Recent and upcoming publications:
Novel uncultivated labyrinthulomycetes revealed by 18S rDNA sequences from seawater and sediment samples Enixy Collado-Mercado, JoAnn C. Radway and Jackie L. Collier AQUATIC MICROBIAL ECOLOGY IN PRESS
ABSTRACT: Labyrinthulomycetes (Labyrinthulea) are ubiquitous marine osmoheterotrophic protists that appear to be important in decomposition of both allochthonous and autochthonous organic matter. We used a cultivation-independent method based on the labyrinthulomycete-specific primer LABY-Y to PCR amplify, clone, and sequence 68 nearly full-length 18S rDNA amplicons from four sediment and three seawater samples collected in estuarine habitats around Long Island, NY, USA. Phylogenetic analyses revealed that all 68 amplicons belonged to the Labyrinthulea. Only 15 of the 68 amplicons belonged to the thraustochytrid phylogenetic group (Thraustochytriidae). None of these 15 was similar to cultivated strains, and eleven formed a novel group. The remaining 53 amplicons belonged either to the labyrinthulid phylogenetic group (Labyrinthulidae) or to other families of Labyrinthulea that have not yet been described. 37 of these amplicons were closely related to previously cultivated Aplanochytrium spp. and Oblongichytrium spp. Members of these two genera were also cultivated from one of the sediment samples. The 16 other amplicons were not closely related to cultivated strains, and 15 belonged to five groups of apparently novel labyrinthulomycetes. Most of the novel groups of amplicons also contained environmental sequences from surveys of protist diversity using universal 18S rDNA primers. Because the primer LABY-Y is biased against several groups of labyrinthulomycetes, particularly among the thraustochytrids, these results may underestimate the undiscovered diversity of labyrinthulomycetes.
Diversity of urea-degrading microorganisms in open-ocean and estuarine planktonic communities Jackie L. Collier, Kristopher M. Baker, and Sheryl L. Bell ENVIRONMENTAL MICROBIOLOGY IN PRESS
Summary: Urea is an important and dynamic natural component of marine nitrogen cycling and also a major contributor to anthropogenic eutrophication of coastal ecosystems, yet little is known about the identities or diversity of ureolytic marine microorganisms. Primers targeting the gene encoding urease were used to PCR amplify, clone and sequence 709 unique urease gene fragments from 31 plankton samples collected at both estuarine and open ocean locations. 286 amplicons belonged to 22 distinct sequence types that were closely enough related to named organisms to be identified, and included urease sequences both from typical marine planktonic organisms and from bacteria usually associated with terrestrial habitats. The remaining 423 amplicons were not closely enough related to named organisms to be identified, and belonged to 96 distinct sequence types of which 43 types were found in two or more different samples. The distributions of unidentified urease sequence types suggested that some represented truly marine microorganisms while others were restricted to low-salinity estuarine areas. The urease primers revealed a great diversity of ureolytic organisms because they were able to amplify many previously unknown, environmentally relevant urease genes, and will support new approaches for exploring the role of urea in marine ecosystems.
Quantitative Real-Time PCR Assay for QPX (Thraustochytriidae), a Parasite of the Hard Clam (Mercenaria mercenaria) Liu QQ (Liu, Qianqian), Allam B (Allam, Bassem), Collier JL (Collier, Jackie L.)APPLIED AND ENVIRONMENTAL MICROBIOLOGY 75(14): 4913-4918
Abstract: We developed a real-time quantitative PCR (qPCR) assay targeting the rRNA internal transcribed spacer region of the hard clam pathogen QPX. The qPCR assay was more sensitive than was histology in detecting clams with light QPX infections. QPX was detected in 4 of 43 sediment samples but in none of 40 seawater samples.
