Microbial Community Structure and Function on Sinking Particles in the North Pacific Subtropical Gyre
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Sequence from B4 Sponge with (A) the First BLAST Hit Asbestopluma Lycopodium and (B) the Sequence of M
Supplementary Material Figure S1. Alignments of CO1 (PorCOI2fwd/PorCOI2rev) sequence from B4 sponge with (A) the first BLAST hit Asbestopluma lycopodium and (B) the sequence of M. acerata displaying low query cover. 1 Figure S2. Alignment of CO1 (dgLCO1490/dgHCO2198) sequence from B4 sponge with the first BLAST hit (M. acerata). 2 Figure S3. Alignment of CO1 (dgLCO1490/dgHCO2198) sequence from D4 sponge with the first BLAST hit (H. pilosus). 3 Figure S4. Taxonomy Bar Plot, reporting the relative frequencies (in percentage, %) of the bacteria taxons more representative for each of the four sponges under analysis . Sample code: B4= M. (Oxymycale) acerata; D4= H. pilosus, D6= M. sarai, C6= H. (Rhizoniera) dancoi. Each taxon is highlighted by a different color. 4 Figure S5. Krona plot at the seven increasing complexity levels: (a) Regnum, (b) Phylum, (c) Class, (d) Order, (e) Family, (f) Genus and (g) Species. a) 5 b) 6 c) 7 d) 8 e) 9 f) 10 g) 11 Figure S6. Distribution of ASV’s frequencies. 12 Figure S7. Distribution of ASV’s frequencies for each sample (reported as a blue bar). 13 Table S1. BLAST results from B4 sponge (Mycale (Oxymycale) acerata). The primer names, sequence length in base pairs (bp), first hits (highlighted in bold), hits at low significance displaying the correct species (where present), query cover and identity percentages (%) were reported. Sequence Query Identity Primers BLAST results length (bp) cover (%) (%) Mycale macilenta voucher 0CDN7203‐O small subunit 18S A/B 1700 99 98 ribosomal RNA gene, partial sequence Mycale -
Interactions in Self-Assembled Microbial Communities Saturate with Diversity
bioRxiv preprint doi: https://doi.org/10.1101/347948; this version posted June 16, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Interactions in self-assembled microbial communities saturate with diversity Xiaoqian Yu1, Martin F. Polz2*, Eric J. Alm2,3,4,5* 1. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 2. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 3. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 4. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 5. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA *Correspondence should be addressed to: E.J.A. ([email protected]) or M.F.P. ([email protected]) Abstract How the diversity of organisms competing for or sharing resources influences community production is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. -
Labile Dissolved Organic Matter Compound Characteristics Select
http://www.diva-portal.org This is the published version of a paper published in Frontiers in Microbiology. Citation for the original published paper (version of record): Pontiller, B., Martinez-Garcia, S., Lundin, D., Pinhassi, J. (2020) Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription Frontiers in Microbiology, 11: 1-19 https://doi.org/10.3389/fmicb.2020.588778 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-98814 fmicb-11-588778 September 24, 2020 Time: 19:52 # 1 ORIGINAL RESEARCH published: 25 September 2020 doi: 10.3389/fmicb.2020.588778 Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription Benjamin Pontiller1, Sandra Martínez-García2, Daniel Lundin1 and Jarone Pinhassi1* 1 Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden, 2 Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, Spain Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced Edited by: changes in bacterial growth, activity, and transcription related to DOM characteristics. -
Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia
molecules Article Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia Nadezhda Chernysheva, Evgeniya Bystritskaya, Galina Likhatskaya , Olga Nedashkovskaya and Marina Isaeva * G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia; [email protected] (N.C.); [email protected] (E.B.); [email protected] (G.L.); [email protected] (O.N.) * Correspondence: [email protected]; Tel.: +7-423-231-1168 Abstract: We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus- specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs. Keywords: Zobellia; genomes; polysaccharide lyase family 7; alginate utilization system; paralogs; orthologs Citation: Chernysheva, N.; Bystritskaya, E.; Likhatskaya, G.; Nedashkovskaya, O.; Isaeva, M. Genome-Wide Analysis of PL7 1. Introduction Alginate Lyases in the Genus Zobellia. Marine algal polysaccharides are an important nutrient source for marine bacteria. To Molecules 2021, 26, 2387. -
