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Thomas Wichard

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I am a research group leader at the Institute for Inorganic and Analytical Chemistry of the Friedrich Schiller University Jena. The main focus of our research group is to elucidate the mutualistic interactions between bacteria and the marine macroalga Ulva (“cross-kingdom-cross-talk”). The group applies various methodologies in analytical chemistry, chemical ecology and molecular biology to understand the basis of eco-physiological processes.

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Jayjit Majumdar

University of Kalyani

University College Cork

Politecnico di Milano

girolamo fiorentino

University of Salento

George Papachristos

Technische universiteit Eindhoven

Shabib H . Syed

University of the Punjab, Lahore, Pakistan

Hungarian Academy of Sciences

University of Sarajevo

Christian-Albrechts-Universität zu Kiel

The University Of Jordan

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Papers by Thomas Wichard

Algal growth and morphogenesis-promoting factors released by cold-adapted bacteria contribute to the resilience and morphogenesis of the seaweed Ulva (Chlorophyta) in Antarctica (Potter Cove)

bioRxiv (Cold Spring Harbor Laboratory), Jul 6, 2024

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

Beilstein Journal of Organic Chemistry

Aromatic prenylated metabolites have important biological roles and activities in all living orga... more Aromatic prenylated metabolites have important biological roles and activities in all living organisms. Compared to their importance in all domains of life, we know relatively little about their substrate scopes and metabolic functions. Here, we describe a new UbiA-like prenyltransferase (Ptase) Ubi-297 encoded in a conserved operon of several bacterial taxa, including marine Flavobacteria and the genus Sacchromonospora. In silico analysis of Ubi-297 homologs indicated that members of this Ptase group are composed of several transmembrane α-helices and carry a conserved and distinct aspartic-rich Mg2+-binding domain. We heterologously produced UbiA-like Ptases from the bacterial genera Maribacter, Zobellia, and Algoriphagus in Escherichia coli. Investigation of their substrate scope uncovered the preferential farnesylation of quinoline derivatives, such as 8-hydroxyquinoline-2-carboxylic acid (8-HQA) and quinaldic acid. The results of this study provide new insights into the abundan...

High-temperature stress induces bacteria-specific adverse and reversible effects on Ulva (Chlorophyta) growth and its chemosphere in a reductionist model system

Botanica Marina

Axenic cultures of the green seaweed Ulva mutabilis were inoculated with bacteria providing essen... more Axenic cultures of the green seaweed Ulva mutabilis were inoculated with bacteria providing essential algal growth and morphogenesis-promoting factors (AGMPFs) and were exposed to temperature shifts from 18 °C to 30 °C. The temperature-dependent effect of bacteria on longitudinal algal growth and the molecular composition of the chemosphere in the algal culture medium was explored. The reductionist tripartite model system of U. mutabilis, Roseovarius sp. MS2, and Maribacter sp. MS6 was applied as a reference and has been changed by substituting Roseovarius with isolates that phenocopy this strain. Rathayibacter festucae IH2 and Roseovarius aestuarii G8 boosted growth at 18 °C but slowed it down at 30 °C. Additional inoculation of Roseovarius sp. MS2 mitigated these adverse bacterial effects partially. At 30 °C, the molecular profile of the chemosphere differed dramatically between all tested tripartite communities, indicating different traits of the same bacterium with changing temp...

Insights into the potential for mutualistic and harmful host–microbe interactions affecting brown alga freshwater acclimation

Molecular Ecology, Nov 23, 2022

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Chapter 18. Metabolomics of intra- and extracellular metabolites from micro- and macroalgae using GC-MS and LC-MS