UREASE GENE SEQUENCES FROM ALGAE AND HETEROTROPHIC BACTERIA IN AXENIC AND NONAXENIC PHYTOPLANKTON CULTURES Baker KM (Baker, Kristopher M.), Gobler CJ (Gobler, Christopher J.), Collier JL (Collier, Jackie L.) JOURNAL OF PHYCOLOGY 45(3): 625-634
Abstract: While urea has long been recognized as an important form of nitrogen in planktonic ecosystems, very little is known about how many or which phytoplankton and bacteria can use urea as a nitrogen source. We developed a method, targeting the gene encoding urease, for the direct detection and identification of ureolytic organisms and tested it on seven axenic phytoplankton cultures (three diatoms, two prymnesiophytes, a eustigmatophyte, and a pelagophyte) and on three nonaxenic Aureococcus anophagefferens Hargraves et Sieburth cultures (CCMP1784 and two CCMP1708 cultures from different laboratories). The urease amplicon sequences from axenic phytoplankton cultures were consistent with genomic data in the three species for which both were available. Seven of 12 phytoplankton species have one or more introns in the amplified region of their urease gene(s). The 63 urease amplicons that were cloned and sequenced from nonaxenic A. anophagefferens cultures grouped into 17 distinct sequence types. Eleven types were related to alpha-Proteobacteria, including three types likely belonging to the genus Roseovarius. Four types were related to gamma-Proteobacteria, including two likely belonging to the genus Marinobacter, and two types were related to beta-Proteobacteria. Terminal restriction fragment length polymorphism (TRFLP) analyses suggested that the sequenced amplicons represented approximately half of the diversity of bacterial urease genes present in the nonaxenic cultures. While many of the bacterial urease sequence types were apparently lab- or culture-specific, others were found in all three nonaxenic cultures, suggesting the possibility of specific relationships between these bacteria and A. anophagefferens.
Ocean urea fertilization for carbon credits poses high ecological risks Glibert PM (Glibert, Patricia M.), Azanza R (Azanza, Rhodora), Burford M (Burford, Michele), Furuya K (Furuya, Ken), Abal E (Abal, Eva), Al-Azri A (Al-Azri, Adnan), Al-Yamani F (Al-Yamani, Faiza), Andersen P (Andersen, Per), Anderson DM (Anderson, Donald M.), Beardall J (Beardall, John), Berg GM (Berg, G. Mine), Brand L (Brand, Larry), Bronk D (Bronk, Deborah), Brookes J (Brookes, Justin), Burkholder JM (Burkholder, Joann M.), Cembella A (Cembella, Allan), Cochlan WP (Cochlan, William P.), Collier JL (Collier, Jackie L.), Collos Y (Collos, Yves), Diaz R (Diaz, Robert), Doblin M (Doblin, Martina), Drennen T (Drennen, Thomas), Dyhrman S (Dyhrman, Sonya), Fukuyo Y (Fukuyo, Yasuwo), Furnas M (Furnas, Miles), Galloway J (Galloway, James), Graneli E (Graneli, Edna), Ha DV (Ha, Dao Viet), Hallegraeff G (Hallegraeff, Gustaaf), Harrison J (Harrison, John), Harrison PJ (Harrison, Paul J.), Heil CA (Heil, Cynthia A.), Heimann K (Heimann, Kirsten), Howarth R (Howarth, Robert), Jauzein C (Jauzein, Cecile), Kana AA (Kana, Austin A.), Kana TM (Kana, Todd M.), Kim H (Kim, Hakgyoon), Kudela R (Kudela, Raphael), Legrand C (Legrand, Catherine), Mallin M (Mallin, Michael), Mulholland M (Mulholland, Margaret), Murray S (Murray, Shauna), O'Neil J (O'Neil, Judith), Pitcher G (Pitcher, Grant), Qi YZ (Qi, Yuzao), Rabalais N (Rabalais, Nancy), Raine R (Raine, Robin), Seitzinger S (Seitzinger, Sybil), Salomon PS (Salomon, Paulo S.), Solomon C (Solomon, Caroline), Stoecker DK (Stoecker, Diane K.), Usup G (Usup, Gires), Wilson J (Wilson, Joanne), Yin KD (Yin, Kedong), Zhou MJ (Zhou, Mingjiang), Zhu MY (Zhu, Mingyuan) MARINE POLLUTION BULLETIN 56(6): 1049-1056
Abstract: The proposed plan for enrichment of the Sulu Sea, Philippines, a region of rich marine biodiversity, with thousands of tonnes of urea in order to stimulate algal blooms and sequester carbon is flawed for multiple reasons. Urea is preferentially used as a nitrogen source by some cyanobacteria and dinoflagellates, many of which are neutrally or positively buoyant. Biological pumps to the deep sea are classically leaky, and the inefficient burial of new biomass makes the estimation of a net loss of carbon from the atmosphere questionable at best. The potential for growth of toxic dinoflagellates is also high, as many grow well on urea and some even increase their toxicity when grown on urea. Many toxic dinoflagellates form cysts which can settle to the sediment and germinate in subsequent years, forming new blooms even without further fertilization. If large-scale blooms do occur, it is likely that they will contribute to hypoxia in the bottom waters upon decomposition. Lastly, urea production requires fossil fuel usage, further limiting the potential for net carbon sequestration. The environmental and economic impacts are potentially great and need to be rigorously assessed.