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ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage

L. Kelly, K. H. Huang, H. Ding, S. W. Chisholm
2011 Nucleic Acids Research  
Comparative genomics of ecotypes within Prochlorococcus, (1-3) and its sister group Synechococcus (26) (27) (28) (29) have provided a rich resource for analysis of genome evolution (3, 30) , and for  ...  ProPortal currently integrates extensive metagenomic data available from the GOS database (32), a valuable resource for understanding the ecology, diversity and biogeography of these groups.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr1022 pmid:22102570 pmcid:PMC3245167 fatcat:imz5vcjmtzcrfgd6kfpbf77apy

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

Miguel A. Hernández-Prieto, Trudi A. Semeniuk, Matthias E. Futschik
2014 Frontiers in Genetics  
Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools.  ...  Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes  ...  ProPortal (http://proportal.mit.edu/) aims to provide easy access to the growing genetic database devoted to the cyanobacterium Prochlorococcus and its phages; to facilitate its use as a model system for  ... 
doi:10.3389/fgene.2014.00191 pmid:25071821 pmcid:PMC4079066 fatcat:g7nrds6fzndehaqdlczfw4egoy

Phages of the marine cyanobacterial picophytoplankton: Table 1

Nicholas H. Mann
2003 FEMS Microbiology Reviews  
It is still less than 10 years since the discovery of phages that infect marine Synechococcus and the beginning of the characterisation of these phages and assessment of their ecological impact.  ...  Cyanobacteria of the genera Synechococcus and Prochlorococcus dominate the prokaryotic component of the picophytoplankton in the oceans.  ...  Lenski and Levin [67] showed for chemostat cultures of E. coli infected with phage T4 that a virus-resistant, resource-limited bacterial population becomes established and can persist inde¢nitely.  ... 
doi:10.1016/s0168-6445(03)00016-0 pmid:12697340 fatcat:sffgkkhinjc5rchinmk2bxhham

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

Jessica Tout, Thomas C. Jeffries, Nicole S. Webster, Roman Stocker, Peter J. Ralph, Justin R. Seymour
2014 Microbial Ecology  
SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g.  ...  To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great  ...  Functional Biology and Climate Change Cluster (C3).  ... 
doi:10.1007/s00248-013-0362-5 pmid:24477921 fatcat:yuig5eyzurhwnevl642brlntsi

Host-hijacking and planktonic piracy: how phages command the microbial high seas

Joanna Warwick-Dugdale, Holger H. Buchholz, Michael J. Allen, Ben Temperton
2019 Virology Journal  
Incorporation of these new findings into global biogeochemical models requires experimental evidence from model systems and major improvements in our ability to accurately predict protein function from  ...  We also highlight the mechanisms used when, in challenging environments, a 'batten down the hatches' strategy supersedes that of 'plunder and pillage'.  ...  Acknowledgements The authors would like to thank the anonymous reviewers for their critical and constructive comments.  ... 
doi:10.1186/s12985-019-1120-1 pmid:30709355 pmcid:PMC6359870 fatcat:oouj3hfnrzgsnbbl2vkn72r6ju

Picocyanobacteria Community and Cyanophage Infection Responses to Nutrient Enrichment in a Mesocosms Experiment in Oligotrophic Waters

Alexandra Coello-Camba, Ruben Diaz-Rua, Carlos M. Duarte, Xabier Irigoien, John K. Pearman, Intikhab S. Alam, Susana Agusti
2020 Frontiers in Microbiology  
The subsequent collapse of the bloom pointed to a cyanophage infection on Synechococcus that reduced its competitive capacity, and was then followed by a diatom bloom.  ...  Our results highlight the relevance of host-phage interactions on determining population dynamics and diversity of Synechococcus populations.  ...  Resources Core Laboratory (CMOR) for their help in undertaking the sampling.  ... 
doi:10.3389/fmicb.2020.01153 pmid:32582095 pmcid:PMC7283753 fatcat:misrnlbz5bdnfosfm3ss7etmgi

Marine phage genomics

John H Paul, Matthew B Sullivan, Anca M Segall, Forest Rohwer
2002 Comparative Biochemistry and Physiology - Part B: Biochemistry & Molecular Biology  
diversity and physiological potential of the marine phage community.  ...  The handful of marine phage genomes that have been sequenced to date, along with prophages in marine bacterial genomes, and partial sequencing of uncultivated phages are yielding glimpses of the tremendous  ...  Acknowledgments The authors would like to thank phage and virus researchers who provided unpublished data for this review-Grieg Steward and Christina M.  ... 
doi:10.1016/s1096-4959(02)00168-9 pmid:12470812 fatcat:5lfulrocu5hrfdw3eedjmix4g4

An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure

Ivana Gudelj, Joshua S. Weitz, Tom Ferenci, M. Claire Horner-Devine, Christopher J. Marx, Justin R. Meyer, Samantha E. Forde
2010 Ecology Letters  
Finally, we suggest avenues for research where mathematical modelling, experiments and studies of natural microbial communities provide a unique opportunity to integrate studies of diversity across multiple  ...  In this study, we propose that understanding the intracellular basis for trade-offs in microbial systems can aid in predicting and interpreting patterns of diversity.  ...  For the model system used to analyse temperate phages, phage k, the probability of initiating the latent pathway is not a constant.  ... 
doi:10.1111/j.1461-0248.2010.01507.x pmid:20576029 pmcid:PMC3069490 fatcat:zaaabrgm7rgorbvdlazybhzlhm