Zenodo (CERN European Organization for Nuclear Research), Apr 26, 2018

Comparative metabolomics is an emerging technique suitable for the monitoring of metabolic respon... more Comparative metabolomics is an emerging technique suitable for the monitoring of metabolic responses of organisms to external stimuli or stress factors like biotic interaction partners, nutrient limitation or adverse environmental conditions. Using data from comparative metabolomics, changes in primary metabolism can be unraveled and connected to the regulation of metabolic pathways. However, the technique is also suitable for an untargeted screening of primary and secondary metabolites. Thereby candidate metabolites can be identified that might play a functional role in the particular stress situation. Especially mass spectrometry-enabled techniques have found their way into many disciplines. Here we describe the extraction, derivatization, gas chromatography-mass spectrometry (GC-MS) as well as liquid chromatography-mass spectrometry (LC-MS) measurement and data analysis for a metabolic profiling of algae. We describe a general protocol for intracellular profiling of microalgae, and germ cells and thalli of macroalgae. The protocol outlines the procedure to extract, derivatize and measure the exo-metabolome of these organisms, i.e., the metabolites exuded into the seawater. 2 The method was initially developed for metabolomics of the diatom Skeletonema marinoi but proved to be suitable for a broad range of micro-and macroalgae after minor adaptations. The entire work-flow can be carried out in laboratories with basic equipment for chemical work and measurements can be recorded on most commercially available GC-MS and LC-MS systems.

Metabolite profiling reveals insights into the species-dependent cold stress response of the green seaweed holobiont Ulva (Chlorophyta)

Environmental and Experimental Botany, Aug 1, 2022

Algae induce siderophore biosynthesis in the freshwater bacterium Cupriavidus necator H16

Biometals, Nov 24, 2018

Cupriachelin is a photoreactive lipopeptide siderophore produced by the freshwater bacterium Cupr... more Cupriachelin is a photoreactive lipopeptide siderophore produced by the freshwater bacterium Cupriavidus necator H16. In the presence of sunlight, the iron-loaded siderophore undergoes photolytic cleavage, thereby releasing solubilized iron into the environment. This iron is not only available to the siderophore producer, but also to the surrounding microbial community. In this study, the cupriachelinbased interaction between C. necator H16 and the freshwater diatom Navicula pelliculosa was investigated. A reporter strain of the bacterium was constructed to study differential expression levels of the cupriachelin biosynthesis gene cucJ in response to varying environmental conditions. Not only iron starvation, but also culture supernatants of N. pelliculosa were found to induce cupriachelin biosynthesis. The transcription factors involved in this differential gene expression were identified using DNA-protein pulldown assays. Besides the well-characterized ferric uptake regulator, a two-component system was found to tune the expression of cupriachelin biosynthesis genes in the presence of diatom supernatants.

Metabolomics of intra- and extracellular metabolites from micro- and macroalgae using GC–MS and LC–MS

CRC Press eBooks, Apr 17, 2018

<i>Ulva</i>: An emerging green seaweed model for systems biology

Journal of Phycology, May 31, 2023

Using O2/Ar ratios as a proxy for biological productivity determinations in an Arctic river

