Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells

Author Posting. © Marine Biological Laboratory, 2006. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 210 (2006): 73-77.Heterotrophic bacteria are commonly found in close associations with photosynthetic cyanobacteria in aquatic ecosystems. Some of these associations can be species-specific and mutualistic, resulting in optimal growth and nitrogen-fixing potential for the cyanobacteria. A two-membered culture, consisting of a heterotrophic, epibiotic bacterium attached to an Anabaena sp. was studied in the work reported here. The epibiotic bacterium was grown in pure culture, and both organisms were identified on the basis of their 16S rRNA gene sequence. The specificity of the epibiont for the Anabaena sp. heterocysts was confirmed by re-association experiments. The epibiont is a member of the Alphaproteobacteria in the order Rhizobiales, with close relatives that include a group of aerobic anoxygenic photosynthetic marine isolates commonly associated with dinoflagellate phytoplankton. The close association of the epibiotic bacterium with its Anabaena host, and its phylogenic affiliation allude to the evolutionary history of association with photosynthetic organisms for a group of Rhizobia and warrant further investigation

Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans

This paper is not subject to U.S. copyright. The definitive version was published in Bayer, B., Kellom, M., Valois, F., Waterbury, J., & Santoro, A. Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans. Microbiology Resource Announcements, 11(5), (2022): e00100–e00122, https://doi.org/10.1128/mra.00100-22.The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.This work was supported by a Simons Foundation Early Career Investigator Award (3435889) and a U.S. National Science Foundation award OCE-1924512 to A.E.S. B.B. was supported by the Austrian Science Fund (FWF) project number J4426-B. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under contract number DE-AC02-05CH11231. These data were generated for JGI proposal number 506203 to B.B. and A.E.S

Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic c-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae)

Author Posting. © Society for General Mircobiology, 2002. This article is posted here by permission of Society for General Mircobiology for personal use, not for redistribution. The definitive version was published in International Journal of Systematic Bacteriology 52 (2002): 2261-2269, doi:10.1099/ijs.0.02184-0.A cellulolytic, dinitrogen-fixing bacterium isolated from the gill tissue of a wood-boring mollusc (shipworm) Lyrodus pedicellatus of the bivalve family Teredinidae and 58 additional strains with similar properties, isolated from gills of 24 bivalve species representing 9 of 14 genera of Teredinidae, are described. The cells are Gram-negative, rigid, rods (0<4–0<6x3–6 lm) that bear a single polar flagellum. All isolates are capable of chemoheterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Xylan, pectin, carboxymethylcellulose, cellobiose and a variety of sugars and organic acids also support growth. Growth requires addition of combined nitrogen when cultures are vigorously aerated, but all isolates fix dinitrogen under microaerobic conditions. The pH, temperature and salinity optima for growth were determined for six isolates and are approximately 8<5, 30–35 °C and 0<3 M NaCl respectively. The isolates are marine. In addition to NaCl, growth requires elevated concentrations of Ca2M and Mg2M that reflect the chemistry of seawater. The DNA GMC content ranged from 49 to 51 mol%. Four isolates were identical with respect to small-subunit rRNA sequence over 891 positions compared and fall within a unique clade in the c-subclass of the Proteobacteria. Based on morphological, physiological and phylogenetic characteristics and specific symbiotic association with teredinid bivalves, a new genus and species, Teredinibacter turnerae gen. nov., sp. nov., is proposed. The type strain is T7902T (vATCC 39867TvDSM 15152T).This work was supported by grants from the National Science Foundation no. NSF DEB-9420051 and IBN- 9982982, the Maine Science and Technology Foundation's Center for Innovation in Biotechnology, and the University of Maine's Faculty Research program

Closely related phytoplankton species produce similar suites of dissolved organic matter

© 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): 111, doi:10.3389/fmicb.2014.00111.Production of dissolved organic matter (DOM) by marine phytoplankton supplies the majority of organic substrate consumed by heterotrophic bacterioplankton in the sea. This production and subsequent consumption converts a vast quantity of carbon, nitrogen, and phosphorus between organic and inorganic forms, directly impacting global cycles of these biologically important elements. Details regarding the chemical composition of DOM produced by marine phytoplankton are sparse, and while often assumed, it is not currently known if phylogenetically distinct groups of marine phytoplankton release characteristic suites of DOM. To investigate the relationship between specific phytoplankton groups and the DOM they release, hydrophobic phytoplankton-derived dissolved organic matter (DOMP) from eight axenic strains was analyzed using high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Identification of DOM features derived from Prochlorococcus, Synechococcus, Thalassiosira, and Phaeodactylum revealed DOMP to be complex and highly strain dependent. Connections between DOMP features and the phylogenetic relatedness of these strains were identified on multiple levels of phylogenetic distance, suggesting that marine phytoplankton produce DOM that in part reflects its phylogenetic origin. Chemical information regarding the size and polarity ranges of features from defined biological sources was also obtained. Our findings reveal DOMP composition to be partially conserved among related phytoplankton species, and implicate marine DOM as a potential factor influencing microbial diversity in the sea by acting as a link between autotrophic and heterotrophic microbial community structures.This research was supported by grants to Daniel J. Repeta and Sallie W. Chisholm from the Gordon and Betty Moore Foundation and funding to Daniel J. Repeta, Edward F. DeLong, and Sallie W. Chisholm from the National Science Foundation Science and Technology Center Award 0424599

Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ~40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0452883)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0752291)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0723667)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0928414)National Science Foundation (U.S.). Polar Program (ANT-0732665)United States. Environmental Protection Agency (Star Fellowship)Woods Hole Oceanographic Institution. Ocean Life InstituteCenter for Microbial Oceanography: Research and EducationCenter for Environmental Bioinorganic Chemistr

Portal protein diversity and phage ecology

© 2008 The Authors. This article is distributed under the terms of the Creative Commons License, Attribution 2.5. The definitive version was published in Environmental Microbiology 10 (2008): 2810-2823, doi:10.1111/j.1462-2920.2008.01702.x.Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.This research was supported in part by funding from NSF (CMORE contribution #87), DOE, The Seaver Foundation and the Gordon and Betty Moore Foundation Marine Microbiology Program to S.W.C.; an NIH Bioinformatics Training Grant supported M.B.S.; MIT Undergraduate Research Opportunities Program supported V.Q., J.A.L., G.T., R.F. and J.E.R.; Howard Hughes Medical Institute funded MIT Biology Department Undergraduate Research Opportunities Program supported A.S.D.; NSERC (Canada) Discovery Grant (DG 298394) and a Grant from the Canadian Foundation for Innovation (NOF10394) to J.P.B.; NSF Graduate Fellowship funding supported M.L.C

Corrigendum "Portal protein diversity and phage ecology"

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 13 (2011): 2832, doi:10.1111/j.1462-2920.2011.02616.x

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment