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Sulfate-reducing bacteria (SRB) drive the process of sulfate reduction in low-temperature sedimentary environments. Through the production of sulfide, they promote the formation of iron-sulfide (Fe-S) minerals when Fe(II) is available. The negative charge of the cell surface of bacteria can promote the binding of Fe(II), leading to the precipitation of Fe-S minerals at the surface of SRB when sulfide is released from cells. We evaluated interactions between Fe-S minerals and the surface of SRB using transmission electron microscopy (TEM) in cultures of Maridesulfovibrio hydrothermalis AM13 grown with 4 mM of Fe(II) over 1 month of incubation. On average, 18% ± 10% of cells were encrusted in cultures collected during the exponential phase. Fe-S mineral deposition occurred at the surface of cells while cells were growing and producing sulfide in the presence of Fe(II), but mineral crusts were removed from most cells shortly after deposition. Cells removed crusts from their surface through the formation of membrane vesicles, which were apparently only produced during growth. Mineralized and non-mineralized membrane vesicles were preserved in mineral aggregates in stationary-phase cultures. On average, 17% ± 7% of cells were encrusted in cultures collected during the stationary phase, indicating that Fe-S minerals precipitated during the exponential phase and removed from the cell surface did not aggregate back onto cells. On the contrary, they formed large aggregates away from cells. When Fe-S mineral precipitation occurred in non-growing cell suspensions that were first exposed to Fe(II) then to sulfide, the proportion of encrusted cells increased to 95% ± 6%, indicating that resting or non-growing cells were not able to remove mineral crusts from their surface. The metabolic status of SRB therefore plays a role in their ability to escape Fe-S mineral entombment.

Tecticornia is the most species-rich genus within the tribe Salicornieae. These halophytes are distributed across the Australian continent along coastlines and inland salt lake shores, playing a key ecological role in these hostile habitats. However, species delimitation within the genus remains controversial and little is known about infrageneric phylogenetic relationships. Therefore, the primary aim of this study was to infer the evolutionary history of Tecticornia and to genetically assess the reliability of current species concepts. We sampled multiple accessions per taxon from nearly all currently recognized species in Australia. We used a target enrichment approach with two bait sets: Angiosperms353 and a custom Salicornieae bait set (Salibaits). Analyses were performed using HybPiper, and we addressed paralogy using a tree-based approach. In addition, we tested the potential influence of missing data and/or missing gene trees on the topology of the final phylogenetic tree. Despite extensive gene tree discordance and the presence of short branches, the customized Salibaits set consistently produced better-resolved trees than the Angiosperms353 bait set. Missing data were found to have a negligible effect on the final tree inference. These data highlight that there is genetic support for lineages in line with observed morphological variation, suggesting markedly more taxon diversity than is currently circumscribed. While we have shown there is genetic evidence to support the characterization of several new species awaiting formal description, it is clear that further molecular and morphological investigation is required to resolve continent-wide species aggregates, each comprising multiple novel taxa. The target enrichment method effectively addressed the challenges of species delimitation in Tecticornia posed by reduced morphology and high ecological plasticity. We have shown that while there are several complexes constituting variants widely distributed across the Australian continent, some well-defined taxa have highly restricted distributions, which may represent conservation priorities.

The history of Earth's atmospheric oxygen is a cornerstone of evolutionary biology. While unequivocal evidence for an increase in atmospheric O2 marks the Great Oxidation Event (GOE) roughly 2.4 billion years ago, evidence underlying proposals for pre-GOE O2 accumulation is debated. Here we have investigated the distribution of genes for oxygen reductases, the enzymes that consume O2 in respiratory chains, across independently generated molecular timescales of prokaryotic evolution. The data indicate that cytochrome bd-oxidases, heme-copper oxidases and alternative oxidases arose in the wake of the GOE ca. 2.4 billion years ago, after which the genes were subjected to abundant lateral gene transfer, a reflection of their utility in redox balance and membrane bioenergetics. The data lead us to propose a straightforward four-stage model for O2 accumulation surrounding the GOE: (i) Negligible O2 existed prior to the GOE. (ii) Cyanobacterial O2 production started at the GOE, yet was capped at 2 % [v/v] atmospheric O2, the threshold at which cyanobacterial nitrogenase is inhibited by O2. (iii) Production of 0.02 atm of O2 (2 % [v/v]) at the GOE buried roughly the entire atmospheric CO2 inventory, causing sudden enrichment of 13C in dissolved inorganic carbon (the Lomagundi 13C anomaly), through RuBisCO isotope discrimination, without atmospheric O2 exceeding 2 % [v/v]. (iv) High atmospheric 12C at the end of the Lomagundi excursion marks the origin of oxygen reductases, their rapid spread via function in respiratory CO2 liberation, and the onset of equilibrium between photosynthetic O2 production and respiratory O2 consumption at 2 % atmospheric O2.

Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification rates may vary across both extant and extinct and unsampled lineages. We estimate the parameters of this model in a Bayesian statistical framework from phylogenies of exclusively extant lineages. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical primates dataset, which reveal that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a statistically coherent model.

Phylogenetic tip-dating has been and still is revolutionizing evolutionary biology in several ways. Fossil tip-dating, where fossils are placed into a phylogeny as tips based on morphological and/or molecular character information, provides a more principled approach to infer time-calibrated phylogenies compared with node-dating. Additionally, phylogenetic trees with fossils as tips become more and more important to elucidate evolutionary processes in macroevolutionary studies (e.g., deciphering diversification patterns and directional phenotypic evolution). Fossil tip-dating is slowly gathering popularity in empirical applications and has progressed substantially since its first demonstration in 2011, with respect to improved statistical models, software, and data sets. Nevertheless, executing a phylogenetic fossil tip-dating analysis is complicated and comes with many challenges. Here, we provide an extensive review and overview of methods and models for phylogenetic tip-dating analyses with fossils. We focus both on data collection and preparation and on modeling choices. We start with a survey of all published phylogenetic tip-dating studies to date, showing common data and modeling choices as well as trends toward new approaches. Then, we walk readers through sections of molecular evolution, morphological evolution (both for discrete and continuous data), and lineage evolution (the fossilized birth-death process). In each section, we describe the data and standard models with their underlying assumptions, and provide an outlook and practical recommendations.

Sponges harbor complex and diverse microbiomes that contribute to the host's fitness and, ultimately, the health of the ecosystems sponges inhabit. Using high-throughput 16S and 18S rRNA amplicon sequencing, we explore the prokaryotic and eukaryotic communities associated with three sympatric Mediterranean demosponges, namely Tethya aurantium, Tethya meloni, and Tethya citrina. We found species-specific prokaryotic and eukaryotic communities despite the close sympatry of the three Mediterranean Tethya species studied. This offers further support for the phylogenetic nature of the sponge microbiome, where microbial communities reflect the evolutionary ancestry of their host species. These patterns are both present in the eukaryotic and prokaryotic sponge-associated communities, since both display similar levels of host species specificity.

Cable bacteria are filamentous, sulphur-oxidizing microorganisms of the Desulfobulbaceae family that conduct electrons over centimetre-scale distances, coupling sulphide oxidation in deeper sediments to oxygen reduction near the surface. Geochemical evidence demonstrates high rates of aerobic sulphide oxidation in sediments inhabited by cable bacteria. Still, the underlying physiological and molecular basis of this electrogenic sulphur metabolism remains unresolved. Previous genomic analysis proposed that cable bacteria oxidize sulphide by reversing the canonical dissimilatory sulphite reduction (Dsr) pathway. We evaluated the sulphur metabolism of cable bacteria and related Desulfobulbales through comparative genomics, using an expanded set of 31 quality-filtered cable bacteria genomes, including 7 closed assemblies. We showed that cable bacteria encode a complete Dsr pathway, including the previously missing dsrD and dsrT genes, as well as a novel gene cluster with DsrOP homologues. All Dsr genes were classified as reductive-type, and phylogenetic analyses indicated a close affiliation with those of other Desulfobulbaceae (sulphate-reducing and/or sulphur-disproportionating bacteria). In addition, several other previously unrecognized sulphur-metabolism genes were identified in both cable bacteria and closely related Desulfobulbales, including a novel subtype of sulphide:quinone oxidoreductase (SQR), a putative rhodanese–persulphide dioxygenase fusion (Rho–PDO), and a YTD gene cluster (consisting of five genes) previously proposed to be characteristic of sulphur-disproportionation lineages. Structural predictions indicate that three uncharacterized YTD-encoded proteins assemble into a DsrEFH-like double heterotrimer, albeit with highly divergent, non-orthologous sequences. Finally, we integrated publicly available transcriptomic and proteomic data to confirm the in vivo expression of these genes, with expression patterns mirroring those of Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus. Cable bacteria show minimal genetic divergence and little differential expression in their sulphur-metabolism genes compared to related organisms. Together, our findings challenge the idea that sulphide oxidation occurs via a reversed Dsr pathway. We propose a unique sulphur metabolism model for cable bacteria, in which a canonical reductive/disproportionating sulphur-metabolism repertoire (similar to Desulfolithobacter dissulfuricans and Desulfurivibrio alkaliphilus) is coupled to net sulphide oxidation through long-distance electron transport. Key steps include sulphide oxidation to polysulphide by SQR, putative conversion to sulphite via Rho–PDO and/or proteins encoded in the YTD cluster, and subsequent disproportionation through the Dsr pathway, where sulphide re-enters the cycle. Net sulphide oxidation and sulphate production arise because electrons are efficiently drained via long-distance electron transport, effectively coupling the metabolism to oxygen reduction. The online version contains supplementary material available at 10.1186/s12864-026-12675-1.

The nitrogen metabolism genes and associated microorganisms in polar oceans and hydrothermal vents remain insufficiently studied. In this study, metagenomic data were analyzed to characterize the geographical and biological features of 16 key nitrogen-cycling genes. NasA/B, narG, and nxrB were consistently abundant in both environments. Polar oceans were dominated by common nitrogen-cycling taxa, whereas hydrothermal vents hosted species linked to sulfur and methane metabolism. Environmental extremes exerted a stronger influence on nitrogen cycling than depth. Distinct co-occurrence networks (centralized vs. redundant) and accurate habitat classification (>95 %) highlighted strong environmental shaping. Differences in amino acid preferences and enzyme thermal stability reflected evolutionary divergence and adaptation to extreme temperatures. Overall, depth and environmental conditions structured community networks, while genetic variation supported ecological adaptation. These findings reveal contrasting nitrogen-cycling strategies and adaptations, with potential implications for biotechnological applications.

Halite pinnacles from the Yungay area in the hyperarid core of the Atacama Desert harbor cryptoendolithic microbial colonies. A cross-section of a halite pinnacle was investigated using Raman spectroscopic imaging as the principal analytical technique, complemented by advanced fluorescence microscopy and CT-scan-based 3D visualization. Transversal section images were analyzed to track spatial variations in biomolecular responses, with particular emphasis on pigment composition. Overall, this study provides (a) new insights into complex halite architecture characterized by heterogeneous porosity, (b) the distribution of minor evaporitic components within the rock, specifically Ca-sulfate (gypsum) and Na-Ca sulfate (glauberite), (c) a characteristic umbrella-like pattern of scytonemin distribution revealed by both Raman and fluorescence imaging, and (d) changes in scytonemin Raman features that are interpreted as putative oxidative transformation of the pigment.

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We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.

