Seasonal succession of free-living bacterial communities in coastal waters of the Western Antarctic Peninsula

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR

Comparative Molecular Microbial Ecology of the Spring Haptophyte Bloom in a Greenland Arctic Oligosaline Lake

The Arctic is highly sensitive to increasing global temperatures and is projected to experience dramatic ecological shifts in the next few decades. Oligosaline lakes are common in arctic regions where evaporation surpasses precipitation, however these extreme microbial communities are poorly characterized. Many oligosaline lakes, in contrast to freshwater ones, experience annual blooms of haptophyte algae that generate valuable alkenone biomarker records that can be used for paleoclimate reconstruction. These haptophyte algae are globally important, and globally distributed, aquatic phototrophs yet their presence in microbial molecular surveys is scarce. To target haptophytes in a molecular survey, we compared microbial community structure during two haptophyte bloom events in an arctic oligosaline lake, Lake BrayaSø in southwestern Greenland, using high-throughput pyrotag sequencing. Our comparison of two annual bloom events yielded surprisingly low taxon overlap, only 13% for bacterial and 26% for eukaryotic communities, which indicates significant annual variation in the underlying microbial populations. Both the bacterial and eukaryotic communities strongly resembled high-altitude and high latitude freshwater environments. In spite of high alkenone concentrations in the water column, and corresponding high haptophyte rRNA gene copy numbers, haptophyte pyrotag sequences were not the most abundant eukaryotic tag, suggesting that sequencing biases obscured relative abundance data. With over 170 haptophyte tag sequences, we observed only one haptophyte algal Operational Taxonomic Unit, a prerequisite for accurate paleoclimate reconstruction from the lake sediments. Our study is the first to examine microbial diversity in a Greenland lake using next generation sequencing and the first to target an extreme haptophyte bloom event. Our results provide a context for future explorations of aquatic ecology in the warming arctic

A molecular approach to questions in the phylogeny of planktonic sarcodines

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1996.Includes bibliographical references.by Linda Angela Amaral Zettler.Ph.D

Distribution and seasonal variability in the benthic eukaryotic community of Río Tinto (SW, Spain), an acidic, high metal extreme environment

Author Posting. © The Author(s), 2007. 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 Systematic and Applied Microbiology 30 (2007): 531-546, doi:10.1016/j.syapm.2007.05.003.The eukaryotic community of Río Tinto (SW, Spain) was surveyed fall, winter, and spring through the combined use of traditional microscopy and molecular approaches including Denaturing Gradient Gel Electrophoresis (DGGE) and sequence analysis of 18S rRNA gene fragments. We compared eukaryotic assemblages of surface sediment biofilms collected in January, May and September 2002 from 13 sampling stations along the river. Physicochemical data revealed extremely acidic conditions (pH ranged from 0.9 to 2.5) with high concentrations of heavy metals including up to 20 g l-1 Fe, 317 mg l-1 Zn, 47 mg l-1 As, 42 mg l-1 Cd, and 4 mg l-1 Ni. In total, 20 taxa were identified, including members of the Bacillariophyta, Chlorophyta, and Euglenophyta phyla as well as ciliates, cercomonads, amoebae, stramenopiles, fungi, heliozoan and rotifers. In general, total cell abundances were highest in fall and spring decreasing drastically in winter and the sampling stations with the most extreme conditions showed the lowest number of cells as well as the lowest diversity. Species diversity does not vary much during the year. Only the filamentous algae showed a dramatic seasonal change almost disappearing in winter and reaching the highest biomass during the summer. PCA showed a high inverse correlation between pH and most of the heavy metals analyzed as well as Dunaliella sp., while Chlamydomonas sp. is directly related to pH during May and September. Three heavy metals (Zn, Cu and Ni) remained separate from the rest and showed an inverse correlation with most of the species analyzed except for Dunaliella sp.A.A was supported by the Spanish Ministry of Education and Science through the Ramón y Cajal program. This work has been supported by grant CGL2005-05470/BOS and grants to the Centro de Astrobiología at the Instituto National de Técnica Aeroespacial

Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 7 (2017): 516–525, doi:10.1002/ece3.2630.Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created “golden tides” that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification. We generated full-length mitogenomes and partial chloroplast genomes of all representative holopelagic Sargassum species, S. fluitans III and S. natans I alongside the putatively rare S. natans VIII, to demonstrate small but consistent differences between S. natans I and VIII (7 bp differences out of the 34,727). Our comparative analyses also revealed that both S. natans I and S. natans VIII share a very close phylogenetic relationship with S. fluitans III (94- and 96-bp differences of 34,727). We designed novel primers that amplified regions of the cox2 and cox3 marker genes with consistent polymorphic sites that enabled differentiation between the two S. natans forms (I and VIII) from each other and both from S. fluitans III in over 150 Sargassum samples including those from the 2014 golden tide event. Despite remarkable gene synteny and sequence conservation, the three Sargassum forms differ in morphology, ecology, and distribution patterns, warranting more extensive interrogation of holopelagic Sargassum genomes as a whole.This work was supported by a US National Science Foundation (NSF) collaborative grant to LAA-Z (OCE-1155571) and ERZ (OCE-1155379), and an NSF TUES grant (DUE-1043468) to LAA-Z and ER

Microbial diversity and potential pathogens in onamental fish aquarium water

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e39971, doi:10.1371/journal.pone.0039971.Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species

The biogeography of the Plastisphere : implications for policy

Author Posting. © Ecological Society of America, 2015. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Frontiers in Ecology and the Environment 13 (2015): 541–546, doi:10.1890/150017.Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid-ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) and the rise in plastic production, the impacts of plastic on marine ecosystems will likely increase. Microscopic life (the “Plastisphere”) thrives on these tiny floating “islands” of debris and can be transported long distances. Using next-generation DNA sequencing, we characterized bacterial communities from water and plastic samples from the North Pacific and North Atlantic subtropical gyres to determine whether the composition of different Plastisphere communities reflects their biogeographic origins. We found that these communities differed between ocean basins – and to a lesser extent between polymer types – and displayed latitudinal gradients in species richness. Our research reveals some of the impacts of microplastics on marine biodiversity, demonstrates that the effects and fate of PMD may vary considerably in different parts of the global ocean, and suggests that PMD mitigation will require regional management efforts.This work was supported by a US National Science Foundation (NSF) collaborative grant to LAA-Z (OCE-1155571), ERZ (OCE-1155379), and TJM (OCE-1155671), and was partially funded by an NSF TUES grant (DUE-1043468) to LAA-Z and ERZ, and by the Richard Saltonstall Charitable Foundation to TJM. GP was funded through the OCE-1155379 grant and assisted with identification of plastic resins via ATR-FTIR

Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR

Modeling submerged biofouled microplastics and their vertical trajectories

The fate of (micro)plastic particles in the open ocean is controlled by physical and biological processes. Here, we model the effects of biofouling on the subsurface vertical distribution of spherical, virtual plastic particles with radii of 0.01–1 mm. For the physics, four vertical velocity terms are included: advection, wind-driven mixing, tidally induced mixing, and the sinking velocity of the biofouled particle. For the biology, we simulate the attachment, growth and loss of algae on particles. We track 10,000 particles for one year in three different regions with distinct biological and physical properties: the low productivity region of the North Pacific Subtropical Gyre, the high productivity region of the Equatorial Pacific and the high mixing region of the Southern Ocean. The growth of biofilm mass in the euphotic zone and loss of mass below the euphotic zone result in the oscillatory behaviour of particles, where the larger (0.1–1.0 mm) particles have much shorter average oscillation lengths ( 5000 m). Our results show that the vertical movement of particles is mainly affected by physical (wind-induced mixing) processes within the mixed layer and biological (biofilm) dynamics below the mixed layer. Furthermore, positively buoyant particles with radii of 0.01–1.0 mm can sink far below the euphotic zone and mixed layer in regions with high near-surface mixing or high biological activity. This work can easily be coupled to other models to simulate open-ocean biofouling dynamics, in order to reach a better understanding of where ocean (micro)plastic ends up

Envisioning a marine biodiversity observation network

Author Posting. © University of California Press and American Institute of Biological Sciences, 2013. This article is posted here by permission of University of California Press and American Institute of Biological Sciences for personal use, not for redistribution. The definitive version was published in BioScience 63 (2013): 350-361, doi:10.1525/bio.2013.63.5.8.Humans depend on diverse ocean ecosystems for food, jobs, and sustained well-being, yet many stressors threaten marine life. Extensive research has demonstrated that maintaining biodiversity promotes ocean health and service provision; therefore, monitoring the status and trends of marine biodiversity is important for effective ecosystem management. However, there is no systematic sustained program for evaluating ocean biodiversity. Coordinating existing monitoring and building a proactive marine biodiversity observation network will support efficient, economical resource management and conservation and should be a high priority. A synthesis of expert opinions suggests that, to be most effective, a marine biodiversity observation network should integrate biological levels, from genes to habitats; link biodiversity observations to abiotic environmental variables; site projects to incorporate environmental forcing and biogeography; and monitor adaptively to address emerging issues. We summarize examples illustrating how to leverage existing data and infrastructure to meet these goals