The Natural History of Ooliths: Franz Ernst Brückmann’s Treatise of 1721 and its Significance for the Understanding of Oolites

Franz Brückmann schrieb 1721 seine erste Abhandlung über Oolithe. Wir stellen hier eine Übersetzung des lateinischen Originaltextes ins Englische vor. Brückmann beschreibt die Herkunft des Namens Oolith und seine Synonyme; interpretiert Oolithe als Ansammlung von Fisch-Eiern; klassifiziert sie als Steine; gibt Auftreten und Häufigkeit an; erklärt das Ablagerungsmilieu und Prozesse der Versteinerung und die große Menge der gefundenen Eier; beweist ihre biologische Herkunft und ihre biologischen Beziehungen; unterscheidet die Oolithe von den Pisolithen und gibt Orte an, wo sie gefunden werden. Wir kommentieren Brückmanns Text, besprechen die Wirkung seines Werkes und verfolgen die Forschung über Oolithe bis zum frühen 20. Jahrhundert. Wir schließen, dass Brückmanns Abhandlung am besten als Überblick anzusehen ist, der eine Grundlage für spätere Forschungen bildete. Sein wichtigster Beitrag war, Oolithe eher als Anhäufungen von biologischen Überresten als „Spiele der Natur“ (lusus naturae) anzusehen. Einige von Brückmanns Zeitgenossen, wie Da Costa und De Saussure zweifelten, dass Fischeier versteinern könnenund – obgleich sie die biologische Herkunft einräumten – zogen es vor, sie als mineralische Konkretionen zu betrachten. Große Neuerungen in der Stratigraphie, Paläontologie, Mikrobiologie, Mikroskopie, vergleichenden Sedimentologie und Petrologie mußten stattfinden, bevor im 19. Jahrhundert signifikante Fortschritte von Brückmanns Interpretationen gemacht werden konnten.Franz Brückmann wrote his treatise on oolites in 1721. We present here an English translation of his Latin text which describes the following topics; derivation of the name “oolith” and its synonyms; interpretation as accumulations of fish-eggs; classification as stones; occurrence and diversity; environments of deposition and processes of lithification; explanations for the large quantities of eggs found; evidence for their biological origin; evidence for their biological associations; the distinction between ooliths and pisoliths; and localities of occurrence. We provide a commentary on Brückmann’s text, and then review the impact of his work by tracing the subsequent development of research on Oolites up to the early twentieth century. We conclude that Brückmann’s treatise is best regarded as a review paper that provided a platform for later research. His most significant contribution was to view oolites as accumulations of petrified biological remains rather than as “sports of nature”. Some of Brückmann’s near contemporaries such as Da Costa and De Saussure doubted that fish eggs could lithify and, although conceding their sedimentary origin, preferred to regard them as mineral concretions. Major developments in the sciences of stratigraphy, palaeontology, microbiology, microscopy, comparative sedimentology, and petrology would be required before more significant advances could be made on Brückmann’s interpretations

The Role and Significance of Authigenic Magnesium Silicates in the Organomineralisation of Microbialites in the Yalgorup Lakes, Western Australia

