Biology subjects

von Meijenfeldt, F. A. B.

Publications and source records attributed to von Meijenfeldt, F. A. B..

9 recordsLinked to original sources

bioRxiv2025

Substantial contribution of in-situ produced bacterial lipids to the sedimentary lipidome

The sedimentary lipid pool is comprised of a myriad of individual components. Due to their importance for organic carbon sequestration and their application in paleoclimatic and geobiological reconstructions, its composition has been studied for many decades with targeted approaches but an overall view on its composition is still lacking. In part this uncertainty relates to the different sources of sedimentary lipids, they can be both delivered from the overlying water column by sedimentation, but also produced in-situ by sediment dwelling organisms. Another uncertainty relates to the differing degree of preservation, both between lipid groups and relative to other organic matters. Here we conduct an untargeted analysis of the sedimentary lipidome in the Black Sea using high resolution mass spectrometry. Besides commonly reported phytoplankton-derived fossil lipids, a diverse and abundant set of sphingolipids was discovered, accounting for [~]20% of the sedimentary lipidome. These sphingolipids are produced in situ by sedimentary anaerobic bacteria, which probably used sphingolipids instead of phospholipids, likely because of the deficiency of phosphate in the anoxic sediments. Our results suggest that while phytoplankton-derived lipids contribute 50-60% of the sedimentary lipidome, the importance of bacterial lipids, particularly in-situ produced sphingolipids, may have been overlooked.

microbiology↗

bioRxiv2024

Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system

Bacterial membrane lipids have been traditionally defined as fatty acids (FAs) bilayers linked through ester bonds, while those of Archaea as ether-linked isoprenoids forming bilayers or monolayers of membrane spanning lipids (MSLs) known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). This paradigm has been challenged with the discovery of branched GDGTs (brGDGTs), membrane spanning ether-bound branched alkyl FAs, that are of bacterial origin but whose specific producers in the environment are often unknown. The limited number of available microbial cultures restricts the knowledge of the biological sources of membrane lipids, which in turn limits their potential applicability as biomarkers. To address this limitation, we detected membrane lipids in the Black Sea using high resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also detected brGDGTs and overly branched GDGTs in the suboxic and euxinic waters, which are potentially attributed, to members of the Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota--all anaerobic microorganisms. These results open a new chapter in the use of specific brGDGTs as biomarkers of anoxic conditions in marine settings and of the role of these membrane lipids in microbial adaptation.

microbiology↗

bioRxiv2024

Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria

Paleontological and phylogenomic observations have shed light on the evolution of cyanobacteria. Nevertheless, the emergence of heterocytes, specialized cells for nitrogen fixation, remains unclear. Heterocytes are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Here, by comprehensive HG identification and screening of HG biosynthesis genes throughout cyanobacteria, we identify HG analogs produced by specific and distantly related non-heterocytous cyanobacteria. These structurally less complex molecules probably acted as precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Subsequently, HG chemical structure evolved convergently in response to environmental pressures. Our results open a new chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.

microbiology↗

bioRxiv2024

Coupled metalipidomics-metagenomics reveal structurally diverse sphingolipids produced by a wide variety of marine bacteria

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply for the first time metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1,623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Genomic analysis revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a fourfold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response and cell wall remodeling. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.

microbiology↗

bioRxiv2022

On specialists and generalists: niche range strategies across the tree of life

Generalists can survive in many environments whereas specialists have a limited distribution. Although a classical concept in ecology, niche breadth has remained challenging to quantify because it depends on an objective definition of the environment. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative social niche breadth score for all microbial taxa. At the level of genera, we explored niche range strategies across the tree of life. We found that generalists include opportunists that stochastically dominate local communities, while specialists are stable but low in abundance. Generalists have a more diverse and open pan genome than specialists, but we found no global correlation between niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our global analysis shines a new, data-driven light on microbial niche range strategies.

bioinformatics↗

bioRxiv2022

Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of unusual Membrane-spanning and Ether lipids in Bacteria

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea possess membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this lipid divide are the production by some bacterial species of (ether-bound) MSLs, formed by tail-tail condensation of fatty acids resulting in the formation of (iso) diabolic acids (DAs), which are the likely precursors of paleoclimatological relevant branched glycerol dialkyl glycerol tetraether molecules. However, the enzymes responsible for their production are unknown. Here, we report the discovery of bacterial enzymes responsible for the condensation reaction of fatty acids and for ether bond formation, and confirm that the building blocks of iso-DA are branched iso-FAs. Phylogenomic analyses of the key biosynthetic genes reveal a much wider diversity of potential MSL (ether)-producing bacteria than previously thought, with significant implications for our understanding of the evolution of lipid membranes.

microbiology↗

bioRxiv2020

Nutrition or nature: disentangling the complex forces shaping prokaryote pan-genomes

Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes often exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of genes with each other and with their external environments. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Here, we use pan-reactomes as proxies for pan-genomes since they can explicitly represent the interactions between the genes that code for metabolic reactions and simulate complex phenotypes that interact with the metabolic environment. We interpreted pan-reactomes as dynamic pools of metabolic reactions that are potentially gained or lost and simulated the routes along which different lineages lose reactions in alternative environments. We performed these simulations on the pan-reactomes of 46 bacterial and archaeal families covering a broad taxonomic range. These simulations allowed us to disentangle metabolic reactions whose presence does, and does not depend on the metabolite composition of the external environment, allowing us to identify reactions constrained "by nutrition" and "by nature", respectively. By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages in their evolutionary past. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Together, we introduce a computational framework for analyzing and interpreting pan-reactomes that provides new insights into the ecological and evolutionary drivers of pan-genome composition.

evolutionary biology↗

bioRxiv2019

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high-quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. In a real-world challenge, we apply BAT to over 900 MAGs from a recent rumen metagenomics study and classified 97% consistently with prior phylogeny-based classifications, but in a fully automated fashion.

bioinformatics↗

bioRxiv2018

Bridging the divide: bacteria synthesizing archaeal membrane lipids

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol, while Bacteria/Eukarya produce membranes consisting of ester-bound fatty acids. This dichotomy in membrane lipid composition or lipid divide is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a mixed heterochiral archaeal/bacterial membrane, however no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) group superphylum and related candidate phyla encode a complete pathway for archaeal membrane lipid biosynthesis in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in E. coli resulted in the formation of a mixed archaeal/bacterial membrane. Our results support the existence of mixed membranes in natural environments and their stability over large evolutionary timescales, thereby bridging a once-thought fundamental divide in biology.

evolutionary biology↗