Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bernhard, J. M., Wit, J. C., Starczak, V. R., Beaudoin, D. J., Phalen, W. G., & McCorkle, D. C. Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming. Frontiers in Marine Science, 8, (2021): 643339, https://doi.org/10.3389/fmars.2021.643339.Ocean chemistry is changing as a result of human activities. Atmospheric carbon dioxide (CO2) concentrations are increasing, causing an increase in oceanic pCO2 that drives a decrease in oceanic pH, a process called ocean acidification (OA). Higher CO2 concentrations are also linked to rising global temperatures that can result in more stratified surface waters, reducing the exchange between surface and deep waters; this stronger stratification, along with nutrient pollution, contributes to an expansion of oxygen-depleted zones (so called hypoxia or deoxygenation). Determining the response of marine organisms to environmental changes is important for assessments of future ecosystem functioning. While many studies have assessed the impact of individual or paired stressors, fewer studies have assessed the combined impact of pCO2, O2, and temperature. A long-term experiment (∼10 months) with different treatments of these three stressors was conducted to determine their sole or combined impact on the abundance and survival of a benthic foraminiferal community collected from a continental-shelf site. Foraminifera are well suited to such study because of their small size, relatively rapid growth, varied mineralogies and physiologies. Inoculation materials were collected from a ∼77-m deep site south of Woods Hole, MA. Very fine sediments (<53 μm) were used as inoculum, to allow the entire community to respond. Thirty-eight morphologically identified taxa grew during the experiment. Multivariate statistical analysis indicates that hypoxia was the major driving factor distinguishing the yields, while warming was secondary. Species responses were not consistent, with different species being most abundant in different treatments. Some taxa grew in all of the triple-stressor samples. Results from the experiment suggest that foraminiferal species’ responses will vary considerably, with some being negatively impacted by predicted environmental changes, while other taxa will tolerate, and perhaps even benefit, from deoxygenation, warming and OA.This work was supported by the US NSF SEES-OA grant OCE-1219948 to JB and the Investment in Science Program at WHOI. DM also received support from the NSF Independent Research and Development Program

Two spatial scales in a bleaching event : corals from the mildest and the most extreme thermal environments escape mortality

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1531-1545, doi:10.4319/lo.2013.58.5.1531.In summer 2010, a bleaching event decimated the abundant reef flat coral Stylophora pistillata in some areas of the central Red Sea, where a series of coral reefs 100–300 m wide by several kilometers long extends from the coastline to about 20 km offshore. Mortality of corals along the exposed and protected sides of inner (inshore) and mid and outer (offshore) reefs and in situ and satellite sea surface temperatures (SSTs) revealed that the variability in the mortality event corresponded to two spatial scales of temperature variability: 300 m across the reef flat and 20 km across a series of reefs. However, the relationship between coral mortality and habitat thermal severity was opposite at the two scales. SSTs in summer 2010 were similar or increased modestly (0.5°C) in the outer and mid reefs relative to 2009. In the inner reef, 2010 temperatures were 1.4°C above the 2009 seasonal maximum for several weeks. We detected little or no coral mortality in mid and outer reefs. In the inner reef, mortality depended on exposure. Within the inner reef, mortality was modest on the protected (shoreward) side, the most severe thermal environment, with highest overall mean and maximum temperatures. In contrast, acute mortality was observed in the exposed (seaward) side, where temperature fluctuations and upper water temperature values were relatively less extreme. Refuges to thermally induced coral bleaching may include sites where extreme, high-frequency thermal variability may select for coral holobionts preadapted to, and physiologically condition corals to withstand, regional increases in water temperature.J.C.B.S. was partially supported by Fundac¸a˜o para a Cieˆncia e a Tecnologia (project PEst-C/MAR/LA0015/2011) and by the European Regional Development Fund through the Operational Competitiveness Programme (National Strategic Reference Framework). Kristen Davis was partially supported by a Woods Hole Oceanographic Institution postdoctoral scholarship. This research was supported by KAUST with awards USA 00002 and KSA 00011

A crab swarm at an ecological hotspot : patchiness and population density from AUV observations at a coastal, tropical seamount

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 4 (2016): e1770, doi:10.7717/peerj.1770.A research cruise to Hannibal Bank, a seamount and an ecological hotspot in the coastal eastern tropical Pacific Ocean off Panama, explored the zonation, biodiversity, and the ecological processes that contribute to the seamount’s elevated biomass. Here we describe the spatial structure of a benthic anomuran red crab population, using submarine video and autonomous underwater vehicle (AUV) photographs. High density aggregations and a swarm of red crabs were associated with a dense turbid layer 4–10 m above the bottom. The high density aggregations were constrained to 355–385 m water depth over the Northwest flank of the seamount, although the crabs also occurred at lower densities in shallower waters (∼280 m) and in another location of the seamount. The crab aggregations occurred in hypoxic water, with oxygen levels of 0.04 ml/l. Barcoding of Hannibal red crabs, and pelagic red crabs sampled in a mass stranding event in 2015 at a beach in San Diego, California, USA, revealed that the Panamanian and the Californian crabs are likely the same species, Pleuroncodes planipes, and these findings represent an extension of the southern endrange of this species. Measurements along a 1.6 km transect revealed three high density aggregations, with the highest density up to 78 crabs/m2, and that the crabs were patchily distributed. Crab density peaked in the middle of the patch, a density structure similar to that of swarming insects.This work was sponsored by a grant from the Dalio Foundation, Inc, through the Woods Hole Oceanographic Institution

Oxidation products of 5-methyl cytosine are decreased in senescent cells and tissues of progeroid mice

5-Hydroxymethylcytosine and 5-formylcytosine are stable DNA base modifications generated from 5-methylcytosine by the ten-eleven translocation protein family that function as epigenetic markers. 5-Hydroxymethyluracil may also be generated from thymine by ten-eleven translocation enzymes. Here, we asked if these epigenetic changes accumulate in senescent cells, since they are thought to be inversely correlated with proliferation. Testing this in ERCC1-XPF-deficient cells and mice also enabled discovery if these DNA base changes are repaired by nucleotide excision repair. Epigenetic marks were measured in proliferating, quiescent and senescent wild-type (WT) and Ercc1−/− primary mouse embryonic fibroblasts. The pattern of epigenetic marks depended more on the proliferation status of the cells than their DNA repair capacity. The cytosine modifications were all decreased in senescent cells compared to quiescent or proliferating cells, whereas 5-(hydroxymethyl)-2′-deoxyuridine was increased. In vivo, both 5-(hydroxymethyl)-2′-deoxyuridine and 5-(hydroxymethyl)-2′-deoxycytidine were significantly increased in liver tissues of aged WT mice compared to young adult WT mice. Livers of Ercc1-deficient mice with premature senescence and aging had reduced level of 5-(hydroxymethyl)- 2′-deoxycytidine and 5-formyl-2′-deoxycytidine compared to aged-matched WT controls. Taken together, we demonstrate for the first time, that 5-(hydroxymethyl)-2′-deoxycytidine is significantly reduced in senescent cells and tissue, potentially yielding a novel marker of senescence

Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments

© 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.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.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

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. R-loops are nucleic acid structures formed by an RNA:DNA hybrid and unpaired single-stranded DNA that represent a source of genomic instability in mammalian cells1–4. Here we show that N6-methyladenosine (m6A) modification, contributing to different aspects of messenger RNA metabolism5,6, is detectable on the majority of RNA:DNA hybrids in human pluripotent stem cells. We demonstrate that m6A-containing R-loops accumulate during G2/M and are depleted at G0/G1 phases of the cell cycle, and that the m6A reader promoting mRNA degradation, YTHDF2 (ref. 7), interacts with R-loop-enriched loci in dividing cells. Consequently, YTHDF2 knockout leads to increased R-loop levels, cell growth retardation and accumulation of γH2AX, a marker for DNA double-strand breaks, in mammalian cells. Our results suggest that m6A regulates accumulation of R-loops, implying a role for this modification in safeguarding genomic stability

Tolerance of allogromiid Foraminifera to severely elevated carbon dioxide concentrations : implications to future ecosystem functioning and paleoceanographic interpretations

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Global and Planetary Change 65 (2009): 107-114, doi:10.1016/j.gloplacha.2008.10.013.Increases in the partial pressure of carbon dioxide (pCO2) in the atmosphere will significantly affect a wide variety of terrestrial fauna and flora. Because of tight atmospheric-oceanic coupling, shallow-water marine species are also expected to be affected by increases in atmospheric carbon dioxide concentrations. One proposed way to slow increases in atmospheric pCO2 is to sequester CO2 in the deep sea. Thus, over the next few centuries marine species will be exposed to changing seawater chemistry caused by ocean-atmospheric exchange and/or deep-ocean sequestration. This initial case study on one allogromiid foraminiferal species (Allogromia laticollaris) was conducted to begin to ascertain the effect of elevated pCO2 on benthic Foraminifera, which are a major meiofaunal constituent of shallow- and deep-water marine communities. Cultures of this thecate foraminiferan protist were used for 10-14-day experiments. Experimental treatments were executed in an incubator that controlled CO2 (15 000; 30 000; 60 000; 90 000; 200 000 ppm), temperature and humidity; atmospheric controls (i.e., ~375 ppm CO2) were executed simultaneously. Although the experimental elevated pCO2 values are far above foreseeable surface water pCO2, they were selected to represent the spectrum of conditions expected for the benthos if deep-sea CO2 sequestration becomes a reality. Survival was assessed in two independent ways: pseudopodial presence/absence and measurement of adenosine triphosphate (ATP), which is an indicator of cellular energy. Substantial proportions of A. laticollaris populations survived 200 000 ppm CO2 although the mean of the median [ATP] of survivors was statistically lower for this treatment than for that of atmospheric control specimens. After individuals that had been incubated in 200 000 ppm CO2 for 12 days were transferred to atmospheric conditions for ~24 hours, the [ATP] of live specimens (survivors) approximated those of the comparable atmospheric control treatment. Incubation in 200 000 ppm CO2 also resulted in reproduction by some individuals. Results suggest that certain Foraminifera are able to tolerate deep-sea CO2 sequestration and perhaps thrive as a result of elevated pCO2 that is predicted for the next few centuries, in a high-pCO2 world. Thus, allogromiid foraminiferal “blooms” may result from climate change. Furthermore, because allogromiids consume a variety of prey, it is likely that they will be major players in ecosystem dynamics of future coastal sedimentary environments.This work was funded by US Department of Energy grant # DE-FG02-03ER63696 (to J. Kennett and J. Bernhard), NSF OCE-0725966, and the WHOI Summer Student Fellow Program, which is funded by NSF Research Experience for Undergraduates Program grant #OCE-0139423

Otolith geochemistry does not reflect dispersal history of clownfish larvae

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Coral Reefs 29 (2010): 883-891, doi:10.1007/s00338-010-0652-z.Natural geochemical signatures in calcified structures are commonly employed to retrospectively estimate dispersal pathways of larval fish and invertebrates. However, the accuracy of the approach is generally untested due to the absence of individuals with known dispersal histories. We used genetic parentage analysis (genotyping) to divide 110 new recruits of the orange clownfish, Amphiprion percula, from Kimbe Island, Papua New Guinea, into two groups: “self-recruiters” spawned by parents on Kimbe Island and “immigrants” that had dispersed from distant reefs (>10km away). Analysis of daily increments in sagittal otoliths found no significant difference in PLDs or otolith growth rates between self-recruiting and immigrant larvae. We also quantified otolith Sr/Ca and Ba/Ca ratios during the larval phase using laser ablation inductively coupled plasma mass spectrometry. Again, we found no significant differences in larval profiles of either element between self-recruits and immigrants. Our results highlight the need for caution when interpreting otolith dispersal histories based on natural geochemical tags in the absence of water chemistry data or known-origin larvae with which to test the discriminatory ability of natural tags.Research was supported by the Australian Research Council, the Coral Reef Initiatives for the Pacific (CRISP), the Global Environmental Facility CRTR Connectivity Working Group, the Total Foundation, a National Science Foundation grant (#0424688) to SRT, and a National Science Foundation Graduate Research Fellowship to MLB