Phosphonate production by marine microbes: exploring new sources and potential function [article]

Marianne Acker, Shane L Hogle, Paul M Berube, Thomas Hackl, Ramunas M Stepanauskas, Sallie W Chisholm, Daniel J Repeta
2020 bioRxiv   pre-print
Phosphonates, organic compounds with a C-P bond, constitute 20-25% of phosphorus in high molecular weight dissolved organic matter and are a significant phosphorus source for marine microbes.  ...  Surprisingly, one strain of Prochlorococcus (SB) can allocate more than 40% of its cellular P-quota towards phosphonate production.  ...  Overall it appears that a modest proportion of highly abundant beginning at 100 m depth.  ... 
doi:10.1101/2020.11.04.368217 fatcat:waisgou2zvdahlre27373yyqfa

Bacteriophages presence in nature and their role in the natural selection of bacterial populations

Zakira Naureen, Astrit Dautaj, Kyrylo Anpilogov, Giorgio Camilleri, Kristjana Dhuli, Benedetta Tanzi, Paolo Enrico Maltese, Francesca Cristofoli, Luca De Antoni, Tommaso Beccari, Munis Dundar, Matteo Bertelli
2020 Acta bio-medica : Atenei Parmensis  
Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions.  ...  Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations.  ...  M13 neither lyses the cell nor exists as a prophage and maintains its DNA as an extrachromosomal element, thus utilizing bacterial resources for its continuous replication and packaging into new M13 particles  ... 
doi:10.23750/abm.v91i13-s.10819 pmid:33170167 pmcid:PMC8023132 fatcat:g6znqa24cbbwbd3h73epcaddj4

Riboregulators and the role of Hfq in photosynthetic bacteria

Wolfgang R Hess, Bork A Berghoff, Annegret Wilde, Claudia Steglich, Gabriele Klug
2014 RNA Biology  
Whereas Anabaena 7120 is a well-established model system for bacterial developmental biology and for the study of dinitrogen fixation (for reviews, see refs. 3 and 42) , N. spumigena is of ecological  ...  that the induction of host RNase E transcript may help the phage by generating a source of nucleotides that are utilized by the phage for its own replication.  ... 
doi:10.4161/rna.28035 pmid:24651049 pmcid:PMC4152350 fatcat:fhxhhkspujcu7atyxeiigc34oe

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus

Paul M Berube, Anna Rasmussen, Rogier Braakman, Ramunas Stepanauskas, Sallie W Chisholm
2019 eLife  
By mapping this process onto a model of Prochlorococcus' macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation  ...  Intraspecific trait variability has important consequences for the function and stability of marine ecosystems.  ...  This paper is a contribution from the Simons Collaboration on Ocean Processes and Ecology (SCOPE) and from the NSF Center for Microbial Oceanography: Research and Education (C-MORE).  ... 
doi:10.7554/elife.41043 pmid:30706847 pmcid:PMC6370341 fatcat:so2meon7gnbuzdkgssv4ajtri4

The Marine Viromes of Four Oceanic Regions

Florent E Angly, Ben Felts, Mya Breitbart, Peter Salamon, Robert A Edwards, Craig Carlson, Amy M Chan, Matthew Haynes, Scott Kelley, Hong Liu, Joseph M Mahaffy, Jennifer E Mueller (+7 others)
2006 PLoS Biology  
There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed.  ...  Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic.  ...  Acknowledgments The GOM, BBC, and Arctic samples were collected with the generous help of the crew and scientists aboard the research vessels Longhorn, Mirai, Raddisson, Walton Smith, and Vector.  ... 
doi:10.1371/journal.pbio.0040368 pmid:17090214 pmcid:PMC1634881 fatcat:yokkhah6afhvblh23jhzxakcdq

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

M. F. Polz, D. E. Hunt, S. P. Preheim, D. M. Weinreich
2006 Philosophical Transactions of the Royal Society of London. Biological Sciences  
These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving  ...  variable resources; and the passive oligotroph, efficiently using low nutrient concentrations.  ...  This work was supported in part by grants from the DOE Genomes to Life program, NSF Biological Oceanography and the NSF/NIEHS sponsored Woods Hole Centre for Ocean and Human Health.  ... 
doi:10.1098/rstb.2006.1928 pmid:17062417 pmcid:PMC1764928 fatcat:dr6efbpxrvhx5n264uxeolz6ba

Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus

Erik R. Zinser, Debbie Lindell, Zackary I. Johnson, Matthias E. Futschik, Claudia Steglich, Maureen L. Coleman, Matthew A. Wright, Trent Rector, Robert Steen, Nathan McNulty, Luke R. Thompson, Sallie W. Chisholm (+1 others)
2009 PLoS ONE  
cycle, it does provide us with a valuable framework upon which to build when the Prochlorococcus proteome and metabolome become available.  ...  To better understand the tempo and choreography of this minimal phototroph, we studied the entire transcriptome of the cell over a simulated daily light-dark cycle, and placed it in the context of diagnostic  ...  Acknowledgments We thank George Church, Kyriacos Leptos, Xiaoxia Lin, and other members of the Church laboratory, and Julia Holtzendorff and Gabrielle Rocap for advice and technical assistance.  ... 
doi:10.1371/journal.pone.0005135 pmid:19352512 pmcid:PMC2663038 fatcat:ea6aqd4h6jacjiyawluppvbd4m
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