This work re-examines samples of modern microbialites collected in the 1980s from Lakes Clifton and Preston, two of the Yalgorup Lakes in southwest Western Australia. Lake Clifton contains the first convincing modern examples of thrombolites to have been recognized. It was known that aragonite mineralisation took place in these structures within near-surface biofilms. New research reveals that stevensite, a Mg-rich trioctahedral smectite, is the principal primary phase that establishes the initial structural rigidity of Lake Clifton thrombolites. Aragonite microcrystals then grow within the stevensite matrix. In adjacent Lake Preston, lithified, centimetre-scale, coniform structures occur that are similar to pinnacle-like microbial mats that grow intermittently in a small pond adjacent to the lake. Microstructures within the lithified cones confirm their microbial origin, but they have undergone four phases of mineralization; an amorphous Mg silicate phase (of smectite-like composition); some areas of Mg silicate were then partially transformed into authigenic serpentine (chrysotile and/or lizardite); aggregates of aragonite microcrystals then overprinted much of the fabric; and finally high-magnesium calcite grew as void fills and rims, as well as overprinting some of the remaining areas of the Mg silicate phase. It is concluded that syngenetic and early diagenetic carbonate mineralisation of microbialites may effectively obscure all traces of the original microbial communities, leaving only faint evidence for their organo-sedimentary origin. Secondary carbonate mineralisation of microbialites may thus eliminate the evidence of primary organomineralisation. Many published examples of apparently abiogenic but microbialite-like carbonates should be re-examined for traces of early silicate mineralisation. The discovery of microbial permineralisation of modern microbialites by Mg silicates in Lakes Clifton and Preston raises the possibility that phyllosilicates could have contributed to the early structural rigidity of some Proterozoic Stromatolites such as Conophyton. Reexamination of the literature on Conophyton tends supports this hypothesis. Finally, the significance of this research is considered in relation to ; clarifying the role of Mg silicates in microbialite organomineralisation; examining the evidence that apparently abiotic crystalline carbonate may be of secondary origin; understanding the nature of the supposed “microbialites” in Cretaceous pre-salt sequences of the proto-Atlantic rift; assessing the continuing relevance of the “microbialite” concept; and clarifying evidence for the recognition of the earliest signs of life on Earth

The evolution of microbialite forms during the Early Triassic transgression: A case study in Chongyang of Hubei Province, South China

The widespread development of microbialites in shallow areas of the Tethys Ocean at the start of the Early Triassic reflects the deterioration of marine ecosystems in the aftermath of the extinction that marked the demise of the majority of Palaeozoic marine faunas. Here we present a study of the evolving microbialite forms and associated biotic assemblages of this pioneering microbialite interval from exposures at Chongyang, Hubei Province, China. This research provides a perspective on the effects of eustatic transgression on marine ecosystems as water depths increased at the beginning of Mesozoic, through the study of the changing forms, microfacies and distribution of microbialites. Microbialite forms evolved from stratiform stromatolites to a sequence of tabular thrombolites (with an intercalated layer of columnar stromatolites), followed by domical thrombolites that were overlain, in turn, by oolites. The stratiform stromatolites contain poorly preserved remains of calcified cyanobacteria, but microfossils with chambered structure can also be seen. Metazoan fossils increased from the base of the overlying tabular thrombolite, reflecting increasing biodiversity with deepening of seawater. The occurrence of columnar stromatolites within the tabular thrombolite may indicate a temporary sea-level shallowing. Foraminiferans and other metazoans are absent within the columnar stromatolites, but spherical cyanobacterial remains are extremely abundant. Well-preserved calcified cyanobacteria may reflect an absence of metazoan predation and/or carbonate supersaturation of seawater. As water deepened, domical thrombolites developed and the more complex seafloor relief created varied niches between and within the domes that harboured more ecologically diverse communities. During the process of transgression within the microbialite interval, carbon isotopes exhibit a negative relationship with biodiversity, implying that upwelling of anoxic deep-ocean water, if associated with the negative excursion of carbon isotope values, did not inhibit the diversification of benthic organisms at least on shallow carbonate platforms in the period immediately after the end-Permian mass extinction.This study was jointly supported by the National Natural Science Foundationof China (Grants No. 41730320 and No. 41572001) and the 111 project(B08030

Biofilm formation and virulence expression by Streptococcus mutans are altered when grown in dual-species model

<p>Abstract</p> <p>Background</p> <p>Microbial cell-cell interactions in the oral flora are believed to play an integral role in the development of dental plaque and ultimately, its pathogenicity. The effects of other species of oral bacteria on biofilm formation and virulence gene expression by <it>Streptococcus mutans</it>, the primary etiologic agent of dental caries, were evaluated using a dual-species biofilm model and RealTime-PCR analysis.</p> <p>Results</p> <p>As compared to mono-species biofilms, biofilm formation by <it>S. mutans </it>was significantly decreased when grown with <it>Streptococcus sanguinis</it>, but was modestly increased when co-cultivated with <it>Lactobacillus casei</it>. Co-cultivation with <it>S. mutans </it>significantly enhanced biofilm formation by <it>Streptococcus oralis </it>and <it>L. casei</it>, as compared to the respective mono-species biofilms. RealTime-PCR analysis showed that expression of <it>spaP </it>(for multi-functional adhesin SpaP, a surface-associated protein that <it>S. mutans </it>uses to bind to the tooth surface in the absence of sucrose), <it>gtfB </it>(for glucosyltransferase B that synthesizes α1,6-linked glucan polymers from sucrose and starch carbohydrates) and <it>gbpB </it>(for surface-associated protein GbpB, which binds to the glucan polymers) was decreased significantly when <it>S. mutans </it>were co-cultivated with <it>L. casei</it>. Similar results were also found with expression of <it>spaP </it>and <it>gbpB</it>, but not <it>gtfB</it>, when <it>S. mutans </it>was grown in biofilms with <it>S. oralis</it>. Compared to mono-species biofilms, the expression of <it>luxS </it>in <it>S. mutans </it>co-cultivated with <it>S. oralis </it>or <it>L. casei </it>was also significantly decreased. No significant differences were observed in expression of the selected genes when <it>S. mutans </it>was co-cultivated with <it>S. sanguinis</it>.</p> <p>Conclusions</p> <p>These results suggest that the presence of specific oral bacteria differentially affects biofilm formation and virulence gene expression by <it>S. mutans</it>.</p

A biofilm and organomineralisation model for the growth and limiting size of ooids

Ooids are typically spherical sediment grains characterised by concentric layers encapsulating a core. There is no universally accepted explanation for ooid genesis, though factors such as agitation, abiotic and/or microbial mineralisation and size limitation have been variously invoked. Here we examine the possible influence of microbial organomineralisation on the formation of some naturally occurring ooids. We develop a mathematical model for ooid growth, inspired by work on avascular brain tumours, that assumes mineralisation in a biofilm to form a central core which then nucleates the progressive growth of concentric laminations. The model predicts a limiting size with the sequential width variation of growth rings comparing favourably with those observed in experimentally grown ooids generated from biomicrospheres. In reality, this model pattern may be complicated during growth by syngenetic aggrading neomorphism of the unstable mineral phase, followed by diagenetic recrystallisation that further complicates the structure. Our model provides a potential key to understanding the genetic archive preserved in the internal structures of some ooids.The work of F.L. has been supported by the National Natural Science Foundation of China (Grant No. 41502115). R.V.B. acknowledges the support of a Visiting Professorship at Université de Lausanne supported by funds from the Fondation Herbette and a Guest Professorship at Chongqing University. Te work of M.T.B. has been supported by the 1000 Talents Program of China

Genetic Analysis of the Functions and Interactions of Components of the LevQRST Signal Transduction Complex of Streptococcus mutans

Transcription of the genes for a fructan hydrolase (fruA) and a fructose/mannose sugar:phosphotransferase permease (levDEFG) in Streptococcus mutans is activated by a four-component regulatory system consisting of a histidine kinase (LevS), a response regulator (LevR) and two carbohydrate-binding proteins (LevQT). The expression of the fruA and levD operons was at baseline in a levQ mutant and substantially decreased in a levT null mutant, with lower expression with the cognate inducers fructose or mannose, but slightly higher expression in glucose or galactose. A strain expressing levQ with two point mutations (E170A/F292S) did not require inducers to activate gene expression and displayed altered levD expression when growing on various carbohydrates, including cellobiose. Linker-scanning (LS) mutagenesis was used to generate three libraries of mutants of levQ, levS and levT that displayed various levels of altered substrate specificity and of fruA/levD gene expression. The data support that LevQ and LevT are intimately involved in the sensing of carbohydrate signals, and that LevQ appears to be required for the integrity of the signal transduction complex, apparently by interacting with the sensor kinase LevS

Phylogenomics and the dynamic genome evolution of the genus Streptococcus

The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group

RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms

Early childhood caries (ECC), which can lead to rampant tooth-decay that is painful and costly to treat, is one of the most prevalent infectious diseases affecting children worldwide. Previous studies support that interactions between Streptococcus mutans and Candida albicans are associated with the pathogenesis of ECC. The presence of Candida enhances S. mutans growth, fitness and accumulation within biofilms in vitro, although the molecular basis for these behaviors is undefined. Using an established co-cultivation biofilm model and RNA-Seq, we investigated how C. albicans influences the transcriptome of S. mutans. The presence of C. albicans dramatically altered gene expression in S. mutans in the dual-species biofilm, resulting in 393 genes differentially expressed, compared to mono-species biofilms of S. mutans. By Gene Ontology analysis, the majority of up-regulated genes were related to carbohydrate transport and metabolic/catabolic processes. KEGG pathway impact analysis showed elevated pyruvate and galactose metabolism, suggesting that co-cultivation with C. albicans influences carbohydrate utilization by S. mutans. Analysis of metabolites confirmed the increases in carbohydrate metabolism, with elevated amounts of formate in the culture medium of co-cultured biofilms. Moreover, co-cultivation with C. albicans altered transcription of S. mutans signal transduction (comC and ciaRH) genes associated with fitness and virulence. Interestingly, the expression of genes for mutacins (bacteriocins) and CRISPR were down-regulated. Collectively, the data provide a comprehensive insight into S. mutans transcriptomic changes induced by C. albicans, and offer novel insights into how bacterial–fungal interactions may enhance the severity of dental caries

Oscillatory underpinnings of mismatch negativity and their relationship with cognitive function in patients with schizophrenia.

BACKGROUND: Impairments in mismatch negativity (MMN) generation have been consistently reported in patients with schizophrenia. However, underlying oscillatory activity of MMN deficits in schizophrenia and the relationship with cognitive impairments have not been investigated in detail. Time-frequency power and phase analyses can provide more detailed measures of brain dynamics of MMN deficits in schizophrenia. METHOD: 21 patients with schizophrenia and 21 healthy controls were tested with a roving frequency paradigm to generate MMN. Time-frequency domain power and phase-locking (PL) analysis was performed on all trials using short-time Fourier transforms with Hanning window tapering. A comprehensive battery (CANTAB) was used to assess neurocognitive functioning. RESULTS: Mean MMN amplitude was significantly lower in patients with schizophrenia (95% CI 0.18 - 0.77). Patients showed significantly lower EEG power (95% CI -1.02 - -0.014) in the ~4-7 Hz frequency range (theta band) between 170 and 210 ms. Patients with schizophrenia showed cognitive impairment in multiple domains of CANTAB. However, MMN impairments in amplitude and power were not correlated with clinical measures, medication dose, social functioning or neurocognitive performance. CONCLUSION: The findings from this study suggested that while MMN may be a useful marker to probe NMDA receptor mediated mechanisms and associated impairments in gain control and perceptual changes, it may not be a useful marker in association with clinical or cognitive changes. Trial-by-trial EEG power analysis can be used as a measure of brain dynamics underlying MMN deficits which also can have implications for the use of MMN as a biomarker for drug discovery

The Streptococcus mutans Cid and Lrg systems modulate virulence traits in response to multiple environmental signals

The tight control of autolysis by Streptococcus mutans is critical for proper virulence gene expression and biofilm formation. A pair of dicistronic operons, SMU.575/574 (lrgAB) and SMU.1701/1700 (designated cidAB), encode putative membrane proteins that share structural features with the bacteriophage-encoded holin family of proteins, which modulate host cell lysis during lytic infection. Analysis of S. mutans lrg and cid mutants revealed a role for these operons in autolysis, biofilm formation, glucosyltransferase expression and oxidative stress tolerance. Expression of lrgAB was repressed during early exponential phase and was induced over 1000-fold as cells entered late exponential phase, whereas cidAB expression declined from early to late exponential phase. A two-component system encoded immediately upstream of lrgAB (LytST) was required for activation of lrgAB expression, but not for cid expression. In addition to availability of oxygen, glucose levels were revealed to affect lrg and cid transcription differentially and significantly, probably through CcpA (carbon catabolite protein A). Collectively, these findings demonstrate that the Cid/Lrg system can affect several virulence traits of S. mutans, and its expression is controlled by two major environmental signals, oxygen and glucose. Moreover, cid/lrg expression is tightly regulated by LytST and CcpA