Challenging to engineer in synthetic glues, wet adhesion is critical for many technical and biomedical applications. Mussels, however, have evolved underwater glues that adhere effectively onto slippery seashore surfaces. Past research on mussel adhesion highlights the importance of the post-translationally modified amino acid 3,4-dihydroxyphenylalanine (DOPA), found in abundance in mussel glue proteins. Yet, DOPA alone is insufficient to match native adhesion in synthetic mimics. Here, we provide evidence that a previously uncharacterized histidine-rich protein (mefp-12) plays a crucial role in the formation, curing, and performance of mussel glue. Biochemical analysis localizes mefp-12 within vesicles of the mussel glue secretory glands, while AI-assisted modeling of its sequence predicts Zn-stabilized coiled coil conformation and several domains resembling zinc-finger motifs. In vitro investigation of a His-rich α-helical peptide from mefp-12 shows Zn- and pH-dependent liquid-liquid phase separation (LLPS), coalescence, and spreading over the substrate. Exposure to seawater pH induces subsequent self-organization of the fluid condensates into solid nanoporous networks resembling the structure of the native mussel glue. Based on these findings we gain a deeper mechanistic understanding of mussel glue formation and function that challenges the dominant DOPA-centric paradigm, providing inspiration for design of bio-inspired wet adhesives.

Observations of morphology are commonly used to evaluate the biogenicity of terrestrial microfossils and could constitute a crucial line of evidence for extraterrestrial life-detection missions in the future. However, evaluating the origin of morphological features in the rock record can be problematic because naturally occurring abiotic structures can resemble biological morphologies, which may lead to false-positive detections of fossilised life. Iron-mineralised chemical gardens have been highlighted as potentially confounding abiotic structures because of their morphological and chemical resemblance to biomineralised filaments. Despite this, the potential for chemical garden structures to be preserved in the fossil record has not been thoroughly investigated. Here, we subjected abiotic iron-mineralised chemical garden structures to artificial maturation using hydrous pyrolysis, in order to evaluate their preservation potential. We found that these abiotic filaments were relatively resistant to degradation caused by maturation when compared with analogous biological material. Additionally, the transformation of ferrihydrite to crystalline iron oxides was found to be relatively inhibited, likely because of the influence of silica. These findings highlight the need for fossilised filamentous material to be distinguished from chemical garden structures before a biological origin can be confidently attributed, particularly when observed in significantly altered rocks.

Phylogenetic comparative methods are a major tool for evaluating macroevolutionary hypotheses. Methods based on the mean-reverting stochastic Ornstein-Uhlenbeck process allow for modelling adaptation on a phenotypic adaptive landscape that itself evolves and where fitness peaks depend on measured characteristics of the external environment and/or other organismal traits. Here, we give an overview of the conceptual framework for the many implementations of these methods and discuss how we might interpret estimated parameters. We emphasize that the ability to model a changing adaptive landscape sets these methods apart from other approaches and discuss why this aspect captures long-term trait evolution more realistically. Recent multivariate extensions of these methods provide a powerful framework for testing evolutionary hypotheses but are also more complicated to use and interpret. We provide some guidance on their usage and put recent literature on the topic in biological rather than mathematical terms. We further show how these methods provide a starting point for modelling reciprocal selection (i.e., coevolution) between interacting lineages. We then briefly review some critiques of the methodologies. Finally, we provide some ideas for future developments that we think will be useful to evolutionary biologists.

Present-day angiosperm plants produce a plethora of metabolites including pigments that serve for important functions such as photosynthesis, protection against light, attraction of pollinators, and defense against microbes and herbivores. However, little is known about phytochemical constituents of ancient angiosperms, their distribution in the fossil record, their stability in deep time, and diagenesis. Outstanding preservation of ancient angiosperms, including exceptional color preservation, has been reported, but chemical analyses of such valuable specimens are limited by the rarity of the fossil material and the small amounts of potentially preserved metabolites. Here we use highly sensitive targeted liquid chromatography-tandem mass spectrometry in multiple reaction monitoring mode to screen for nanogram quantities of intact ancient phytochemical metabolites and their products in exceptionally well-preserved, about 45-Ma-old leaves from the Eocene Geiseltal fossil Lagerstätte, Germany. We show that diverse chlorophyll derivatives and degradation products as well as polyphenolic pigments are preserved in green to yellow colored angiosperm leaves and the brown coal matrix from Geiseltal. Most interesting is the fossil occurrence of the "unstable" green chlorophyll derivative dihydro-132,173-cyclopheophorbide a-enol, since cyclopheophorbide-enols are otherwise known as unique non-fluorescent chlorophyll catabolites of microorganisms in modern aquatic environments. The monopyrrole hematinic acid is interpreted as a stable product of chlorophyll catabolism via linear tetrapyrroles. Moreover, polyphenolic compounds in the fossil angiosperms are represented by the flavonoid pigments apigenin and luteolin. Our results demonstrate the potential of paleometabolomic-like screening of individual plant fossils to trace the fate of phytochemical constituents and to understand the processes of fossilization at the molecular level.

