Biology subjects

Sipkema, D.

Publications and source records attributed to Sipkema, D..

9 recordsLinked to original sources

bioRxiv2026

Elucidating biosynthetic pathways related to the synthesis of small halogenated peptidic natural products in marine sponge microbiomes

Marine sponges are known sources of bioactive natural products (NPs), many of which are produced by associated bacterial symbionts via encoded biosynthetic gene clusters (BGCs). A particularly interesting subclass of sponge-derived NPs is comprised of small, brominated alkaloids, which are recovered from diverse habitats and host sponge taxonomies. Despite having been described decades ago, most of these NPs do not have an elucidated biosynthetic origin. We queried metagenomes of several sponge species by making use of a minimal set of core enzymes that we postulate to be necessary to produce these small peptidic NPs: an FADH2-dependent halogenase and an AMP-binding adenylation enzyme. This revealed a variety of novel BGC architectures, many of which showed conservation among sponge host phylogenies and were encoded in the genomes of diverse sponge-associated bacteria. Furthermore, we identified a BGC in the sponge G. barretti that is potentially linked to the production of the iconic barettins, given its enzymatic machinery and specific acidobacterial origin. The present work contributes to the challenging quest to link orphan brominated NPs to their parent BGCs in the sponge holobiont and beyond.

bioinformatics↗

bioRxiv2026

Carbon monoxide utilisation by Thermanaeromonas species and description of Thermobium azorense gen. nov., sp. nov.

Syngas fermentation by carbon monoxide (CO)-utilising acetogens offers a sustainable route for converting gasified waste materials into value-added chemicals. In this study, we isolated a novel thermophilic CO-utilising bacterium, strain AZ2, from marine hydrothermal sediment collected on the island of Sao Miguel, Azores, Portugal. Strain AZ2 is an obligately anaerobic, spore-forming bacterium. Average nucleotide identity (ANI; 78.4-86.7%) and digital DNA-DNA hybridization (dDDH; 23.4-32.5 %) analyses indicate that strain AZ2 represents a novel species within a previously uncharacterised lineage represented by the GTDB placeholder genus UBA2545 in the Neomoorellaceae family. Strain AZ2 was able to grow fermentatively on CO, producing acetate. We further demonstrated that its closest isolated relatives - Thermanaeromonas toyohensis, T. burensis, and Thermanaeromonas sp. strain 9S - are capable of growing on CO, producing either acetate or hydrogen gas (H2). Additionally, we unveiled the genomic potential for CO utilisation within other members of the GTDB placeholder class DSM-521 (previously Moorellia) to which our isolate belongs, expanding the list of possible thermophilic CO-utilising acetogens. We propose that strain AZ2T represents the type strain of a novel genus and species, named Thermobium azorense gen. nov., sp. nov. (= DSM 121889T = JCM 39698T).

microbiology↗

bioRxiv2026

Distinct taxonomic groups of sponge symbionts have the biosynthetic capacity for the production of ether lipids

The marine sponge holobiont, composed of the sponge host and its microbial symbionts, is a known source of abundant and diverse ether lipids (ELs). Apart from their structural role in the cytoplasmic membrane of archaea and some bacteria, ELs have often been linked to signaling functions and defense against pathogens. Despite the relevance of ELs, their biosynthesis, as well as the identity of their producers, remain elusive. Here, we report the analysis of potential ether lipid producing genes and gene clusters, detected in marine sponge metagenomes as well as public sponge genomes. We show that the sponge holobiont has the capacity to synthesize ELs via several pathways, and suggest the ability of the sponge holobiont to synthesize ELs under different O2 levels. Finally, targeted lipidome analysis confirmed that ELs are present in the lipid profiles of all of the studied sponge holobiont samples, and indicates that the biosynthesis of the plasmalogens detected is likely restricted to the sponge host itself, based on the detected hydrocarbon chain lengths. This work provides a basis for the challenging quest to decipher intricate EL biosynthesis in marine sponges and their associated microbes.

microbiology↗

bioRxiv2026

Bacteria orchestrate gametophyte growth, oogenesis and sporophyte development in Saccharina latissima in a sex-dependent manner

