Fossilized bacteria in a Cretaceous pterosaur headcrest

Pinheiro F.L., Horn B.L.D., Schultz C.L., de Andrade J.A.F.G. and Sucerquia P.A., 2012: Fossilized bacteria in a Cretaceous pterosaur headcrest. Lethaia, Vol. 45, pp. 495–499. We report herein the first evidence of bacterial autolithification in the Crato Formation of Araripe Basin, Brazil. The fossilized bacteria are associated with a tapejarid pterosaur skull, replacing the soft‐tissue extension of the headcrest. EDS analyses indicate that the bacteria were replaced by phosphate minerals, probably apatite. The bacterial biofilm was likely part of the prokaryotic mat that decomposed the pterosaur carcass at the bottom of the Araripe lagoon. This work suggests that bacterial autolithification could have played a key‐role on soft‐tissue preservation of Crato Formation Lagerstätte. □Bacterial autolithification, Crato Formation, phosphatization, pterosaur, soft‐tissue preservation.     

Decay and mineralization of soft tissue in Early Devonian boring ctenostome bryozoans

The Early Devonian of Podolia, Ukraine, has yielded phosphatized colonies of the boring ctenostome bryozoan Podoliapora doroshivi with 3‐D preservation of soft tissues. However, the feeding zooids are not anatomically complete, their preserved soft tissues comprising decay‐resistant structures such as the protective cuticular polypide sacs with presumed parietal muscles inside the wall of the sacs, the setigerous collars, the membranous orificial walls and remains of the muscle tissues. Early diagenetic apatite mineralization occured in numerous feeding zooids of Podoliapora at different stages of decay and may be important for the interpretation of decay processes in these colonial soft‐bodied fossil organisms. A setigerous collar, which is a characteristic of extant ctenostomes, occurs in P. doroshivi in several stages of decay showing progressive collapse and eventual complete loss. This study indicates that the morphological changes of collars induced by decay often resulted in connection with the membranous orificial wall, producing false anatomical structures, unrelated to structures observed in the earlier stages of decay or to the anatomical structures of extant ctenostomes. The most decay‐resistant cuticular polypide sacs mineralized as cryptocrystalline apatite in early stage of decay became degraded in later stages of decay. These data provide evidence that the anatomical interpretation of soft‐bodied fossils preserved only in the later stages of decay may have led to imprecise morphological interpretations.     

Organic preservation of fossil musculature with ultracellular detail

The very labile (decay-prone), non-biomineralized, tissues of organisms are rarely fossilized. Occurrences thereof are invaluable supplements to a body fossil record dominated by biomineralized tissues, which alone are extremely unrepresentative of diversity in modern and ancient ecosystems. Fossil examples of extremely labile tissues (e.g. muscle) that exhibit a high degree of morphological fidelity are almost invariably replicated by inorganic compounds such as calcium phosphate. There is no consensus as to whether such tissues can be preserved with similar morphological fidelity as organic remains, except when enclosed inside amber. Here, we report fossilized musculature from an approximately 18 Myr old salamander from lacustrine sediments of Ribesalbes, Spain. The muscle is preserved organically, in three dimensions, and with the highest fidelity of morphological preservation yet documented from the fossil record. Preserved ultrastructural details include myofilaments, endomysium, layering within the sarcolemma, and endomysial circulatory vessels infilled with blood. Slight differences between the fossil tissues and their counterparts in extant amphibians reflect limited degradation during fossilization. Our results provide unequivocal evidence that high-fidelity organic preservation of extremely labile tissues is not only feasible, but likely to be common. This is supported by the discovery of similarly preserved tissues in the Eocene Grube Messel biota.     

Carvacrol and eugenol effectively inhibit Rhizopus stolonifer and control postharvest soft rot decay in peaches

Aims

This study aimed to investigate the antifungal mechanism of carvacrol and eugenol to inhibit Rhizopus stolonifer and the control of postharvest soft rot decay in peaches.

Methods and Results

To investigate the antifungal mechanism, the effects of carvacrol and eugenol on the mycelium growth, leakages of cytoplasmic contents, mycelium morphology, cell membrane and membrane composition of R. stolonifer were studied. Carvacrol and eugenol both exhibited dose‐dependent antifungal activity against R. stolonifer, carvacrol at a concentration of 2 μl per plant and eugenol at a concentration of 4 μl per plant inhibited fungal growth completely. The two essential oils (EOs) increased cell membrane penetrability and caused the leakage of cytoplasm, nucleic acid and protein content. The observation using scanning electron microscopy and fluorescent microscopy showed modification of the hyphal morphology and breakage of the cell plasma membrane. Decreased ergosterol contents confirmed that the two EOs could destroy the membrane of R. stolonifer. For the in vivo test, the inhibition of soft rot disease and the induction of defence‐related enzymes were investigated. Carvacrol and eugenol significantly reduced the incidence and severity of soft rot decay in inoculated peaches. The best treatments for controlling soft rot decay were obtained at 0·5 μl l^?1 for carvacrol and 1 μl l^?1 for eugenol. The activities of defence‐related enzymes in peaches were also enhanced by fumigation with two EOs.

Conclusion

This study showed that carvacrol and eugenol could effectively inhibit the growth of R. stolonifer in vitro and successfully control the incidence of soft rot decay in honey peaches.

Significance and Impact of the Study

The above findings may be the main antifungal mechanism of carvacrol and eugenol on R. stolonifer. Furthermore, carvacrol and eugenol are helpful for their commercial application on the preservation of fresh fruit.     

Preservation of phosphatic wood remains in marine deposits of the Brentskardhaugen Bed (Middle Jurassic) from Svalbard (Boreal Realm)

The exceptional record of well-preserved wood remains from the Middle Jurassic of Svalbard is studied from the taphonomic point of view. These remains were recovered from the Brentskardhaugen Bed, a conglomerate with phosphatic nodules, which constitutes the record of the eroded deposits corresponding to the Toarcian–Early Bathonian gap. The wood remains occur in the cores of these nodules. These wood fragments are preserved as phosphate (francolite) and as charcoals. The well preservation allows us to identify xenoxyloid cross-field pits and xenoxylean pitting on the radial wall of tracheid, characterizing the species Xenoxylon phyllocladoides. Phosphatic nodules originated as the result of early phosphate precipitation filling the inter-particle pore space of the sandy quartz sediment around the wood fragments (and other organic-rich nucleation centers) below the sediment–water interface. This phosphatization involved a sudden burial of the wood remains in the sea-bottom, the subsequent decay of the lignin, and a fast growth of carbonate fluorapatite forming phosphatic inner moulds. Fossil microbial biofilms induced the phosphatization. The dissolution/decay of the lignin is not possible in charcoal, and phosphatic casts did not develop in charcoalified parts. Some remains were not totally charred, with the lignin preserved only in reduced relicts that were later replaced by phosphate. The phosphate precipitation occurred in recurrent episodes during the Toarcian–Callovian as a result of distinct sea-level rises and the associated nutrification of the shelf. The phosphatic nodules were developed and reworked during the transgressive–regressive cycle of the Toarcian–Early Bathonian, as well as during the final transgression of the Late Bathonian–Earliest Callovian, which resulted in the Brentskardhaugen Bed.     

PHOSPHATIZED SOFT-TISSUE IN TRIASSIC BIVALVES

Abstract: Exceptionally preserved specimens of the genera Myophoria, Neoschizodus and Trigonodus (Bivalvia, Palaeoheterodonta, Trigonioida) from carbonate sediments of the Muschelkalk (Anisian, Ladinian) contain phosphatized soft‐tissues. This is the oldest record of soft‐tissue preservation in bivalves and the first from the German Muschelkalk. The phosphatized remains are here interpreted as relics of the originally chitinous gill supports, the gill axis, the labial palps (?), the adductor muscles, the pedal retractor muscles, the mantle margin including the radial mantle musculature, and the ‘siphons’. According to microprobe analysis, the mineral replacing the soft‐tissue is mainly apatite and, more rarely, francolite. Additionally, quartz filled voids within the gill supports, and in one sample it occurs in minute crystals in the phosphatized remains of the adductor muscle of Neoschizodus. Myophoria, Neoschizodus and Trigonodus were soft‐bottom dwellers and five of the specimens were discovered in life position. This is indicated by geopetal structures in three specimens.     

Buoyancy mechanisms limit preservation of coleoid cephalopod soft tissues in Mesozoic Lagerstätten

Coleoid cephalopods are characterized by internalization of their shell, and are divided into the ten‐armed Decabrachia (squids and cuttlefish) and the eight‐armed Vampyropoda (octopuses and vampire squid). They have a rich fossil record predominantly of the limited biomineralized skeletal elements they possess: arm hooks, statoliths, mouthparts (the buccal mass) and internal shell (gladius or pen), although exquisitely preserved soft tissue coleoids are known from several Lagerstätten worldwide. Recent studies have shown that although morphological similarities between extant decabrachian gladii and fossil examples exist, no known examples of fossil decabrachians are currently known. However, molecular clock data and phylogenetic bracketing suggest that they should be present in Lagerstätten that are rich in vampyropod soft tissue fossils (i.e. Hâkel and Hâdjoula Lagerstätten, Cretaceous, Lebanon). We propose that a hitherto unknown taphonomic bias pertaining to the differing methods of buoyancy control within coleoid groups limits preservation potential. Both negatively and neutrally buoyant decabrachians use chemical buoyancy control (ammonia) whereas vampyropods do not. In the event of rapid burial in an environment conducive to exceptional preservation, ammonia dramatically decreases the ability of the decabrachian carcass to generate the required pH for authigenic calcium phosphate replacement, limiting its preservation potential. Moreover, the greater surface area and comparatively fragile dermis further decrease the potential for fossilization. This taphonomic bias may have contributed to the lack of preserved labile soft‐tissues in other cephalopods groups such as the ammonoids.     

Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record

An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).     

Exceptionally preserved tadpoles from the Miocene of Libros,Spain: ecomorphological reconstruction and the impact of ontogeny upon taphonomy

McNamara, M.E., Orr, P.J., Kearns, S.L., Alcalá, L., Anadón, P. & Peñalver‐Mollá, E. 2010: Exceptionally preserved tadpoles from the Miocene of Libros, Spain: ecomorphological reconstruction and the impact of ontogeny upon taphonomy. Lethaia, Vol. 43, pp. 290–306. The Libros exceptional biota from the Upper Miocene of NE Spain includes abundant frog tadpoles (Rana pueyoi) preserved in finely laminated lacustrine mudstones. The tadpoles exhibit a depressed body, short tail, low tail fins, dorso‐laterally directed eyes and jaw sheaths; these features identify the Libros tadpoles as members of the benthic lentic ecomorphological guild. This, the first ecomorphological reconstruction of a fossil tadpole, supports phylogenetic evidence that this ecology is a conserved ranid feature. The soft‐tissue features of the Libros tadpoles are characterized by several modes of preservation. The space occupied previously by the brain is defined by calcium carbonate, the nerve cord is defined by calcium phosphate, and jaw sheaths and bone marrow are preserved as organic remains. Gut contents (and coprolites adjacent to specimens) comprise ingested fine‐grained sedimentary detritus and epiphyton. The body outline and the eyespots, nares, abdominal cavity, notochord, caudal myotomes and fins are defined by a carbonaceous bacterial biofilm. A similar biofilm in adult specimens of R. pueyoi from Libros defines only the body outline, not any internal anatomical features. In the adult frogs, but not in the tadpoles, calcium phosphate and calcium sulphate precipitated in association with integumentary tissues. These differences in the mode of preservation between the adult frogs and tadpoles reflect ontogenetic factors. □Anuran, ecology, soft‐tissue, tadpoles, taphonomy.     

Precambrian animal life: Taphonomy of phosphatized metazoan embryos from southwest China

Phosphatized fossils from the Neoproterozoic Doushantuo Formation have provided valuable insight into the early evolution of metazoans, but the preservation of these spectacular fossils is not yet fully understood. This research begins to address this issue by performing a detailed specimen-based taphonomic analysis of the Doushantuo Formation phosphatized metazoan embryos. A total of 206 embryos in 65 thin sections from the Weng'an Phosphorite Member of the Doushantuo Formation were examined and their levels of pre-phosphatization decay estimated. The data produced from this examination reveal a strong taphonomic bias toward earlier (2-cell and 4-cell) cleavage stages, which tend to be well-preserved, and away from later (8-cell and 16-cell) cleavage stages, which tend to exhibit evidence for slight to intense levels of organic decay. In addition, the natural abundances of these embryos tend to decrease with advancement in cleavage stage, and no evidence of more advanced (beyond 16-cell) cleavage stages or eventual adult forms were found in this study. One possible explanation for this taphonomic bias toward early cleavage stages is that later cleavage stages and adult forms were more physically delicate, allowing them to be more easily damaged during burial and reworking, allowing for more rapid decay. The spectacular preservation of these embryos was probably aided by their likely internal enrichment in phosphate-rich yolk, which would have caused their internal dissolved phosphate levels to reach critical levels with only miniscule organic decay, thereby hastening phosphatization. If internal sources of phosphate did indeed play a role in the phosphatization of these embryos, it may explain their prolific abundance in these rocks compared to other phosphatized fossils as well as indicating that metazoans lacking such internal phosphate sources were likely much more difficult to preserve. The phosphatic fossils of the Doushantuo Formation, therefore, provide an indispensable, yet restricted, window into Neoproterozoic life and metazoan origins.     

The cuticle of the enigmatic arthropod Phytophilaspis and biomineralization in Cambrian arthropods

Lin, J.‐P., Ivantsov, A.Y. & Briggs, D.E.G. 2011: The cuticle of the enigmatic arthropod Phytophilaspis and biomineralization in Cambrian arthropods. Lethaia, Vol. 44, pp. 344–349. Many non‐trilobite arthropods occur in Cambrian Burgess Shale‐type (BST) biotas, but most of these are preserved in fine‐grained siliciclastics. Only one important occurrence of Cambrian non‐trilobite arthropods, the Sinsk biota (lower Sinsk Formation, Botomian) from the Siberian Platform, has been discovered in carbonates. The chemical compositions of samples of the enigmatic arthropod Phytophilaspis pergamena Ivantsov, 1999 and the co‐occurring trilobite Jakutus primigenius Ivantsov in Ponomarenko, 2005 from this deposit were analysed. The cuticle of P. pergamena is composed of mainly calcium phosphate and differs from the cuticle of J. primigenius, which contains only calcium carbonate. Phosphatized cuticles are rare among large Cambrian arthropods, except for aglaspidids and a few trilobites. Based on recent phylogenetic studies, phosphatization of arthropod cuticle is likely to have evolved several times. □arthropod cuticle, Burgess Shale‐type preservation, fossil‐diagenesis, phosphatization.     

Tissue preservation biases in stable isotopes of fishes and molluscs from Patagonian lakes

Field work commonly involves preserving samples for later use; however, most preservation methods distort stable‐isotope (SI) signatures that are of interest to ecologists. Although preservation of muscle samples with table salt and rubbing alcohol affected the SI (δ¹³C and δ¹⁵N) of important consumers in Patagonian lakes (molluscs and fishes), variation among individuals and lakes generally exceeded that among preservation treatments. Mathematical corrections for these preservation biases are provided, and a potentially bias‐free preservation by air‐drying is suggested.     

Experimentally observed soft‐tissue preservation near a marine brine seep

A sea urchin placed on the sea floor near an active brine seep was recovered after 13 years with detailed soft‐tissue preservation. Growth of an amorphous calcium carbonate solid with small amounts of the mineral bassanite occurred on the spines and test. The solid also exhibits striations at both the macro‐ and microscopic scales that preserve the muscle texture of the sea urchin. Such soft‐tissue replacement and mineralization could lead to exquisite fossilization. Soft‐tissue mineralization has been previously replicated in controlled laboratory conditions; however, this is the first report of the lithologic replication of soft tissues in an open marine experiment. Examples of extraordinary fossil preservation, or Lagersätten, give a distinct snapshot of the past and have led to a greater understanding of the history of life. Soft‐tissue lithification occurs in special circumstances in which local chemical conditions (often mediated by decay or bacterial factors) promote early diagenetic mineralization, the first steps of which are observed in this instance. The preservation of articulated skeletons, especially within echinoderms, is normally attributed to rapid burial, but that may not be necessary given that this urchin was at or very near the sediment–water interface for 13 years.     

ULTRASTRUCTURAL AND PALEOBIOCHEMICAL CORRELATIONS AMONG FOSSIL LEAF TISSUES FROM THE ST. MARIES RIVER (CLARKIA) AREA,NORTHERN IDAHO,USA

Miocene angiosperm leaf tissues of Betula, Hydrangea, Platanus, and Quercus, and of Castanea, Persea, and gymnospermous tissues from offshore and onshore lacustrine sediments, respectively, reveal various states of ultrastructural detail in preservation which correlate with their paleobiochemical profiles. Excellent cytologic preservation of membrane-bound organelles in offshore tissue samples is correlated with relatively mild chlorophyll and fatty acid degradation (chlorins, unsaturated hydrocarbons), while progressive deterioration of ultrastructure seen in onshore specimens is concomitant with extensive chlorophyll degradation and saturation of hydrocarbons. Comparative studies between fossils found in pyroclastic (Succor Creek Flora, Miocene) and lacustrine (Clarkia Flora) environments indicate that the degree of pre- and post-depositional hydration of tissues is a less significant factor in determining preservation than redox potential and secondary metabolites (tannic acids, chlorophyll derivatives). A sequence of organelle degradation in leaf tissues is given, and it is suggested that chloroplasts and cell walls are the most stable cellular constituents, while the endoplasmic reticulum, nuclei, and mitochondria are the most labile.     

Taphonomy of the middle Cambrian (Drumian) Ravens Throat River Lagerstätte,Rockslide Formation,Mackenzie Mountains,Northwest Territories,Canada

The Middle Cambrian (series 3, Drumian, Bolaspidella Biozone) Ravens Throat River Lagerstätte in the Rockslide Formation of the Mackenzie Mountains, northwestern Canada, contains a Burgess Shale‐type biota of similar age to the Wheeler and Marjum formations of Utah. The Rockslide Formation is a unit of deep‐water, mixed carbonate and siliciclastic facies deposited in a slope setting on the present‐day northwestern margin of Laurentia. At the fossil‐bearing locality, the unit is about 175 m thick and the lower part onlaps a fault scarp cutting lower Cambrian sandstones. It consists of a succession of shale, laminated to thin‐bedded lime mudstone, debris‐flow breccias, minor calcareous sandstone, greenish‐coloured calcareous mudstone and dolomitic siltstone, overlain by shallow‐water dolostones of the Broken Skull Formation, which indicates an overall progradational sequence. Two ~1‐m‐thick units of greenish calcareous mudstone in the upper part exhibit soft‐bodied preservation, yielding a biota dominated by bivalved arthropods and macrophytic algae, along with hyoliths and trilobites. It represents a low‐diversity in situ community. Most of the fossils occur in the lower unit, and only the more robust components are preserved. Branching burrows are present under the carapaces of some arthropods, and common millimetre‐sized disruptions of laminae are interpreted as bioturbation. The fossiliferous planar‐laminated calcareous mudstone consists of chlorite, illite, quartz silt, calcite and dolomite and is an anomalous facies in the succession. It was deposited via hemipelagic fallout of a mixture of platform‐derived and terrestrial mud. Geochemical analysis and trace‐element proxies indicate oxic bottom waters that only occasionally might have become dysoxic. Productivity in the water column was dominated by cyanobacteria. Fragments of microbial mats are common as carbonaceous seams. Complete decay of soft tissues was interrupted due to the specific sediment composition, providing support for the role of clay minerals, possibly chlorite, in the taphonomic process.     

Effects of freezing on white perch Morone americana (Gmelin, 1789): implications for multivariate morphometrics

This study tested the hypothesis that duration of freezing differentially affects whole‐body morphometrics of a derived teleost. Whole‐body morphometrics are frequently analyzed to test hypotheses of different species, or stocks within a species, of fishes. Specimens used for morphometric analyses are typically fixed or preserved prior to analysis, yet little research has been done on how fixation or preservation methods or duration of preservation of specimens might affect outcomes of multivariate statistical analyses of differences in shape. To determine whether whole‐body morphometrics changed as a result of freezing, 23 whole‐body morphometrics of age‐1 white perch (Morone americana) from western Lake Erie (n = 211) were analyzed immediately after capture, after being held on ice overnight, and after freezing for 100 or 200 days. Discriminant function analysis revealed that all four groups differed significantly from one another (P < 0.0001). The first canonical axis reflected long‐axis morphometrics, where there was a clear pattern of positive translation along this axis with duration of preservation. Re‐classification analysis demonstrated fish were typically assigned to their original preservation class except for fish frozen 100 days, which assigned mostly to frozen 200 days. Morphometric comparisons using frozen fish must be done on fish frozen for identical periods of time to avoid biases related to the length of time they were frozen. Similar experiments should be conducted on other species and also using formalin‐ and alcohol‐preserved specimens.     

Preservation of soft tissues in Silurian graptolites from Latvia

The contractile stalks of graptoloid zooids are preserved as organic carbon residues in thecae of the middle Llandovery graptoloid graptolites Rastrites geinitzii and Neolagarograptus? sp. from the Aizpute‐41 core, Latvia. The contractile stalks are surrounded by equant pyrite crystals, resulting in three‐dimensional preservation of the graptolite rhabdosomes, and are associated with sediment of similar composition to, and derived from, the adjacent matrix. Matrix entered the thecae after pyrite crystal growth and filled some of the space left by collapse of the contractile stalks and some intercrystalline cavities; other space is partially infilled by diagenetic minerals. The contractile stalks are parallel‐sided and occupy up to one‐half the metathecal width, which is not inconsistent, assuming post‐mortem shrinkage, with the suggestion that graptoloid zooids filled their thecal tubes in life. The location of the preserved soft tissues, towards the distal ends of the metathecae, is very different from that predicted by decay experiments on the extant pterobranch hemichordate Rhabdopleura; the latter's soft tissues may thus not be a reliable analogue for those of these Silurian graptoloids.     

Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans

In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy, we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key question of codon usage. Received: 18 June 2000 / Accepted: 10 November 2000