Zettler and Leslie Murphy). Victor Schmidt was supported during this work by an NSF IGERT fellowship (DGE 0966060, Dr. David Rand, PI).
    Keywords: Oligotyping ; Vibrio ecology ; Host-microbe interactions ; Illumina sequencing ; 16S rRNA analysis ; Plastisphere ; Aquaculture pathogens ; Meta-analysis
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    Does elevated CO2 alter silica uptake in trees? (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Plant Science 5 (2015): 793, doi:10.3389/fpls.2014.00793.
    Description: Human activities have greatly altered global carbon (C) and Nitrogen (N) cycling. In fact, atmospheric concentrations of carbon dioxide (CO2) have increased 40% over the last century and the amount of N cycling in the biosphere has more than doubled. In an effort to understand how plants will respond to continued global CO2 fertilization, long-term free-air CO2 enrichment experiments have been conducted at sites around the globe. Here we examine how atmospheric CO2 enrichment and N fertilization affects the uptake of silicon (Si) in the Duke Forest, North Carolina, a stand dominated by Pinus taeda (loblolly pine), and five hardwood species. Specifically, we measured foliar biogenic silica concentrations in five deciduous and one coniferous species across three treatments: CO2 enrichment, N enrichment, and N and CO2 enrichment. We found no consistent trends in foliar Si concentration under elevated CO2, N fertilization, or combined elevated CO2 and N fertilization. However, two-thirds of the tree species studied here have Si foliar concentrations greater than well-known Si accumulators, such as grasses. Based on net primary production values and aboveground Si concentrations in these trees, we calculated forest Si uptake rates under control and elevated CO2 concentrations. Due largely to increased primary production, elevated CO2 enhanced the magnitude of Si uptake between 20 and 26%, likely intensifying the terrestrial silica pump. This uptake of Si by forests has important implications for Si export from terrestrial systems, with the potential to impact C sequestration and higher trophic levels in downstream ecosystems.
    Description: This research was supported in part by the Sloan Foundation in a fellowship to Robinson W. Fulweiler. The Duke Forest FACE was supported by his study was supported by the US Department of Energy (Grant No. DE-FG02-95ER62083) through the Office of Biological and Environmental Research (BER) and its National Institute for Global Environmental Change (NIGEC), Southeast Regional Center (SERC) at the University of Alabama, and by the US Forest Service through both the Southern Global Climate Change Program and the Southern Research Station. Adrien C. Finzi acknowledges ancillary support from the US NSF (DEB0236356).
    Keywords: Elevated CO2 ; Silicon ; Forest Si uptake ; Terrestrial Si pump ; Active Si accumulation ; Si cycling
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    Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity (2015)
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    OprG Harnesses the Dynamics of its Extracellular Loops to Transport Small Amino Acids across the Outer Membrane of Pseudomonas aeruginosa (2015)
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    An Isoform-Specific Myristylation Switch Targets Type II PKA Holoenzymes to Membranes (2015)
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    The PTEN Tumor Suppressor Forms Homodimers in Solution (2015)
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    A Native-like Intermediate Serves as a Branching Point between the Folding and Aggregation Pathways of the Mouse Prion Protein (2015)
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    Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features (2015)
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    Light Signaling Mechanism of Two Tandem Bacteriophytochromes (2015)
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    From Shellfish Poisoning to Neuroscience (2015)
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    Ribosome Subunit Joining Frozen in Time (2015)
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    Molecular Mechanism of Resolving Trinucleotide Repeat Hairpin by Helicases (2015)
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    In This Issue (2015)
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    In This Issue (2015)
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    The Molecular Basis for the Substrate Specificity of Protein Tyrosine Phosphatase PTPN3 (2015)
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    Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase (2015)
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    Growing an Editorial Board for an Ever Expanding Field (2015)
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    Splicing and Proteolytic Processing in VEGF Signaling: Now It Is the Coreceptor’s Turn (2015)
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    May the Force Be With You: Unfolding Lipid-Protein Interactions By Single-Molecule Force Spectroscopy (2015)
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    Crystal Structure of the Human 20S Proteasome in Complex with Carfilzomib (2015)
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    Helix-Helix Interactions: Is the Medium the Message? (2015)
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    In This Issue (2015)
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    Time to Fold: Tom1 Uses New Tricks to Regulate Lipid Binding of Tollip (2015)
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    Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa (2018)
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