The Mannitol Utilization System of the Marine Bacterium Zobellia Galactanivorans Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon
The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon To cite this version: Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon. The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans. Applied and Environmental Microbiology, Ameri- can Society for Microbiology, 2015, 81, pp.1799 - 1812. 10.1128/AEM.02808-14. hal-01116467 HAL Id: hal-01116467 https://hal.archives-ouvertes.fr/hal-01116467 Submitted on 13 Feb 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 1 The mannitol utilization system of the marine bacterium Zobellia galactanivorans 2 3 4 Agnès Groisillier,a,b, Aurore Labourel,a,b,*, Gurvan Michel,a,b and Thierry Tonona,b,# 5 6 Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine 7 Models, Station Biologique de Roscoff, Francea; CNRS, UMR 8227, Integrative Biology of 8 Marine Models, Station Biologique de Roscoff, Franceb 9 10 Running title: Mannitol degradation by Zobellia galactanivorans 11 12 #Address correspondence to Thierry Tonon, [email protected] 13 14 *Present address: University of Newcastle, Cell and Molecular Biosciences, Medical School, 15 Cookson Bidg, Framligton Place, NE2 4HH Newcastle upon Tyne, United Kingdom 16 17 A.G. -
Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In
Table S8. Species identified by random forests analysis of shotgun sequencing data that exhibit significant differences in their representation in the fecal microbiomes between each two groups of mice. (a) Species discriminating fecal microbiota of the Soil and Control mice. Mean importance of species identified by random forest are shown in the 5th column. Random forests assigns an importance score to each species by estimating the increase in error caused by removing that species from the set of predictors. In our analysis, we considered a species to be “highly predictive” if its importance score was at least 0.001. T-test was performed for the relative abundances of each species between the two groups of mice. P-values were at least 0.05 to be considered statistically significant. Microbiological Taxonomy Random Forests Mean of relative abundance P-Value Species Microbiological Function (T-Test) Classification Bacterial Order Importance Score Soil Control Rhodococcus sp. 2G Engineered strain Bacteria Corynebacteriales 0.002 5.73791E-05 1.9325E-05 9.3737E-06 Herminiimonas arsenitoxidans Engineered strain Bacteria Burkholderiales 0.002 0.005112829 7.1580E-05 1.3995E-05 Aspergillus ibericus Engineered strain Fungi 0.002 0.001061181 9.2368E-05 7.3057E-05 Dichomitus squalens Engineered strain Fungi 0.002 0.018887472 8.0887E-05 4.1254E-05 Acinetobacter sp. TTH0-4 Engineered strain Bacteria Pseudomonadales 0.001333333 0.025523638 2.2311E-05 8.2612E-06 Rhizobium tropici Engineered strain Bacteria Rhizobiales 0.001333333 0.02079554 7.0081E-05 4.2000E-05 Methylocystis bryophila Engineered strain Bacteria Rhizobiales 0.001333333 0.006513543 3.5401E-05 2.2044E-05 Alteromonas naphthalenivorans Engineered strain Bacteria Alteromonadales 0.001 0.000660472 2.0747E-05 4.6463E-05 Saccharomyces cerevisiae Engineered strain Fungi 0.001 0.002980726 3.9901E-05 7.3043E-05 Bacillus phage Belinda Antibiotic Phage 0.002 0.016409765 6.8789E-07 6.0681E-08 Streptomyces sp. -
Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed
fmicb-10-02870 January 6, 2020 Time: 15:52 # 1 ORIGINAL RESEARCH published: 15 January 2020 doi: 10.3389/fmicb.2019.02870 Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed Mahasweta Saha1,2,3*, Robert M. W. Ferguson2, Shawn Dove4,5, Sven Künzel6, Rafael Meichssner7,8, Sven C. Neulinger9, Finn Ole Petersen10 and Florian Weinberger1 1 Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 The School of Life Sciences, University of Essex, Colchester, United Kingdom, 3 Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom, 4 Centre for Biodiversity and Environment Research, University College London, London, United Kingdom, 5 Institute of Zoology, Zoological Society of London, London, United Kingdom, 6 Max Planck Institute for Evolutionary Biology, Plön, Germany, 7 Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany, 8 Coastal Research & Management, Kiel, Germany, 9 omics2view.consulting GbR, Kiel, Germany, 10 Department of Biology, Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany The establishment of epibacterial communities is fundamental to seaweed health and Edited by: fitness, in modulating ecological interactions and may also facilitate adaptation to Olga Lage, University of Porto, Portugal new environments. Abiotic factors like salinity can determine bacterial abundance, Reviewed by: growth and community composition. However, influence of salinity as a driver of Hanzhi Lin, epibacterial community composition (until species level) has not been investigated for University of Maryland Center for Environmental Science (UMCES), seaweeds and especially under long time scales. We also do not know how abiotic United States stressors may influence the ‘core’ bacterial species of seaweeds. -
Transfer of Carbohydrate-Active Enzymes from Marine Bacteria to Japanese Gut Microbiota
Vol 464 | 8 April 2010 | doi:10.1038/nature08937 LETTERS Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Jan-Hendrik Hehemann1,2{, Gae¨lle Correc1,2, Tristan Barbeyron1,2, William Helbert1,2, Mirjam Czjzek1,2 & Gurvan Michel1,2 Gut microbes supply the human body with energy from dietary not possess the critical residues needed for recognition of agarose or polysaccharides through carbohydrate active enzymes, or k-carrageenan12. CAZymes1, which are absent in the human genome. These enzymes To identify their substrate specificity we cloned and expressed these target polysaccharides from terrestrial plants that dominated diet five GH16 genes in Escherichia coli. However, only Zg1017 and the throughout human evolution2. The array of CAZymes in gut catalytic module of Zg2600 were expressed as soluble proteins and microbes is highly diverse, exemplified by the human gut symbiont could be further analysed (Supplementary Fig. 2). As predicted, these Bacteroides thetaiotaomicron3, which contains 261 glycoside proteins had no activity on commercial agarose (Supplementary hydrolases and polysaccharide lyases, as well as 208 homologues Fig. 3) or k-carrageenan. Consequently, we screened their hydrolytic of susC and susD-genes coding for two outer membrane proteins activity against natural polysaccharides extracted from various marine involved in starch utilization1,4. A fundamental question that, to macrophytes (data not shown). Zg2600 and Zg1017 were found to be our knowledge, has yet to be addressed is how this diversity evolved active only on extracts from the agarophytic red algae Gelidium, by acquiring new genes from microbes living outside the gut. Here Gracilaria and Porphyra, as shown by the release of reducing ends we characterize the first porphyranases from a member of the (Fig. -
Morphogenesis of Ulva Mutabilis (Chlorophyta) Induced by Maribacter Species (Bacteroidetes, Flavobacteriaceae)
Botanica Marina 2017; 60(2): 197–206 Short communication Open Access Anne Weiss, Rodrigo Costa and Thomas Wichard* Morphogenesis of Ulva mutabilis (Chlorophyta) induced by Maribacter species (Bacteroidetes, Flavobacteriaceae) DOI 10.1515/bot-2016-0083 related Flavobacteriaceae and a Maribacter strain isolated Received 31 July, 2016; accepted 11 January, 2017; online first from a red alga did not possess any activity. 17 February, 2017 Keywords: bacteroidetes; cell differentiation; green mac- Abstract: Growth and morphogenesis of the sea lettuce Ulva roalga; morphogens; thallusin. (Chlorophyta) depends on the combination of regulative morphogenetic compounds released by specific associated bacteria. Axenic Ulva gametes develop parthenogenetically The green macroalga Ulva mutabilis Føyn (Chlorophyta) is into callus-like colonies consisting of undifferentiated cells not able to develop and differentiate into blade, stem and without normal cell walls. In Ulva mutabilis Føyn, two bac- rhizoid cells under axenic conditions, or when its microbi- terial strains, Maribacter sp. strain MS6 and Roseovarius ome is not appropriate. Instead, the alga forms callus-like, strain MS2, can restore the complete algal morphogenesis slow growing structures with colourless protrusions from forming a tripartite symbiotic community. Morphogenetic the exterior cell wall (Spoerner et al. 2012, Wichard 2015). compounds ( = morphogens) released by the MS6-strain Early experiments of Provasoli (1958) have already pointed induce rhizoid formation and cell wall development in U. out that treatment of Ulva with antibiotics results in abnor- mutabilis, while several bacteria of the Roseobacter clade, mal growth. Further experiments examined the role of including the MS2-strain, promote blade cell division and isolated bacteria in activating developmental and growth thallus elongation. -
Chemical Interactions Between Marine Macroalgae and Bacteria
Vol. 409: 267–300, 2010 MARINE ECOLOGY PROGRESS SERIES Published June 23 doi: 10.3354/meps08607 Mar Ecol Prog Ser REVIEW Chemical interactions between marine macroalgae and bacteria Franz Goecke, Antje Labes, Jutta Wiese, Johannes F. Imhoff* Kieler Wirkstoff-Zentrum at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, Kiel 24106, Germany ABSTRACT: We review research from the last 40 yr on macroalgal–bacterial interactions. Marine macroalgae have been challenged throughout their evolution by microorganisms and have devel- oped in a world of microbes. Therefore, it is not surprising that a complex array of interactions has evolved between macroalgae and bacteria which basically depends on chemical interactions of vari- ous kinds. Bacteria specifically associate with particular macroalgal species and even to certain parts of the algal body. Although the mechanisms of this specificity have not yet been fully elucidated, eco- logical functions have been demonstrated for some of the associations. Though some of the chemical response mechanisms can be clearly attributed to either the alga or to its epibiont, in many cases the producers as well as the mechanisms triggering the biosynthesis of the biologically active compounds remain ambiguous. Positive macroalgal–bacterial interactions include phytohormone production, morphogenesis of macroalgae triggered by bacterial products, specific antibiotic activities affecting epibionts and elicitation of oxidative burst mechanisms. Some bacteria are able to prevent biofouling or pathogen invasion, or extend the defense mechanisms of the macroalgae itself. Deleterious macroalgal–bacterial interactions induce or generate algal diseases. To inhibit settlement, growth and biofilm formation by bacteria, macroalgae influence bacterial metabolism and quorum sensing, and produce antibiotic compounds. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
A Highly Active Phosphate-Insensitive Phosphatase Is Widely Distributed in Nature 2 3 4 Ian D.E.A
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.27.457942; this version posted August 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 A highly active phosphate-insensitive phosphatase is widely distributed in nature 2 3 4 Ian D.E.A. Lidbury1*, David J. Scanlan2, Andrew R. J. Murphy2, Joseph A. Christie-Oleza3, Maria 5 M. Aguilo-Ferretjans3, Andrew HitchcocK4, TiM Daniell1 6 1 Department of AniMal and Plant Sciences, University of Sheffield, Sheffield, UK 7 2 School of Life Sciences, University of WarwicK, Gibbet Hill Road, Coventry, UK 8 3 University of the Balearic Islands, PalMa, Spain 9 4 Department of Molecular BioloGy and BiotechnoloGy, University of Sheffield, Sheffield, UK 10 11 Abstract (250 max) 12 The reGeneration of bioavailable phosphate froM iMMobilised orGanophosphorus represents 13 a Key process in the Global phosphorus cycle and is facilitated by enzyMes Known as 14 phosphatases. Most bacteria possess at least one of three Major phosphatases, Known as 15 PhoA, PhoX and PhoD, whose activity is optiMal under alKaline conditions. The production 16 and activity of these three phosphatase families is neGatively reGulated by phosphate 17 availability and thus these enzyMes play a Major role in scavenGinG phosphorus only during 18 tiMes of phosphate scarcity. Here, we reveal a previously overlooKed phosphate-insensitive 19 phosphatase, PafA, prevalent in Bacteroidetes, which is hiGhly abundant in nature and 20 represents a Major route for the reMineralisation of phosphate in the environMent.