&amp;lt;p&amp;gt;The biogeochemical cycling of carbon in Arctic rivers is perturbed as mo... more &amp;lt;p&amp;gt;The biogeochemical cycling of carbon in Arctic rivers is perturbed as more terrestrial organic carbon and nutrients are released upon active layer and permafrost thaw. The majority of the carbon dioxide (CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) in rivers is emitted into the atmosphere, but it can also be utilized during photosynthesis, especially with more availability of nutrients, influencing the carbon flow and aquatic ecosystem metabolism. However, the timing and amount of photosynthetic primary production in Arctic rivers are unknown.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Water samples from the Kolyma River in Northeast Siberia were collected in June (late freshet) and August (summer) 2019. For the first time in an Arctic river, we measured biological oxygen supersaturations using the relative oxygen-to-argon ratio above equilibrium, &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar), which is an indicator of the presence of biologically produced oxygen. This ratio is influenced in approximately equal parts by physical processes, while biological processes unilaterally influence the oxygen content.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In addition, we measured the partial pressure of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;), dissolved oxygen and inorganic nutrients concentrations. Mass spectrometry was employed to chemically characterize the composition of dissolved organic matter (DOM) and better understand its origin. Microbial communities were elucidated using 16S and metagenomic based sequencing approaches.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In June, the oxygen saturation in turbid and warm waters (average: 14 &amp;amp;#176;C) in the main river channel was on average 10% above atmospheric equilibrium. The &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) values were well above equilibrium (2000 &amp;amp;#181;atm). Unlike oxygen saturation, &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar) was negative (undersaturation); thus, physical processes contributed most to the total oxygen supersaturation (up to 20%), apparently due to contributions of freshet cold gas-rich meltwater, while the net biological oxygen concentration was between &amp;amp;#8211;10 and &amp;amp;#8211;15%.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In August, the water was colder (3 &amp;amp;#176;C drop), and the total oxygen was mostly undersaturated (up to &amp;amp;#8211;10%). However, lower &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) and a decrease in the biological oxygen deficit (between 0 and &amp;amp;#8211;5%) indicated net biological oxygen input. At the confluence of the main river channel and some tributaries, an algal bloom was observed resulting in up to 6.4% supersaturation in &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar) and &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) near atmospheric equilibrium.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Concentrations of nitrate and silica were higher in August than in June. Dissolved phosphate concentrations were low at both sampling times, but apparently did not limit primary productivity. The microbial community composition varied greatly between sampling times, with differential shifts across the transect. Compared to June, the DOM pattern in August was less diverse in the river due to more stable stream conditions and defined hydrologic connectivity between land and river, promoting also nutrient supply for biological productivity.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Unlike anticipated, the O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar ratios suggested that net biological oxygen production in the river did not profit during the late freshet, despite unlimited light and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; availability and warm temperatures. Contrastingly, the summer low-flow allowed for photosynthetically-driven oxygen production and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; uptake in some sites. We conclude that the O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar ratios were essential for quantifying the contribution of biological production, and understand better the fate of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; in an Arctic river influenced by thawing permafrost, as well as the land-aquatic-continuum in the context of climate change.&amp;lt;/p&amp;gt;

Permafrost Arctic streams are effective pathways for the emissions of allochthonous and autochthonous greenhouse gases to the atmosphere during the open water season: a holistic study in Ambolikha river, Northeast Siberia

AGU Fall Meeting Abstracts, Dec 1, 2020

Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

EGU General Assembly Conference Abstracts, Apr 1, 2017

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms

The ISME Journal, Jul 20, 2020

Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments wi... more Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or-oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H 2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.

Stereoselektive Totalsynthese von (−)‐Thallusin zur Bioaktivitätsprofilierung

Angewandte Chemie, Aug 24, 2022

Influence of diatoms on copepod reproduction. III. Consequences of abnormal oocyte maturation on reproductive factors in Calanus helgolandicus

Marine Biology, May 4, 2007

Observations of gonads and oocyte development stages (OS) have been achieved in Calanus helgoland... more Observations of gonads and oocyte development stages (OS) have been achieved in Calanus helgolandicus females fed diVerent algal diets and starved in Wltered sea water under laboratory conditions during 8 days. The eVects of 20 diets on egg production rates (EPR), hatching success (HS) and proportion of abnormal larvae (AL, development stages N1-2) were examined. With the control diet Prorocentrum minimum EPR and HS values were high, while AL was very low, coinciding with intact cell structures in oogonia (OO) and normal OS (OS1-OS4). With the other diets, oocyte maturation, EPR, HS and AL patterns were partially or totally impaired. Decrease of EPR coincided with the arrest of OS3 maturation and oocyte degradations, characterised by cell fragmentation, presence of apoptotic bodies in the OS3, degradation of cytoplasm in OS3 and OS4 and consequently the arrest of OS4 formation. These degradations were reversible when females were fed a favourable diet. Results reXect the presence of two distinct inhibitory mechanisms. Inhibition mechanism (1) impairs egg production. It was induced by starvation or by several species belonging to Bacillariophyceae (Chaetoceros calcitrans, Guinardia delicatula, Guinardia striata, Odontella regia, Rhizosolenia setigera, Stephanopyxis turris, Thalassiosira pseudonana) and mixed-diatom assemblages (collected in the Weld) and to the prymnesiophyte Pavlova lutherii. Remarkably other diatoms like Navicula sp., Nitzschia sp., Skeletonema costatum and Thalassiosira rotula did not induce mechanism (1) Inhibitory mechanism (2) aVected exclusively HS and AL and was triggered by species independent of the production of polyunsaturated aldehydes (PUA), which are supposed to have adverse impacts on HS and larval development. Communicated by O. Kinne.

