MALDI imaging data uploaded to Metaspace and ProteomeExchange platforms (2016)

MALDI-imaging datasets from different animals (Bathymodiolus spp., Kentrophoros sp., Lumbricus terrestris, Olavius algarvensis, Paracatenula sp.) that were uploaded to Metaspace (http://52.19.27.255/) and ProteomeXchange (http://Proteomexchange.org/) platforms until October 2016

Metallothioneins may not be enough - the role of phytochelatins in invertebrate metal detoxification

'Viewpoint' article

Fed-batch process for the psychrotolerant marine bacterium Pseudoalteromonas haloplanktis

<p>Abstract</p> <p>Background</p> <p><it>Pseudoalteromonas haloplanktis </it>is a cold-adapted γ-proteobacterium isolated from Antarctic sea ice. It is characterized by remarkably high growth rates at low temperatures. <it>P. haloplanktis </it>is one of the model organisms of cold-adapted bacteria and has been suggested as an alternative host for the soluble overproduction of heterologous proteins which tend to form inclusion bodies in established expression hosts. Despite the progress in establishing <it>P. haloplanktis </it>as an alternative expression host the cell densities obtained with this organism, which is unable to use glucose as a carbon source, are still low. Here we present the first fed-batch cultivation strategy for this auspicious alternative expression host.</p> <p>Results</p> <p>The key for the fed-batch cultivation of <it>P. haloplanktis </it>was the replacement of peptone by casamino acids, which have a much higher solubility and allow a better growth control. In contrast to the peptone medium, on which <it>P. haloplanktis </it>showed different growth phases, on a casamino acids-containing, phosphate-buffered medium <it>P. haloplanktis </it>grew exponentially with a constant growth rate until the stationary phase. A fed-batch process was established by feeding of casamino acids with a constant rate resulting in a cell dry weight of about 11 g l^-1(OD₅₄₀= 28) which is a twofold increase of the highest densities which have been obtained with <it>P. haloplanktis </it>so far and an eightfold increase of the density obtained in standard shake flask cultures.</p> <p>The cell density was limited in the fed-batch cultivation by the relatively low solubility of casamino acids (about 100 g l^-1), which was proven by pulse addition of casamino acid powder which increased the cell density to about 20 g l^-1(OD₅₄₀= 55).</p> <p>Conclusion</p> <p>The growth of <it>P. haloplanktis </it>to higher cell densities on complex medium is possible. A first fed-batch fermentation strategy could be established which is feasible to be used in lab-scale or for industrial purposes. The substrate concentration of the feeding solution was found to influence the maximal biomass yield considerably. The bottleneck for growing <it>P. haloplanktis </it>to high cell densities still remains the availability of a highly concentrated substrate and the reduction of the substrate complexity. However, our results indicate glutamic acid as a major carbon source, which provides a good basis for further improvement of the fed-batch process.</p

Fucoid brown algae inject fucoidan carbon into the ocean

Peer reviewe

Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schorn, S., Ahmerkamp, S., Bullock, E., Weber, M., Lott, C., Liebeke, M., Lavik, G., Kuypers, M. M. M., Graf, J. S., & Milucka, J. Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proceedings of the National Academy of Sciences of the United States of America, 119(9), (2022): e2106628119, https://doi.org/10.1073/pnas.2106628119.Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m−2 ⋅ d−1. Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.This project was funded by theMax Planck Society

Aromatic metabolites from the coelomic fluid of Eisenia earthworm species

Earthworms from the genus Eisenia express coelomic fluid when under severe stress. This coelomic fluid contains a complex mixture of small-molecule metabolites, including aromatic metabolites which are known to be species-specific, yet their actual identities remain unknown. We have aimed to characterize selected high-concentration coelomic fluid metabolites. The major aromatic compound in Eisenia veneta coelomic fluid is the rare metabolite a-nicotinamide riboside; and the major aromatic compound for Eisenia fetida is closely related to the (already characterized) metabolite of Eisenia andrei, which consists of two aromatic quinazoline-2,4-dione ring structures linked by N-acetylspermine. The biological function(s) of these metabolites in earthworms is unknown, but we hypothesize that they represent remnants of larger molecules, possibly bacterial in origin, that are recalcitrant to metabolism by earthworm enzymes. (C) 2016 The Authors. Published by Elsevier Masson SAS

Ecological drivers influence the distributions of two cryptic lineages in an earthworm morphospecies

Substantial genetic diversity exists within earthworm morphotypes, such that traditional species designations may be incomplete. It is, however, currently not known whether these different genetic variants show ubiquity or specialty in their distribution across separated sites subject to different climatic, biotic or soil physicochemical factors. Here we report on the results of a survey in which individuals of the Lumbricus rubellus morphotype, a species known to comprise two deeply divergent genetic lineages in England and Wales, were sampled from 26 plots. Sequences from the mitochondrial cytochrome oxidase I gene were used to distinguish lineages for 787 individuals. In conjunction, a range of geographic, climatic, biotic and soil physiochemical variables were also collected for each locality. Genotyping indicated that Lineage A was more common than Lineage B, comprising 58% of the collected L. rubellus. Six site populations comprised only Lineage A, while only a single site comprised entirely Lineage B. The remaining 20 sites contained both lineages. A multivariate ordination of site variables identified major difference between sites were associated with low pH, organic-rich soils in Western wet upland areas and pollutant levels associated with sites in the South. Earthworm genotype (as proportion of Lineage A) was not correlated with either of these major environmental axes. When individual variables of soil pH and the percentage of soil organic matter, which are known to be key driver of soil species distributions, were investigated as single variables significant relationship with lineage frequency were found. Soil organic matter content was significantly negatively correlated with Lineage A proportion, while pH was significantly positively correlated. This lineage preference may be related to lineage metabolism and/or behavioral differences. Measurement of tissue metal concentrations in worms from 17 sites identified a significant site effect in all cases, but a lineage effect only for arsenic (higher Lineage B). Tissue arsenic concentrations varied between lineages, supporting previous observations that there are differences in the way the two lineages have adapted to manage exposure to this metalloid

Unique metabolites protect earthworms against plant polyphenols

All higher plants produce polyphenols, for defence against above-ground herbivory. These polyphenols also influence the soil micro- and macro-fauna that break down plant leaf litter. Polyphenols therefore indirectly affect the fluxes of soil nutrients and, ultimately, carbon turnover and ecosystem functioning in soils. It is unknown how earthworms, the major component of animal biomass in many soils, cope with high-polyphenol diets. Here, we show that earthworms possess a class of unique surface-active metabolites in their gut, which we term ‘drilodefensins’. These compounds counteract the inhibitory effects of polyphenols on earthworm gut enzymes, and high-polyphenol diets increase drilodefensin concentrations in both laboratory and field populations. This shows that drilodefensins protect earthworms from the harmful effects of ingested polyphenols. We have identified the key mechanism for adaptation to a dietary challenge in an animal group that has a major role in organic matter recycling in soils worldwide

Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm’s Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light‐independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high‐resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2·h−1. Single‐cell analyses of lake water incubated with 13CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single‐cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved