<i>Daphnia magna</i>'s Favorite Snack: Biofouled Plastics

The influence of biofouling on zooplankton ingestion rates of plastics in freshwater environments has received limited attention. We investigated how biofouling of microplastics in wastewater effluent and in fresh surface water influences Daphnia magna's microplastic consumption. The differences in ingestion of the biofouled as compared with the virgin microplastics were higher for the surface water by a factor of seven compared with a factor of two for the effluent. The intake of biofouled microplastics by D. magna was higher compared with virgin plastics, but the reason for this preference should be further investigated. Environ Toxicol Chem 2022;41:1977–1981. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC

Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute

A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes

© 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 4 (2009): e6372, doi:10.1371/journal.pone.0006372.Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments. Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.This work was supported by grants from the W.M. Keck Foundation and 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) (LAZ and SH)

Distributions of bacteriohopanepolyols in lakes and coastal lagoons of the Azores Archipelago

Bacteriohopanepolyols (BHPs) are a diverse class of lipids produced by bacteria across a wide range of environments. In this study, we aim to further identify BHPs related to ecological niches and/or specific bacteria by characterizing the distribution of BHPs in suspended particulate matter (SPM) of the water column and in sediments in a range of lakes and coastal lagoons from the Azores Archipelago, as well as in a co-culture enriched for methanotrophs. Sediment samples from Azorean lakes with low-oxygen conditions during the summer months (i.e., Azul, Verde, Funda, and Negra) contain relatively high abundances of BHPs that are typically associated with methane-oxidizing (methanotrophic) bacteria (i.e., aminotetrol, aminopentol, and methylcarbamate-aminopentol), as well as the ethenolamine-BHPs (i.e., ethenolamine-BHpentol and ethenolamine-BHhexol) and the N-formylated aminoBHPs. Both ethenolamine-BHPs and N-formylated aminoBHPs were also detected in a methanotroph–methylotroph co-culture that was enriched from a lake. In the SPM of all water columns, bacteriohopanetetrol (BHT), BHT cyclitol ether, and aminotriol are the dominant BHPs. In SPM from Lake Funda, nucleoside BHPs (i.e., Me-adenosylhopaneHG-diMe (where HG refers to head group), N1-methylinosylhopane, 2Me-N1-inosylhopane, and Me-N1-inosylhopane) are present in low abundance or absent under oxic conditions but increase in concentration near the chemocline, suggesting potential in situ production of these nucleoside BHPs rather than an allochthonous origin. In contrast, sediments from shallow, well-mixed lakes (i.e., Empadadas, São Jorge, and Lomba) contain higher abundances of adenosylhopane and N1-methylinosylhopane, which likely originate from bacteria living in nearby soils. Based on our current results we revised the existing Rsoil index, which was previously used to infer terrestrial inputs to aquatic environments, to exclude any potential nucleosides produced in the lake water column (Rsoil-lake). In the coastal lagoons, Cubres East and Cubres West, methoxylated BHTs were detected, and higher abundances of ethenolamine-BHT were observed. This study highlights the diversity of BHPs in lakes and coastal lagoons and their potential as taxonomic markers for bacteria associated with certain ecological niches, which can be preserved in sedimentary records

Eukaryotic richness in the abyss: insights from pyrotag sequencing

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes.French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundationinfo:eu-repo/semantics/publishedVersio

Culturing of the first 37:4 predominant lacustrine haptophyte : geochemical, biochemical, and genetic implications

Author Posting. © The Author(s), 2011. 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 Geochimica et Cosmochimica Acta 78 (2012): 51–64, doi:10.1016/j.gca.2011.11.024.Long chain alkenones (LCAs) are potential biomarkers for quantitative paleotemperature reconstructions from lacustrine environments. However, progress in this area has been severely hindered by the lack of culture studies of haptophytes responsible for alkenone distributions in lake sediments: the predominance of C37:4 LCA. Here we report the first enrichment culturing of a novel haptophyte phylotype (Hap-A) from Lake George, ND that produces predominantly C37:4-LCA. Hap-A was enriched from its resting phase collected from deep sediments rather than from water column samples. In contrast, enrichments from near surface water yielded a different haptophyte phylotype (Hap-B), closely related to Chrysotila lamellosa and Pseudoisochrysis paradoxa, which does not display C37:4-LCA predominance (similar enrichments have been reported previously). The LCA profile in sediments resembles that of Hap-A enrichments, suggesting that Hap-A is the dominant alkenone producer of the sedimentary LCAs. In enrichments, excess lighting appeared to be crucial for triggering blooms of Hap-A. Both and indices show a linear relationship with temperature for Hap-A in enrichments, but the relationship appears to be dependent on the growth stage. Based on 18S rRNA gene analyses, several lakes from the Northern Great Plains, as well as Pyramid Lake, NV and Tso Ur, Tibetan Plateau, China contain the same two haptophyte phylotypes. The Great Plains lakes show the Hap-A-type LCA distribution, whereas Pyramid and Tso Ur show the Hap-B type distribution. Waters of the Great Plain lakes are dominated by sulfate, whereas those Pyramid and Tso Ur are dominated by carbonate, suggesting that the sulfate to carbonate ratio may be a determining factor for the competitiveness of the Hap-A and Hap-B phylotypes in natural settings.This work was supported by a grant from the National Science Foundation to Y. Huang (EAR06-02325) and a Brown University Graduate School Dissertation Fellowship to J. L. Toney

Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of National Academy of Sciences of the USA for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 104 (2007): 9029-9034, doi:10.1073/pnas.0610552104.Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes. Vibrio and Legionella species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; no evidence of a long-term hurricane-induced algal bloom was observed. Giardia and Cryptosporidium were detected in canal waters. Elevated levels of fecal indicator bacteria observed in sediment could not be solely attributed to impacts from floodwaters, as both flooded and nonflooded areas exhibited elevated levels of fecal indicator bacteria. Evidence from measurements of Bifidobacterium and bacterial diversity analysis suggest that the fecal indicator bacteria observed in the sediment were from human fecal sources. Epidemiologic studies are highly recommended to evaluate the human health effects of the sediments deposited by the floodwaters.This work was funded by NSF-NIEHS Oceans and Human Health Program (NSF OCE0432368, OCE0432479, OCE0430724 and NIEHS P50 ES12736, ES012740, ES012742), the NSF-SGER Program (OCE 0554402, OCE 0554674, OCE 0554850, OCE0600130), the NSF-REU Program, and by the Georgia Sea Grant College Program (NA04OAR170033)

Making Marine Life Count: A New Baseline for Policy

The Census of Marine Life aids practical work of the Convention on Biological Diversity, discovers and tracks ocean biodiversity, and supports marine environmental planning