Influence of diatoms on copepod reproduction. I. Field and laboratory observations related to Calanus helgolandicus egg production

Marine Ecology Progress Series, Feb 16, 2006

Egg production rates (EPR) by Calanus helgolandicus females were investigated with specimens samp... more Egg production rates (EPR) by Calanus helgolandicus females were investigated with specimens sampled weekly, from April to November 2003 and from March to October 2004, at a station located in the English Channel off Roscoff. Comparison of results between 1994, 2003 and 2004 showed that C. helgolandicus was a late spawner in 1994 and became an early spawner in 2003 and 2004. In all cases high variations in EPR were observed, which could not be correlated to phytoplankton biomass, expressed as diatom, chlorophyll a, particulate carbon and nitrogen concentrations in 2003 and 2004. Neither were they correlated to food quality, expressed as C/N ratio. To explain this mismatch between EPR and food concentration, a series of mixed phytoplankton species dominated by diatoms (≥11 µm filtrate representing natural diatom assemblages: NDA) and 7 single diatom species, all occurring during blooms in the field, were assayed as diets with C. helgolandicus females. Ingestion of diatoms by females was estimated by faecal pellet production rates and complementary scanning electron microscopy examinations of diatom remains in pellets. Depending on diatom species in diets, EPR was either increased or depressed 2 to 3 d after food uptake by females had started. The EPR decrease was reversible, when diatom diets were replaced by the dinoflagellate Prorocentrum minimum. This effect was also observed when females were transferred to natural phytoplankton populations from the English coast of the Channel close to Plymouth, where food composition in the field differed compared to that off Roscoff. EPR ceased completely when the concentration of NDA diets was artificially increased, but recovered after a shift to a dinoflagellate diet. These results indicate that phytoplankton dominated by diatoms can impair C. helgolandicus egg production in the field. This effect was not related to the production of polyunsaturated aldehydes by diatoms. Limitations due to unidentified essential compounds not provided by the metabolism of diatoms, or unknown diatom-derived toxins, were probably involved.

Multiples roles of sidrophores in free-living nitrogen-fixing bacteria. Biometals

Furthering knowledge on seaweed growth and development to facilitate sustainable aquaculture

University of Birmingham Research Portal (University of Birmingham), 2017

Where a licence is displayed above, please note the terms and conditions of the licence govern yo... more Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document. When citing, please reference the published version. Take down policy While the University of Birmingham exercises care and attention in making items available there are rare occasions when an item has been uploaded in error or has been deemed to be commercially or otherwise sensitive.

Genome Sequence of <i>Halomonas</i> sp. Strain MS1, a Metallophore-Producing, Algal Growth-Promoting Marine Bacterium Isolated from the Green Seaweed Ulva mutabilis (Chlorophyta)

Microbiology resource announcements, Nov 17, 2022

We report the draft genome sequence of the marine gammaproteobacterium Halomonas sp. strain MS1, ... more We report the draft genome sequence of the marine gammaproteobacterium Halomonas sp. strain MS1, isolated from the green seaweed Ulva mutabilis (Chlorophyta), which releases metallophores fostering macroalga-bacterium interactions. The 4.6-Mbp sequence, which was obtained using PacBio technology, harbors 4,166 predicted coding sequences, including gene clusters for siderophore production.

Effects of Reversal of Water Flow in an Arctic Floodplain River on Fluvial Emissions of CO <sub>2</sub> and CH <sub>4</sub>

Journal Of Geophysical Research: Biogeosciences, 2022

Rivers connect the land with oceans and are effective active pipes where terrestrial carbon under... more Rivers connect the land with oceans and are effective active pipes where terrestrial carbon undergoes numerous transformations (Cole et al., 2007). The majority of the carbon in rivers and streams is emitted into the atmosphere as carbon dioxide (CO 2) (Raymond et al., 2013) and methane (CH 4) (Stanley et al., 2016). Thus, it is estimated that less than 50% (∼0.9 PgC yr −1) of the total carbon export from global inland waters (1.9-3.2 PgC yr −1) reaches the oceans (Abril & Borges, 2019).

Algal growth and morphogenesis-promoting factors released by cold-adapted bacteria contribute to the resilience and morphogenesis of the seaweed Ulva (Chlorophyta) in Antarctica (Potter Cove)

bioRxiv (Cold Spring Harbor Laboratory), Jul 6, 2024

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

Beilstein Journal of Organic Chemistry

Aromatic prenylated metabolites have important biological roles and activities in all living orga... more Aromatic prenylated metabolites have important biological roles and activities in all living organisms. Compared to their importance in all domains of life, we know relatively little about their substrate scopes and metabolic functions. Here, we describe a new UbiA-like prenyltransferase (Ptase) Ubi-297 encoded in a conserved operon of several bacterial taxa, including marine Flavobacteria and the genus Sacchromonospora. In silico analysis of Ubi-297 homologs indicated that members of this Ptase group are composed of several transmembrane α-helices and carry a conserved and distinct aspartic-rich Mg2+-binding domain. We heterologously produced UbiA-like Ptases from the bacterial genera Maribacter, Zobellia, and Algoriphagus in Escherichia coli. Investigation of their substrate scope uncovered the preferential farnesylation of quinoline derivatives, such as 8-hydroxyquinoline-2-carboxylic acid (8-HQA) and quinaldic acid. The results of this study provide new insights into the abundan...

High-temperature stress induces bacteria-specific adverse and reversible effects on Ulva (Chlorophyta) growth and its chemosphere in a reductionist model system

Botanica Marina

Axenic cultures of the green seaweed Ulva mutabilis were inoculated with bacteria providing essen... more Axenic cultures of the green seaweed Ulva mutabilis were inoculated with bacteria providing essential algal growth and morphogenesis-promoting factors (AGMPFs) and were exposed to temperature shifts from 18 °C to 30 °C. The temperature-dependent effect of bacteria on longitudinal algal growth and the molecular composition of the chemosphere in the algal culture medium was explored. The reductionist tripartite model system of U. mutabilis, Roseovarius sp. MS2, and Maribacter sp. MS6 was applied as a reference and has been changed by substituting Roseovarius with isolates that phenocopy this strain. Rathayibacter festucae IH2 and Roseovarius aestuarii G8 boosted growth at 18 °C but slowed it down at 30 °C. Additional inoculation of Roseovarius sp. MS2 mitigated these adverse bacterial effects partially. At 30 °C, the molecular profile of the chemosphere differed dramatically between all tested tripartite communities, indicating different traits of the same bacterium with changing temp...

Insights into the potential for mutualistic and harmful host–microbe interactions affecting brown alga freshwater acclimation

Molecular Ecology, Nov 23, 2022

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Chapter 18. Metabolomics of intra- and extracellular metabolites from micro- and macroalgae using GC-MS and LC-MS

Zenodo (CERN European Organization for Nuclear Research), Apr 26, 2018

Comparative metabolomics is an emerging technique suitable for the monitoring of metabolic respon... more Comparative metabolomics is an emerging technique suitable for the monitoring of metabolic responses of organisms to external stimuli or stress factors like biotic interaction partners, nutrient limitation or adverse environmental conditions. Using data from comparative metabolomics, changes in primary metabolism can be unraveled and connected to the regulation of metabolic pathways. However, the technique is also suitable for an untargeted screening of primary and secondary metabolites. Thereby candidate metabolites can be identified that might play a functional role in the particular stress situation. Especially mass spectrometry-enabled techniques have found their way into many disciplines. Here we describe the extraction, derivatization, gas chromatography-mass spectrometry (GC-MS) as well as liquid chromatography-mass spectrometry (LC-MS) measurement and data analysis for a metabolic profiling of algae. We describe a general protocol for intracellular profiling of microalgae, and germ cells and thalli of macroalgae. The protocol outlines the procedure to extract, derivatize and measure the exo-metabolome of these organisms, i.e., the metabolites exuded into the seawater. 2 The method was initially developed for metabolomics of the diatom Skeletonema marinoi but proved to be suitable for a broad range of micro-and macroalgae after minor adaptations. The entire work-flow can be carried out in laboratories with basic equipment for chemical work and measurements can be recorded on most commercially available GC-MS and LC-MS systems.

Metabolite profiling reveals insights into the species-dependent cold stress response of the green seaweed holobiont Ulva (Chlorophyta)

Environmental and Experimental Botany, Aug 1, 2022

Algae induce siderophore biosynthesis in the freshwater bacterium Cupriavidus necator H16

Biometals, Nov 24, 2018

Cupriachelin is a photoreactive lipopeptide siderophore produced by the freshwater bacterium Cupr... more Cupriachelin is a photoreactive lipopeptide siderophore produced by the freshwater bacterium Cupriavidus necator H16. In the presence of sunlight, the iron-loaded siderophore undergoes photolytic cleavage, thereby releasing solubilized iron into the environment. This iron is not only available to the siderophore producer, but also to the surrounding microbial community. In this study, the cupriachelinbased interaction between C. necator H16 and the freshwater diatom Navicula pelliculosa was investigated. A reporter strain of the bacterium was constructed to study differential expression levels of the cupriachelin biosynthesis gene cucJ in response to varying environmental conditions. Not only iron starvation, but also culture supernatants of N. pelliculosa were found to induce cupriachelin biosynthesis. The transcription factors involved in this differential gene expression were identified using DNA-protein pulldown assays. Besides the well-characterized ferric uptake regulator, a two-component system was found to tune the expression of cupriachelin biosynthesis genes in the presence of diatom supernatants.

Metabolomics of intra- and extracellular metabolites from micro- and macroalgae using GC–MS and LC–MS

CRC Press eBooks, Apr 17, 2018

<i>Ulva</i>: An emerging green seaweed model for systems biology

Journal of Phycology, May 31, 2023

Using O2/Ar ratios as a proxy for biological productivity determinations in an Arctic river

&amp;lt;p&amp;gt;The biogeochemical cycling of carbon in Arctic rivers is perturbed as mo... more &amp;lt;p&amp;gt;The biogeochemical cycling of carbon in Arctic rivers is perturbed as more terrestrial organic carbon and nutrients are released upon active layer and permafrost thaw. The majority of the carbon dioxide (CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) in rivers is emitted into the atmosphere, but it can also be utilized during photosynthesis, especially with more availability of nutrients, influencing the carbon flow and aquatic ecosystem metabolism. However, the timing and amount of photosynthetic primary production in Arctic rivers are unknown.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Water samples from the Kolyma River in Northeast Siberia were collected in June (late freshet) and August (summer) 2019. For the first time in an Arctic river, we measured biological oxygen supersaturations using the relative oxygen-to-argon ratio above equilibrium, &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar), which is an indicator of the presence of biologically produced oxygen. This ratio is influenced in approximately equal parts by physical processes, while biological processes unilaterally influence the oxygen content.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In addition, we measured the partial pressure of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;), dissolved oxygen and inorganic nutrients concentrations. Mass spectrometry was employed to chemically characterize the composition of dissolved organic matter (DOM) and better understand its origin. Microbial communities were elucidated using 16S and metagenomic based sequencing approaches.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In June, the oxygen saturation in turbid and warm waters (average: 14 &amp;amp;#176;C) in the main river channel was on average 10% above atmospheric equilibrium. The &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) values were well above equilibrium (2000 &amp;amp;#181;atm). Unlike oxygen saturation, &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar) was negative (undersaturation); thus, physical processes contributed most to the total oxygen supersaturation (up to 20%), apparently due to contributions of freshet cold gas-rich meltwater, while the net biological oxygen concentration was between &amp;amp;#8211;10 and &amp;amp;#8211;15%.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;In August, the water was colder (3 &amp;amp;#176;C drop), and the total oxygen was mostly undersaturated (up to &amp;amp;#8211;10%). However, lower &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) and a decrease in the biological oxygen deficit (between 0 and &amp;amp;#8211;5%) indicated net biological oxygen input. At the confluence of the main river channel and some tributaries, an algal bloom was observed resulting in up to 6.4% supersaturation in &amp;lt;em&amp;gt;&amp;amp;#916;&amp;lt;/em&amp;gt;(O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar) and &amp;lt;em&amp;gt;p&amp;lt;/em&amp;gt;(CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) near atmospheric equilibrium.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Concentrations of nitrate and silica were higher in August than in June. Dissolved phosphate concentrations were low at both sampling times, but apparently did not limit primary productivity. The microbial community composition varied greatly between sampling times, with differential shifts across the transect. Compared to June, the DOM pattern in August was less diverse in the river due to more stable stream conditions and defined hydrologic connectivity between land and river, promoting also nutrient supply for biological productivity.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Unlike anticipated, the O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar ratios suggested that net biological oxygen production in the river did not profit during the late freshet, despite unlimited light and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; availability and warm temperatures. Contrastingly, the summer low-flow allowed for photosynthetically-driven oxygen production and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; uptake in some sites. We conclude that the O&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;/Ar ratios were essential for quantifying the contribution of biological production, and understand better the fate of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; in an Arctic river influenced by thawing permafrost, as well as the land-aquatic-continuum in the context of climate change.&amp;lt;/p&amp;gt;

