Alice L. Alldredge

Bio: Alice L. Alldredge is an academic researcher from University of California, Santa Barbara. The author has contributed to research in topics: Marine snow & Water column. The author has an hindex of 59, co-authored 92 publications receiving 14589 citations. Previous affiliations of Alice L. Alldredge include University of California & University of California, Davis.

Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages

Abstract: The phylogenetic diversity of macroaggregate-attached vs. free-living marine bacteria, co-occurring in the same water mass, was compared. Bacterial diversity and phylogcnetic identity were inferred by analyzing polymerase chain reaction (PCR) amplified, cloned ribosomal RNA (rRNA) genes. Ribosomal RNA genes from macroaggregatc-associated bacteria were fundamentally different from those of free-living bacterioplankton. Most rRNA types recovered from the free-living bacterioplankton were closely related to a phenotypically undcscribcd (Y Proteobacteria group, previously detected in surface waters of North Pacific and Atlantic central ocean gyres. The results suggest that members of this phylogenetically distinct, (Y proteobacterial group are abundant free-living bactcrioplankters in coastal, as well as open-ocean habitats. In contrast, most macroaggregate-associated rRNA clones were closely related to Cytophuga, Planctomyce.s, or y Proteobacteria, within the domain Bacteria. These data indicate that specific bacterial populations, different from those which predominate in free-living bacterioplankton, develop on marine phytodetrital aggregates. The inferred properties of attached bacterial assemblages have significant implications for models of microbially mediated transformation of particulate organic material.

Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution

Abstract: LARGE, rapidly sinking organic aggregates are an important component of the carbon flux from the ocean's surface to its depths. Marine snow, the main type of large (<0.5 mm) aggregate, is heavily colonized by bacteria in surface waters1, yet the carbon demand of the attached bacteria is so small that months to years are required to consume the aggregates' carbon2–5. This has led to the conclusion that marine aggregates are resistant to degradation by attached bacteria, and thus act as refractory carriers of carbon to the deep ocean. Here we report that aggregates play host to intense activities of hydrolytic enzymes (presumably due to cell surface bound and released enzymes of the attached bacteria), which render the aggregates soluble. Particulate amino acids were hydrolysed rapidly (turnover time 0.2–2.1 days), with very little of the hydrolysate being taken up by the attached bacteria. Our results support the hypothesis6,7 that such 'uncoupled' hydrolysis is a biochemical mechanism for large-scale transfer of organic matter from sinking particles to the dissolved phase, and may supply the slowly degradable dissolved organic matter for downward export postulated by recent models8–10.

The abundance and significance of a class of large, transparent organic particles in the ocean

Abstract: Polysaccharide-specific staining techniques reveal the existence and high abundance of a class of large, discrete, transparent particles in seawater and diatom cultures formed from dissolved exopolymers exuded by phytoplankton and bacteria. Transparent exopolymer particles (TEP), ranged from 28 to 5000 particles ml−1 and 3 to 100s μm in longest dimension at five coastal stations off California. A high percentage of seemingly free-living bacteria (28–68%) were attached to these transparent sheets and films, suggesting that they may alter the distributions and microenvironments of marine microbes in nature. Preliminary coagulation experiments demonstrated that TEP are major agents in the aggregation of diatoms and in the formation of marine snow. The existence of microbial exudates acting as large, discrete particles, rather than as dissolved molecules or as coating on other particles, suggests that the transformation of dissolved organic matter into particulate form in the sea can occur via a rapid abiotic pathway as well as through conventional microbial uptake. The existence of these particles has far reaching implications for food web structure, microbial processes, carbon cycling and particulate flux in the ocean.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Abstract: 16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥ 1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

Environmental Genome Shotgun Sequencing of the Sargasso Sea

Abstract: We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity. Microorganisms are responsible for most of the biogeochemical cycles that shape the environment of Earth and its oceans. Yet, these organisms are the least well understood on Earth, as the ability to study and understand the metabolic potential of microorganisms has been hampered by the inability to generate pure cultures. Recent studies have begun to explore environ

Couplings between changes in the climate system and biogeochemistry

Abstract: Couplings Between Changes in the Climate System and Biogeochemistry Coordinating Lead Authors: Kenneth L. Denman (Canada), Guy Brasseur (USA, Germany) Lead Authors: Amnat Chidthaisong (Thailand), Philippe Ciais (France), Peter M. Cox (UK), Robert E. Dickinson (USA), Didier Hauglustaine (France), Christoph Heinze (Norway, Germany), Elisabeth Holland (USA), Daniel Jacob (USA, France), Ulrike Lohmann (Switzerland), Srikanthan Ramachandran (India), Pedro Leite da Silva Dias (Brazil), Steven C. Wofsy (USA), Xiaoye Zhang (China) Contributing Authors: D. Archer (USA), V. Arora (Canada), J. Austin (USA), D. Baker (USA), J.A. Berry (USA), R. Betts (UK), G. Bonan (USA), P. Bousquet (France), J. Canadell (Australia), J. Christian (Canada), D.A. Clark (USA), M. Dameris (Germany), F. Dentener (EU), D. Easterling (USA), V. Eyring (Germany), J. Feichter (Germany), P. Friedlingstein (France, Belgium), I. Fung (USA), S. Fuzzi (Italy), S. Gong (Canada), N. Gruber (USA, Switzerland), A. Guenther (USA), K. Gurney (USA), A. Henderson-Sellers (Switzerland), J. House (UK), A. Jones (UK), C. Jones (UK), B. Karcher (Germany), M. Kawamiya (Japan), K. Lassey (New Zealand), C. Le Quere (UK, France, Canada), C. Leck (Sweden), J. Lee-Taylor (USA, UK), Y. Malhi (UK), K. Masarie (USA), G. McFiggans (UK), S. Menon (USA), J.B. Miller (USA), P. Peylin (France), A. Pitman (Australia), J. Quaas (Germany), M. Raupach (Australia), P. Rayner (France), G. Rehder (Germany), U. Riebesell (Germany), C. Rodenbeck (Germany), L. Rotstayn (Australia), N. Roulet (Canada), C. Sabine (USA), M.G. Schultz (Germany), M. Schulz (France, Germany), S.E. Schwartz (USA), W. Steffen (Australia), D. Stevenson (UK), Y. Tian (USA, China), K.E. Trenberth (USA), T. Van Noije (Netherlands), O. Wild (Japan, UK), T. Zhang (USA, China), L. Zhou (USA, China) Review Editors: Kansri Boonpragob (Thailand), Martin Heimann (Germany, Switzerland), Mario Molina (USA, Mexico) This chapter should be cited as: Denman, K.L., G. Brasseur, A. Chidthaisong, P. Ciais, P.M. Cox, R.E. Dickinson, D. Hauglustaine, C. Heinze, E. Holland, D. Jacob, U. Lohmann, S Ramachandran, P.L. da Silva Dias, S.C. Wofsy and X. Zhang, 2007: Couplings Between Changes in the Climate System and Biogeochemistry. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M.Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

The Uncultured Microbial Majority

Abstract: ▪ Abstract Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically owing to the sequencing of ribosomal RNA genes cloned from environmental DNA. Currently, only 26 of the approximately 52 identifiable major lineages, or phyla, within the domain Bacteria have cultivated representatives. Evidence from field studies indicates that many of the uncultivated phyla are found in diverse habitats, and some are extraordinarily abundant. In some important environments, including seawater, freshwater, and soil, many biologically and geochemically important organisms are at best only remotely related to any strain that has been characterized by phenotype or by genome sequencing. Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory.