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Cobalamin (vitamin B 12 , herein referred to as B 12 ) is an essential cofactor for most marine prokaryotes and eukaryotes 1 , 2 . Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics 2 – 4 . Here we show that two bacterial B 12 auxotrophs can salvage different B 12 building blocks and cooperate to synthesize B 12 . A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B 12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B 12 . Release of B 12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B 12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B 12 . These complex microbial interactions of ligand cross-feeding and joint B 12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B 12 producers. These findings add new players to our understanding of B 12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems. Two species of auxotrophic marine bacteria are shown to share precursors to synthesize the essential cofactor vitamin B 12 , and such ligand cross-feeding may be a common phenomenon in the ocean and other ecosystems.

The biochemical composition of Antarctic krill, Euphausia superba , is largely determined by their feeding behaviour. As they supply energy for animals of a higher trophic level and are also commercialized for human consumption, the interest in research on the species is high. Lipids, especially phospholipids, make up a high proportion of dry weight in krill. Seasonal changes are well documented in the fingerprint of free fatty acids analysed after hydrolysis of phospholipids, but the underlying intact polar lipids are rarely considered. In this study, we evaluated the compositions of intact phospholipids (IPLs) in the stomach, digestive gland and hind gut of Antarctic krill caught in summer and autumn at the Antarctic Peninsula region. Using high-resolution mass spectrometry, the fatty acid composition of 179 intact phospholipids could be resolved. Most IPLs were phosphatidylcholines, followed by phosphatidylethanolamines. Several very long chain polyunsaturated fatty acids up to 38:8, which have not been reported in krill before, were identified. The composition shifted to higher molecular weight IPLs with a higher degree of unsaturation for summer samples, especially for samples of the digestive gland. The data supplied in this paper provides new insights into lipid dynamics between summer and autumn usually described by free fatty acid biomarkers.

Rapid climate change threatens the relatively pristine environment of the Southern Ocean. The effects on biogeochemical cycles and their subsequent consequences for the organisms in this area are of significant interest. Antarctic krill, Euphausia superba , is the dominant species in the Antarctic ecosystem and a vital component of the Southern Ocean food web. Its metabolism is influenced by the feeding regime, which is governed by environmental conditions. However, little is yet known about the metabolome of Antarctic krill. Here, we investigated metabolite classes that can serve as tracers for documenting variations in the metabolic and biochemical status of krill. To this end, we utilised targeted metabolomics to analyse coenzyme A thioesters, amino acids, B vitamins, and respiratory quinones in the digestive system of Antarctic krill, sampled during two campaigns in the Antarctic summer and autumn. A significant proportion of the detected coenzyme A thioesters were associated with the β-oxidation of fatty acids and, consequently, with lipid metabolism. Propionyl-CoA was particularly abundant in samples from the digestive gland, while malonyl- and succinyl-CoA were more prevalent in stomach and hindgut samples. 3-Hydroxy-3-methylglutaryl-CoA, an intermediate in the metabolism of branched amino acids and the biosynthesis of isoprenoids, occurred almost exclusively in the summer samples. Analyzing the free amino acids, very high levels of the non-proteinogenic amino acid sarcosine were found, which possibly serves as an osmolyte for the Antarctic krill and/or plays a role in its digestive process. Among the B vitamins, there were seasonal fluctuations, particularly in B 1 and B 5 . The respiratory quinones exhibited more homogeneous patterns, with UQ 10:10 as the dominant representative. These seasonal and organ-dependent variations in the composition of the different metabolite classes can serve as a reference point in future studies to better assess the influence of changing conditions in Antarctic waters.

Biotin (vitamin B 7 ) is involved in a wide range of essential biochemical reactions and a crucial micronutrient that is vital for many pro- and eukaryotic organisms. The few biotin measurements in the world’s oceans show that availability is subject to strong fluctuations. Numerous marine microorganisms exhibit biotin auxotrophy and therefore rely on supply by other organisms. Desthiobiotin is the primary precursor of biotin and has recently been detected at concentrations similar to biotin in seawater. The last enzymatic reaction in the biotin biosynthetic pathway converts desthiobiotin to biotin via the biotin synthase (BioB). The role of desthiobiotin as a precursor of biotin synthesis in microbial systems, however, is largely unknown. Here we demonstrate experimentally that bacteria can overcome biotin auxotrophy if they retain the bioB gene and desthiobiotin is available. A genomic search of 1068 bacteria predicts that the biotin biosynthetic potential varies greatly among different phylogenetic groups and that 20% encode solely bioB and thus can potentially overcome biotin auxotrophy. Many Actino - and Alphaproteobacteria cannot synthesize biotin de novo, but some possess solely bioB , whereas the vast majority of Gammaproteobacteria and Flavobacteriia exhibit the last four crucial biotin synthesis genes. We detected high intra- and extracellular concentrations of the precursor relative to biotin in the prototrophic bacterium, Vibrio campbellii , with extracellular desthiobiotin reaching up to 1.09 ± 0.15*10 6 molecules per cell during exponential growth. Our results provide evidence for the ecological role of desthiobiotin as an escape route to overcome biotin auxotrophy for bacteria in the ocean and presumably in other ecosystems.