Permafrost Arctic streams are effective pathways for the emissions of allochthonous and autochthonous greenhouse gases to the atmosphere during the open water season: a holistic study in Ambolikha river, Northeast Siberia

AGU Fall Meeting Abstracts, Dec 1, 2020

Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

EGU General Assembly Conference Abstracts, Apr 1, 2017

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms

The ISME Journal, Jul 20, 2020

Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments wi... more Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or-oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H 2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.

Stereoselektive Totalsynthese von (−)‐Thallusin zur Bioaktivitätsprofilierung

Angewandte Chemie, Aug 24, 2022

Influence of diatoms on copepod reproduction. III. Consequences of abnormal oocyte maturation on reproductive factors in Calanus helgolandicus

Marine Biology, May 4, 2007

Observations of gonads and oocyte development stages (OS) have been achieved in Calanus helgoland... more Observations of gonads and oocyte development stages (OS) have been achieved in Calanus helgolandicus females fed diVerent algal diets and starved in Wltered sea water under laboratory conditions during 8 days. The eVects of 20 diets on egg production rates (EPR), hatching success (HS) and proportion of abnormal larvae (AL, development stages N1-2) were examined. With the control diet Prorocentrum minimum EPR and HS values were high, while AL was very low, coinciding with intact cell structures in oogonia (OO) and normal OS (OS1-OS4). With the other diets, oocyte maturation, EPR, HS and AL patterns were partially or totally impaired. Decrease of EPR coincided with the arrest of OS3 maturation and oocyte degradations, characterised by cell fragmentation, presence of apoptotic bodies in the OS3, degradation of cytoplasm in OS3 and OS4 and consequently the arrest of OS4 formation. These degradations were reversible when females were fed a favourable diet. Results reXect the presence of two distinct inhibitory mechanisms. Inhibition mechanism (1) impairs egg production. It was induced by starvation or by several species belonging to Bacillariophyceae (Chaetoceros calcitrans, Guinardia delicatula, Guinardia striata, Odontella regia, Rhizosolenia setigera, Stephanopyxis turris, Thalassiosira pseudonana) and mixed-diatom assemblages (collected in the Weld) and to the prymnesiophyte Pavlova lutherii. Remarkably other diatoms like Navicula sp., Nitzschia sp., Skeletonema costatum and Thalassiosira rotula did not induce mechanism (1) Inhibitory mechanism (2) aVected exclusively HS and AL and was triggered by species independent of the production of polyunsaturated aldehydes (PUA), which are supposed to have adverse impacts on HS and larval development. Communicated by O. Kinne.

