Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise

Interactions between co-existing microorganisms deeply affect the physiology of the involved organisms and, ultimately, the function of the ecosystem as a whole. Copiotrophic Alteromonas are marine gammaproteobacteria that thrive during the late stages of phytoplankton blooms in the marine environment and in laboratory co-cultures with cyanobacteria such as Trichodesmium. The response of this heterotroph to the sometimes rapid and transient changes in nutrient supply when the phototroph crashes is not well understood. Here, we isolated and sequenced the strain Alteromonas macleodii str. Te101 from a laboratory culture of Trichodesmium erythraeum IMS101, yielding a chromosome of 4.63 Mb and a single plasmid of 237 kb. Increasing salinities to ≥43 ppt inhibited the growth of Trichodesmium but stimulated growth of the associated Alteromonas. We characterized the transcriptomic responses of both microorganisms and identified the complement of active transcriptional start sites in Alteromonas at single-nucleotide resolution. In replicate cultures, a similar set of genes became activated in Alteromonas when growth rates of Trichodesmium declined and mortality was high. The parallel activation of fliA, rpoS and of flagellar assembly and growth-related genes indicated that Alteromonas might have increased cell motility, growth, and multiple biosynthetic activities. Genes with the highest expression in the data set were three small RNAs (Aln1a-c) that were identified as analogs of the small RNAs CsrB-C in E. coli or RsmX-Z in pathogenic bacteria. Together with the carbon storage protein A (CsrA) homolog Te101_05290, these RNAs likely control the expression of numerous genes in responding to changes in the environmentThis work was supported by the EU project MaCuMBA (grant agreement no. 311975) to WRH and FRVby the German Israeli Foundation grant no. 1133 to IB-F and WRHSupport of ML-P by a postdoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (APOSTD/2016/051)of SH by the China Scholarship Council is gratefully acknowledged

Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture

The ocean’s nitrogen is largely fixed by cyanobacteria, including Trichodesmium, which forms aggregates comprising hundreds of filaments arranged in organized architectures. Aggregates often form upon exposure to stress and have ecological and biophysical characteristics that differ from those of single filaments. Here, we report that Trichodesmium aggregates can rapidly modulate their shape, responding within minutes to changes in environmental conditions. Combining video microscopy and mathematical modeling, we discovered that this reorganization is mediated by “smart reversals” wherein gliding filaments reverse when their overlap with other filaments diminishes. By regulating smart reversals, filaments control aggregate architecture without central coordination. We propose that the modulation of gliding motility at the single-filament level is a determinant of Trichodesmium’s aggregation behavior and ultimately of its biogeochemical role in the ocean

Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the southwest Pacific

International audienceMicrobial gene expression was followed for 23 days within a mesocosm (M1) isolating 50m(3) of seawater and in the surrounding waters in the Noumea lagoon, New Caledonia, in the southwest Pacific as part of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) experiment. The aim of VAHINE was to examine the fate of diazotroph-derived nitrogen (DDN) in a low-nutrient, low-chlorophyll ecosystem. On day 4 of the experiment, the mesocosm was fertilized with phosphate. In the lagoon, gene expression was dominated by the cyanobacterium Synechococcus, closely followed by Alphaproteobacteria. In contrast, drastic changes in the microbial community composition and transcriptional activity were triggered within the mesocosm within the first 4 days, with transcription bursts from different heterotrophic bacteria in rapid succession. The microbial composition and activity of the surrounding lagoon ecosystem appeared more stable, although following similar temporal trends as in M1. We detected significant gene expression from Chromerida in M1, as well as the Noumea lagoon, suggesting these photoautotrophic alveolates were present in substantial numbers in the open water. Other groups contributing substantially to the metatranscriptome were affiliated with marine Euryarchaeota Candidatus Thalassoarchaea (inside and outside) and Myoviridae bacteriophages likely infecting Synechococcus, specifically inside M1. High transcript abundances for ammonium transporters and glutamine synthetase in many different taxa (e.g., Pelagibacteraceae, Synechococcus, Prochlorococcus, and Rhodobacteraceae) was consistent with the known preference of most bacteria for this nitrogen source. In contrast, Alteromonadaceae highly expressed urease genes; Rhodobacteraceae and Prochlorococcus showed some urease expression, too. Nitrate reductase transcripts were detected on day 10 very prominently in Synechococcus and in Halomonadaceae. Alkaline phosphatase was expressed prominently only between days 12 and 23 in different organisms, suggesting that the microbial community was not limited by phosphate, even before the fertilization on day 4, whereas the post-fertilization community was. We observed high expression of the Synechococcus sqdB gene, only transiently lowered following phosphate fertilization. SqdB encodes UDP-sulfoquinovose synthase, possibly enabling marine picocyanobacteria to minimize their phosphorus requirements by substitution of phospholipids with sulphur-containing glycerolipids. This result suggests a link between sqdB expression and phosphate availability in situ. Gene expression of diazotrophic cyanobacteria was mainly attributed to Trichodesmium and Richelia intracellularis (diatom-diazotroph association) in the Noumea lagoon and initially in M1. UCYN-A (Candidatus Atelocyanobacterium) transcripts were the third most abundant and declined both inside and outside after day 4, consistent with 16S- and nifH-based analyses. Transcripts related to the Epithemia turgida endosymbiont and Cyanothece ATCC 51142 increased during the second half of the experiment

MGOUN1 Encodes an Arabidopsis Type IB DNA Topoisomerase Required in Stem Cell Regulation and to Maintain Developmentally Regulated Gene Silencing[W]

This work examines the function of MGOUN1 (MGO1) in Arabidopsis stem cell maintenance, showing that mgo1 mutations enhance the specific stem cell defects in hypomorphic wuschel alleles. Positional cloning reveals that MGO1 encodes topoisomerase IB, thereby linking topoisomerase function to the propagation of developmentally regulated gene function

Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

Studies investigating the fate of diazotrophs through the microbial food web are lacking, although N2 fixation can fuel up to 50 % of new production in some oligotrophic oceans. In particular, the role played by heterotrophic prokaryotes in this transfer is largely unknown. In the frame of the VAHINE (VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific) experiment, three replicate large-volume (∼ 50 m3) mesocosms were deployed for 23 days in the new Caledonia lagoon and were intentionally fertilized on day 4 with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. We specifically examined relationships between heterotrophic bacterial production (BP) and N2 fixation or primary production, determined bacterial growth efficiency and established carbon budgets. BP was statistically higher during the second phase of the experiment (P2: days 15–23), when chlorophyll biomass started to increase compared to the first phase (P1: days 5–14). Phosphatase alkaline activity increased drastically during the second phase of the experiment, showing adaptations of microbial populations after utilization of the added DIP. Notably, among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget (27–43 %), was notably higher than generally cited for oligotrophic environments and discussed in links with the presence of abundant species of bacteria expressing proteorhodopsin. The main fates of gross primary production (particulate + dissolved) were respiration (67 %) and export through sedimentation (17 %). BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but was slightly correlated, and only during P2 phase, with N2 fixation rates. Heterotrophic bacterial production was strongly stimulated after mineral N enrichment experiments, suggesting N-limitation of heterotrophic bacteria across the experiment. N2 fixation rates corresponded to 17–37 % of the nitrogen demand of heterotrophic bacteria. Our results suggest that most of the diazotroph-derived nitrogen fuelled the heterotrophic bacterial community through indirect processes generating dissolved organic matter and detritus, like mortality, lysis and grazing of both diazotrophs and non-diazotrophs

Supplementary Datasets for "mdRNA-Seq analysis of marine microbial communities from the northern Red Sea"

<p>This file set contains supplementary datasets for paper "Hou, S.<i> et al.</i> mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci. Rep. 6, 35470; doi: 10.1038/srep35470 (2016)." Please refer to this paper for more information.</p><p><b><u>File Description:</u></b></p> <p><b>Supplemental Dataset S1: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Synechococcus</i> CC9605. <b></b></p><p><b>Supplemental Dataset S2: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Candidatus </i>Pelagibacter sp. HTCC7211.</p> <p><b>Supplemental Dataset S3:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 17 chromosomes, mitochondrial and chloroplast genomes of <i>Micromonas </i>sp. RCC299.</p> <p><b>Supplemental Dataset S</b><b>4:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 149 environmental contigs belonging to the <i>Euryarchaeota</i>.</p> <p><b>Supplemental Dataset S</b><b>5:</b> Alignment of archaeal RNase P RNA sequences including eight euryarchaeal sequences from the Red Sea metatranscriptome. </p> <b>Supplemental Dataset S6:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 52 environmental contigs belonging to the <i>Thaumarchaeota</i>.<div><br></div><div><br></div><div><div><b><u>How to cite this dataset:</u></b></div><div><br></div><div>If you find this dataset useful to your research, please consider to cite the main paper: </div><div>Hou, S. <i>et al</i>. <b>mdRNA-Seq analysis of marine microbial communities from the northern </b><b>Red Sea</b>. <i>Sci. Rep.</i> <b>6</b>, 35470; doi: 10.1038/srep35470 (2016).</div><div><br></div><div><br></div><div><br></div></div

Supplementary Datasets for "Benefit from decline: The primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise"

<p>This file set contains supplementary dataset for paper "Hou, S.<i> et al.</i> <b>Benefit from decline: The primary transcriptome of <i>Alteromonas macleodii </i>str. Te101 during <i>Trichodesmium</i> demise</b>. (<i>accepted</i>)." Please refer to this paper for more information.</p><p><b><u><br></u></b></p><p><b><u>File Description:</u></b></p><p><b>Supplemental Dataset S1:</b> Genome-wide visualization of predicted TSS and coverage for the genome of <i>Alteromonas</i> <i>macleodii</i> str. Te101.</p><p><b>Supplementary Dataset 2: </b>Genome-wide GO assignments of <i>Alteromonas</i> <i>macleodii</i> str. Te101 proteins.</p><div><br></div><div><br></div><div><div><b><u>How To Cite This Dataset:</u></b></div><div><br></div><div>If you find this dataset useful to your research, please consider to cite the main paper: </div><div>Hou, S. <i>et al</i>. <b>Benefit from decline: The primary transcriptome of <i>Alteromonas macleodii</i> str. Te101 when <i>Trichodesmium</i> collapses.</b> (<i>accepted</i>)</div><div><br></div><div><br></div></div