Off-line system for estimation of co-ordinate measurement uncertainty

W artykule zaprezentowano komputerowy system, umożliwiający obliczenie niepewności pomiaru dla kilkudziesięciu zadań pomiarowych. Przez zadanie pomiarowe rozumie się wyznaczenie konkretnej charakterystyki geometrycznej. Różnymi zadaniami pomiarowymi są więc na przykład: pomiar średnicy otworu, pomiar odchyłki płaskości czy pomiar odchyłki równoległości osi do płaszczyzny. Dane wejściowe stanowi informacja o dokładności maszyny pomiarowej i głowicy, o postaci geometrycznej mierzonego przedmiotu i jego usytuowaniu w przestrzeni pomiarowej maszyny oraz o użytych trzpieniach pomiarowych.The paper presents results of investigations conducted within the research & development project. The elaborated computer system enables estimation of the measurement uncertainty for dozens of measurement tasks. The measurement task is understood as determination of the dimension and/or geometrical deviation by means of co-ordinate technique. Examples of different measurement tasks are, for instance, measurement of: hole diameter, flatness deviation, parallelism deviation of axis related to plane, coaxiality deviation. Different measurement tasks are also measurements of different kinds of the same geometrical deviation such as measurement of the parallelism deviation of axis related to axis, axis related to plane, plane related to axis and even measurement of the parallelism deviation of axis related to axis in common plane or in normal to common plane or the parallelism deviation of axis related to axis in case of cylindrical tolerance zone. The input data is information about: the measuring machine (maximum permissible error of the length measurement) and probing system (maximum permissible error of the probing system) accuracy, the workpiece geometrical shape (overall dimensions, mutual arrangement of geometrical features), orientation and location of the measured workpiece in the measuring part of the co-ordinate measuring machine (CMM) and the used styli configuration. The information about the geometrical errors of CMM and probing system is obtained in an experimental way by the procedure similar to CMM calibration. The remaining information is obtained from the elaborated part program of the workpiece

Conclusions from implementation of the EMU software in industry

Oprogramowanie EMU do wyznaczania niepewności pomiarów współrzędnościowych opracowano w Laboratorium Metrologii ATH w ramach projektu badawczo-rozwojowego. Podstawy teoretyczne, na podstawie których powstało oprogramowanie, są opisane we wcześniejszych publikacjach. Oprogramowanie jest bardzo łatwe w użyciu. Parametry konstrukcyjne maszyny oraz dane zawierające informacje o błędach maszyny są wprowadzane przez dostawcę oprogramowania w momencie zakupu licencji. Dane dotyczące błędów maszyny są uaktualniane przez dostawcę po każdym kolejnym wzorcowaniu. Użytkownik oprogramowania tworzy własną bazę używanych trzpieni pomiarowych oraz bazy mierzonych przedmiotów, a w ich obrębie bazy charakterystyk. Najprostszym sposobem przygotowania danych dla wybranej charakterystyki, a równocześnie dokumentowania wyników szacowania niepewności pomiaru, jest następujące postępowanie: wybór modelu, wybór orientacji modelu zgodnie z orientacją mierzonego przedmiotu, wskazanie punktów charakterystycznych na modelu CAD mierzonego przedmiotu, wyznaczenie współrzędnych punktów charakterystycznych w układzie współrzędnych przedmiotu, wyznaczenie współrzędnych globalnych dla początku układu współrzędnych przedmiotu i wykonanie translacji oraz ewentualnie rotacji układu współrzędnych przedmiotu do układu współrzędnych maszyny, wypełnienie odpowiednich pól okna dialogowego. Szczególną zaletą oprogramowania jest to, że kolejne przedmioty i kolejne charakterystyki, dla których wyznacza się niepewność pomiaru, zapisywane są w bazie danych i powtórzenie obliczeń niepewności dla pomiarów wykonanych na danej maszynie, po kolejnych wzorcowaniach maszyny, jest inicjowane naciśnięciem jednego przycisku w menu.The software EMU for coordinate measurement uncertainty estimation was developed at the Laboratory of Metrology of University of Bielsko-Biała within the research grant. Theoretical background on which the software is developed are presented in previous publications. The software is very easy to use. The design-type parameters and the data on the geometrical errors of the CMM are implemented by the software vendor. The data on the geometrical errors of the machine are updated after each calibration of the CMM. The user is able to create a database of the styli used and the measured workpieces with the characteristics. The easiest way to prepare the data for particular characteristic and simultaneously documenting the measuring strategy is following procedure: chose a characteristic model, determine the orientation of the characteristic model with accordance to the measured workpiece, select characteristic points on the CAD model of the measured workpiece, determine the characteristic-points’ coordinates in the workpiece coordinate system, find the transformation between workpiece coordinate system and CMM coordinate system and apply it for the coordinates of the characteristic points, fill the proper fields in the characteristics’ dialog boxes. Particular advantage of the software is the fact that all workpieces and the corresponding characteristics are saved in a data-base and to re-evaluate the measurement uncertainty after CMM calibration can be done by single mouse click