Shrub encroachment has far‐reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning. We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound‐specific carbon (δ13C) and deuterium (δD) isotopes, bulk carbon isotopes (δ13Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution. We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n‐alkane distributions and the δ13C and δ13Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO2 concentration and drought, our vegetation records reflect the impact of broad‐scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling‐resistant taxa. In addition, grain‐size and spore records suggest changes in the erodibility of soils because of reduced grass cover. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state. We present the first multidecadal time series with high taxonomic and temporal resolution, which includes sedaDNA, and that enables the tracking of vegetation and environmental change in a southern African savanna. According to our results, shrub encroachment occurs on a scale of one century and with a phase of transition characterized by a steady turnover of taxa, some of which are restricted to this phase. We discuss further the feedback mechanisms that stabilize the encroached state, as well as the triggers of vegetation change.

Vitamin B 12 (cobalamin, herein B 12 ) is an essential cofactor involved in amino acid synthesis and carbon resupply to the TCA cycle for most prokaryotes, eukaryotic microorganisms, and animals. Despite being required by most, B 12 is produced by only a minor fraction of prokaryotes and therefore leads to complex interaction between prototrophs and auxotrophs. However, it is unknown how B 12 is provided by prototrophs to auxotrophs. In this study, 33 B 12 prototrophic alphaproteobacterial strains were grown in co-culture with Thalassiosira pseudonana , a B 12 auxotrophic diatom, to determine the bacterial ability to support the growth of the diatom by sharing B 12 . Among these strains, 18 were identified to share B 12 with the diatom, while nine were identified to retain B 12 and not support growth of the diatom. The other bacteria either shared B 12 with the diatom only with the addition of substrate or inhibited the growth of the diatom. Extracellular B 12 measurements of B 12 -provider and B 12 -retainer strains confirmed that the cofactor could only be detected in the environment of the tested B 12 -provider strains. Intracellular B 12 was measured by LC-MS and showed that the concentrations of the different B 12 -provider as well as B 12 -retainer strains differed substantially. Although B 12 is essential for the vast majority of microorganisms, mechanisms that export this essential cofactor are still unknown. Our results suggest that a large proportion of bacteria that can synthesise B 12 de novo cannot share the cofactor with their environment.

Background Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called “Keri Lake” in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. Results Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. Conclusions The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.

B vitamins have high microbiological relevance in the marine environment, but their very low concentrations and the chemical heterogeneity of the individual vitamins make their analysis challenging. Mass spectrometric analysis of B vitamins in environmental samples at trace levels has mainly been performed using triple quadrupole mass spectrometers operated in targeted analysis mode. The development of such a method can be laborious and error prone. Additionally, high-resolution mass spectrometers can be used to measure a sample in full scan mode and subsequently search the total ion current chromatogram for extracted ion chromatograms of targeted vitamins. Three different analytical approaches for trace analysis of all B vitamins and some of their biosynthetic precursors were optimized and compared on two different mass spectrometers. A triple quadrupole mass spectrometer in selected reaction monitoring mode, and a high-resolution orbitrap mass spectrometer in parallel reaction monitoring, as well as in full scan mode were employed. Detection limits down to 10 ng/L were achieved with all three techniques. The methods were applied to a marine water sample from the North Sea and to the cell extract of a bacterial culture of Phaeobacter inhibens. Most vitamins and precursors were found in the bacterial cell extract and the seawater sample with all three measuring methods. The results of this study emphasize that, in addition to tandem mass spectrometry, high-resolution full scan mass spectrometry is a promising technique for the simultaneous detection of structurally diverse B vitamins in complex natural samples. This enables highly sensitive measurements without loss of detailed mass spectrometric information, which is inevitable when using a triple quadrupole system in MS/MS mode.

The anaerobic degradation pathway of the saturated hydrocarbon n-hexane in a denitrifying strain (HxN1) was examined by gas chromatography-mass spectrometry of derivatized extracts from cultures grown with unlabeled and deuterated substrate; several authentic standard compounds were included for comparison. The study was focused on possible reaction steps that follow the initial formation of (1-methylpentyl)succinate from n-hexane and fumarate. 4-Methyloctanoic, 4-methyloct-2-enoic, 2-methylhexanoic, 2-methylhex-2-enoic and 3-hydroxy-2-methylhexanoic acids (in addition to a few other methyl-branched acids) were detected in n-hexane-grown but not in n-hexanoate-grown cultures. Labeling indicated preservation of the original carbon chain of n-hexane in these acids. Tracing of the deuterium label of 3- d1-(1-methylpentyl)succinate in tentative subsequent products indicated a deuterium/carboxyl carbon exchange in the succinate moiety. This suggests that the metabolism of (1-methylpentyl)succinate employs reactions analogous to those in the established conversion of succinyl-CoA via methylmalonyl-CoA to propionyl-CoA. Accordingly, a pathway is proposed in which (1-methylpentyl)succinate is converted to the CoA-thioester, rearranged to (2-methylhexyl)malonyl-CoA and decarboxylated (perhaps by a transcarboxylase) to 4-methyloctanoyl-CoA. The other identified fatty acids match with a further degradation of 4-methyloctanoyl-CoA via rounds of conventional beta-oxidation. Such a pathway would also allow regeneration of fumarate (for n-hexane activation) from propionyl-CoA formed as intermediate and hence present a cyclic process.