Influence of diatoms on copepod reproduction. I. Field and laboratory observations related to Calanus helgolandicus egg production

Marine Ecology Progress Series, Feb 16, 2006

Egg production rates (EPR) by Calanus helgolandicus females were investigated with specimens samp... more Egg production rates (EPR) by Calanus helgolandicus females were investigated with specimens sampled weekly, from April to November 2003 and from March to October 2004, at a station located in the English Channel off Roscoff. Comparison of results between 1994, 2003 and 2004 showed that C. helgolandicus was a late spawner in 1994 and became an early spawner in 2003 and 2004. In all cases high variations in EPR were observed, which could not be correlated to phytoplankton biomass, expressed as diatom, chlorophyll a, particulate carbon and nitrogen concentrations in 2003 and 2004. Neither were they correlated to food quality, expressed as C/N ratio. To explain this mismatch between EPR and food concentration, a series of mixed phytoplankton species dominated by diatoms (≥11 µm filtrate representing natural diatom assemblages: NDA) and 7 single diatom species, all occurring during blooms in the field, were assayed as diets with C. helgolandicus females. Ingestion of diatoms by females was estimated by faecal pellet production rates and complementary scanning electron microscopy examinations of diatom remains in pellets. Depending on diatom species in diets, EPR was either increased or depressed 2 to 3 d after food uptake by females had started. The EPR decrease was reversible, when diatom diets were replaced by the dinoflagellate Prorocentrum minimum. This effect was also observed when females were transferred to natural phytoplankton populations from the English coast of the Channel close to Plymouth, where food composition in the field differed compared to that off Roscoff. EPR ceased completely when the concentration of NDA diets was artificially increased, but recovered after a shift to a dinoflagellate diet. These results indicate that phytoplankton dominated by diatoms can impair C. helgolandicus egg production in the field. This effect was not related to the production of polyunsaturated aldehydes by diatoms. Limitations due to unidentified essential compounds not provided by the metabolism of diatoms, or unknown diatom-derived toxins, were probably involved.

Multiples roles of sidrophores in free-living nitrogen-fixing bacteria. Biometals

Furthering knowledge on seaweed growth and development to facilitate sustainable aquaculture

University of Birmingham Research Portal (University of Birmingham), 2017

Where a licence is displayed above, please note the terms and conditions of the licence govern yo... more Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document. When citing, please reference the published version. Take down policy While the University of Birmingham exercises care and attention in making items available there are rare occasions when an item has been uploaded in error or has been deemed to be commercially or otherwise sensitive.

Genome Sequence of <i>Halomonas</i> sp. Strain MS1, a Metallophore-Producing, Algal Growth-Promoting Marine Bacterium Isolated from the Green Seaweed Ulva mutabilis (Chlorophyta)

Microbiology resource announcements, Nov 17, 2022

We report the draft genome sequence of the marine gammaproteobacterium Halomonas sp. strain MS1, ... more We report the draft genome sequence of the marine gammaproteobacterium Halomonas sp. strain MS1, isolated from the green seaweed Ulva mutabilis (Chlorophyta), which releases metallophores fostering macroalga-bacterium interactions. The 4.6-Mbp sequence, which was obtained using PacBio technology, harbors 4,166 predicted coding sequences, including gene clusters for siderophore production.

Effects of Reversal of Water Flow in an Arctic Floodplain River on Fluvial Emissions of CO <sub>2</sub> and CH <sub>4</sub>

Journal Of Geophysical Research: Biogeosciences, 2022

Rivers connect the land with oceans and are effective active pipes where terrestrial carbon under... more Rivers connect the land with oceans and are effective active pipes where terrestrial carbon undergoes numerous transformations (Cole et al., 2007). The majority of the carbon in rivers and streams is emitted into the atmosphere as carbon dioxide (CO 2) (Raymond et al., 2013) and methane (CH 4) (Stanley et al., 2016). Thus, it is estimated that less than 50% (∼0.9 PgC yr −1) of the total carbon export from global inland waters (1.9-3.2 PgC yr −1) reaches the oceans (Abril & Borges, 2019).