O_LIMarine organisms, including green and brown macroalgae, exhibit a broad dependency on their microbiome which has been demonstrated in model species including Ulva compressa and Ectocarpus siliculosus with relatively simple building plans. However, it remains elusive if and how Saccharina latissima, a complex brown macroalgae with high degrees of organ and tissue differentiation, is controlled by its microbiome. C_LIO_LIWe monitored gametophyte cultures of mixed sexes, induced oogenesis and followed sporophyte development both under axenic conditions and in cultures complemented with bacterial isolates from the sugar kelp core microbiome. C_LIO_LIFemale gametophytes generally performed better in the presence of bacteria while males performed worse. Some bacterial isolates inhibit oogenesis in females entirely, whereas others have a stimulating effect. Under axenic conditions sporophytes did form, but growth, pigmentation and the establishment of an apical-basal polarization axis were severely disrupted. These defects could be resolved by complementation with many bacteria from the S. latissima core microbiome. C_LIO_LISugar kelp depends heavily on specific bacterial symbionts for growth, reproduction and development and their effect is sex-dependent in gametophytes. This work provides a platform to investigate the precise methods of cross-kingdom communication which has a large potential in the kelp production industry. C_LI

developmental biology↗

bioRxiv2022

Comparative metagenomic analysis of biosynthetic diversity across sponge microbiomes highlights metabolic novelty, conservation and diversification

Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about their global distribution landscape and the symbionts that produce them. As the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont and measure their diversity across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three sponge species from the Atlantic Ocean and the Mediterranean Sea. This dataset reveals striking novelty in its encoded biosynthetic potential, with less than 1% of the recovered gene cluster families (GCF) showing similarity to any characterized biosynthetic gene cluster (BGC). When zooming in on the microbial communities of each sponge, we observed higher variability of both secondary metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we also identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species, and a true GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases (NRPS) that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts, and to the cryptic biosynthetic potential contained in this environmental niche.

microbiology↗

bioRxiv2021

Genomic diversity and biosynthetic capabilities ofsponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host-interactions remain thus far unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 21.2% of bacterial diversity. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Sorochlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Sponge-associated chlamydiae genomes mostly resembled environmental chlamydial endosymbionts, but not pathogens, and encoded genes for degrading diverse compounds associated with sponges, such as taurine. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an explored reservoir of novel natural products. This finding suggests that chlamydiae may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of this phylum on marine ecosystems.

microbiology↗

bioRxiv2019

Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. The lack of CF removal in the abiotic control cultures without artificial electron donors indicated that the observed CF removal is a biotic process. Metabolite analysis with 13C labelled CF in the sediment-free enrichment cultures (pH 8.5, salinity 5%) revealed that increasing the vitamin B12 concentration from 0.04 to 4 M enhanced CF removal, reduced DCM formation, and increased 13CO2 production, which is likely a product of CF oxidation. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected by quantitative PCR nor metagenomic analysis. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected in the enrichment cultures. Genome-resolved metagenome analysis indicated that their genomes encode enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis that are known to be involved in co-metabolic CF transformation. ImportanceMore than 90% of the global CF emission to the atmosphere originates from natural sources, including saline environments such as salt lake sediments. However, knowledge about the microbial metabolism of CF in such extreme environments is lacking. Here we showed CF transformation potential in a hypersaline lake that was reported as a natural source of CF production. Application of interdisciplinary approaches of microbial cultivation, stable isotope labelling, and metagenomics aided in defining potential chloroform transformation pathways. This study indicates that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere, and expands our knowledge of halogen cycling in extreme hypersaline environments.

microbiology↗

bioRxiv2019

Organohalide-respiring Desulfoluna species isolated from marine environments

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1{top} and D. butyratoxydans MSL71{top} of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third member of this genus from marine intertidal sediment, designed D. spongiiphila strain DBB. All three Desulfoluna strains harbour three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes. Brominated but not chlorinated aromatic compounds were dehalogenated by all three strains. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect OHR. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR (RT-qPCR) revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed differential expression of rdhA1 with 1,4-dibromobenzene, and revealed a possible electron transport chain from lactate dehydrogenases and pyruvate oxidoreductase to RdhA1 via menaquinones and either RdhC, or Fix complex (electron transfer flavoproteins), or Qrc complex (Type-1 cytochrome c3:menaquinone oxidoreductase).

microbiology↗

bioRxiv2017

Succession of embryonic and intestinal bacterial communities of Atlantic salmon

Host-associated microbiota undergoes continuous transition to achieve a stable community, and these modifications are immediately initiated from the birth of the host. In the present study, the succession of early life (eyed egg, embryo, and hatchling stages) and intestinal (the whole intestine at the early freshwater stages and the distal intestine at the late freshwater and seawater stages) bacterial communities of Atlantic salmon (Salmo salar; a prominent farmed fish) were studied using a 16S rRNA gene (V3 region) amplicon sequencing technique.\n\nStage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities were relatively less diverse, but after hatching the diversity increased significantly. A marked transition of the intestinal communities also occurred during the development. The most abundant functional pathways associated with the different stages were not affected by the transition of the community composition A perceptible transition in the community composition occurred during the development of Atlantic salmon. The transition generally did not alter the core functions of the community. Hatching and transfer to seawater are the key events that affect the bacterial diversity and community composition. The contribution of host-derived factors and environment in shaping the bacterial communities need to be confirmed through further studies.

microbiology↗