Multicellular cable bacteria are capable of transferring electrons over centimeter distances through an internal array of conductive fibers. These long, filamentous bacteria function as a living electrochemical cell, performing sulfide oxidation at one end and oxygen reduction at the other end. To investigate how O2 reduction is linked to the long-distance electron transport along the conductive fibers, we performed a detailed electrochemical characterization of native filaments as well as extracted "fiber skeletons" without membranes or cytoplasm. Our data show that fibers skeletons only perform longitudinal electron transport and are not electrochemically active towards oxygen. Still, native cable bacterium filaments are capable of high oxygen reduction rates, thus indicating that dedicated enzyme systems in the periplasm or inner membrane are responsible for O2 reduction. A chemical inhibition assay on native cable bacterium filaments indicates that cytochromes are involved in electron transfer from the conductive fibers towards O2. Together, our data provide empirical support for a model in which diffusible c-type cytochromes mediate electron transport through the periplasm, shuttling electrons between separate respiratory complexes and the conductive fiber network. As such, our study resolves a crucial aspect of the unique electrogenic metabolism in cable bacteria, and clarifies the application potential of the highly conductive fibers in Bio-electrochemical System technologies.

Strong disparity in species richness among organisms is well documented, but heterogeneity in the underlying diversification process is less understood. Using novel probabilistic methods, we investigate clade-specific diversification rate shifts in several species-rich phylogenies, together representing over 300,000 species across the Tree of Life. We find that diversification rate shifts are extremely prevalent across all clades, with more frequent changes in younger clades and an overall excess of upshifts, resulting in an apparent acceleration of net diversification rates. We also reveal that heterogeneity in diversification rates is related to the tempo of diversification itself. While we find support for more prevalent shifts in speciation rates than extinction rates and more upshifts than downshifts, this is partially due to data insufficiency and inference challenges. Our insights are fundamentally enabled by studying numerous large phylogenies with rigorous statistical methods, showing widespread prevalence of diversification rate shifts across the Tree of Life.

The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morphological characters. However, traditional models of morphological character evolution often assume that all characters evolve according to a time-homogeneous Markov process, which applies uniformly across the entire phylogeny. While models incorporating among-character rate variation alleviate the assumption of the same rate for all characters, they still fail to address lineage-specific rate variation for individual characters. The covarion model, originally developed for molecular data to model the invariability of some sites for parts of the phylogeny, provides a promising framework for addressing this issue in morphological phylogenetics. In this study, we extend the covarion model in RevBayes to morphological character evolution, which we call the covariomorph model, and apply it to a diverse range of morphological datasets. Our covariomorph model utilizes multiple rate categories derived from a discretized probability distribution, which scales rate matrices accordingly. Characters are allowed to evolve within any of these rate categories, with the possibility of switching between rate categories during the evolutionary process. We verified our implementation of the covariomorph model with the help of simulations. Additionally, we examined 164 empirical datasets, finding patterns of rate heterogeneity compatible with covarion-like dynamics in approximately half of them. Upon further examination of two focal datasets that exhibited covarion-like rate variation, we found that the covariomorph model provides a more nuanced approach to incorporate rate variation across lineages, significantly affecting the resulting tree topology and branch lengths compared to traditional models. The observed sensitivity of branch lengths to model choice underscores potential implications of this approach for divergence time estimation and evolutionary rate calculations. By accounting for lineage- and character-specific rate shifts, the covariomorph model offers a robust framework to improve the accuracy of morphological phylogenetic inference.

We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria ( Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales ( Candidatus Poriferisodalaceae), among others.