Bioturbation Events Research Articles

Assessing the expansion of the Cambrian Agronomic Revolution into fan-delta environments

The intensity, extent, and ecosystem-level impact of bioturbation (i.e. Agronomic Revolution) at the dawn of the Phanerozoic is a hotly debated issue. Middle Cambrian fan-delta deposits in southwestern Saskatchewan provide insights into the paleoenvironmental extent of the Agronomic Revolution into marginal-marine environments. The studied deposits reveal that several environmental stressors had direct impact on trace-fossil distribution and bioturbation intensities in Cambrian fan deltas. Basal and proximal subaerial deposits are characterized by very coarse grain size and absence of bioturbation. Mid-fan and fan-toe deposits were formed under subaqueous conditions and are characterized by rapid bioturbation events in between sedimentation episodes when environmental stressors were ameliorated, providing evidence of a significant landward expansion of the Agronomic Revolution. Transgressive marine deposits accumulated after the abandonment of the fan-delta system display high levels of bioturbation intensity, reflecting stable environmental conditions that favored endobenthic colonization. The presence of intense bioturbation in both subaqueous fan delta and transgressive deposits provides further support to the view that Cambrian levels of biogenic mixing were high, provided that stable environmental conditions were reached. Our study underscores the importance of evaluating sedimentary facies changes to assess the impact of environmental factors prior to making evolutionary inferences.

Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia.

The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases.

Disappeared almost without a trace: Taphonomic pathways and the recognition of hidden bioturbation events in Eocene storm deposits (Paují Formation, Lake Maracaibo, Venezuela)

Shallow-marine deposits, included in the “Basal Sands” of the Eocene Pauji Formation of the Maracaibo Basin in western Venezuela, record deposition in fore shore to lower off shore settings. These deposits are stacked in coarsening-upward parasequences that reflect variable intensities and frequencies of storms. Of particular interest are sharp-based, amalgamated, hummocky cross-stratified and rippled, very fine-grained sandstone beds, observed in the core MOT-X from the Motatan Field. These beds record storm deposition, under purely oscillatory to combined flows in an offshore-transition setting. The amalgamated nature of the sand stone interval indicates repeated erosion, due to multiple storm events. The ichnofabrics in these tempestites result from a distinctive taphonomic pathway, reflecting the interplay between bioturbation events and storm erosion and deposition. The storm-related trace-fossil suite is represented by Diplocraterion parallelum and local occurrences of Palaeophycus tubularis , Bergaueria isp. and Thalassinoides isp., which is consistent with the relatively high energy of formation of these deposits. Fair-weather deposits are absent from the sand stone interval. However, high densities of Chondrites isp. are present in the infills of Diplocraterion parallelum and, more rarely, Thalassinoides isp. providing the sole evidence of the establishment of a resident fauna during inter-storm intervals. Deposits containing the fair-weather suites were erosionally removed during the subsequent storm. The deep-tier emplacement of Chondrites and the ability of its producer to rework other biogenic structures favour preservation, allowing recognition of a “hidden” bioturbation event that otherwise might have remained undetected.

When and why does bioturbation lead to diffusive mixing?

Bioturbation in aquatic sediments results from many different biological activities, inducing particle displacement over a variety of length and time scales. Despite this inherent complexity, empirical tracer studies show that bioturbational mixing is often well described by a simple diffusive model. To resolve this apparent contradiction between biological complexity and modeling simplicity, we present an investigation into the diffusive nature of bioturbation. To this end, we examine a stochastic description of bioturbation, where particle mixing is described as a sequence of random bioturbation events. Particle movement is governed by three basic variables: the direction of jumping, the jumping distance, and the waiting time between two bioturbation events. A set of gradually more complex random-walk models is constructed by treating these variables consecutively as stochastic. Each time, the conditions are determined under which these random walks generate diffusive behavior. One important criterion is that the tracer should experience a sufficient number of bioturbation events, and so the time scale of observation should be large enough. The full list of conditions needed to arrive at diffusive mixing is different and more extensive than in past examinations of the topic. This analysis clarifies the relation between the biodiffusion model and more sophisticated mixing models, revealing that the conventional distinction between local and nonlocal models is not entirely relevant. Instead, we propose a distinction between “normal“ or “anomalous“ mixing, which is based on the intrinsic nature of the faunal activities causing particle dispersal. Overall, our analysis provides insight into the conditions under which the biodiffusion model can be applied to tracer profiles, and also shows why it sometimes fails, as is the case of sediments dominated by head-down deposit feeders.

Applications of ichnology in lacustrine sequence stratigraphy: Potential and limitations

In comparison with their marine counterparts, lacustrine ichnofaunas have not been extensively used in sequence stratigraphy. Application of trace fossils in continental sequence stratigraphy cannot be based simply on the extrapolation of marine sequence stratigraphy. Marine substrate-controlled ichnofacies, in particular the firmground Glossifungites ichnofacies, develop in stable and cohesive substrates, reflecting erosive exhumation of the sediment. In contrast, in lacustrine sequences, substrate-controlled ichnofossils only rarely indicate erosional exhumation because they are commonly related to desiccation of water bodies. The tripartite division of overfilled, balanced-fill, and underfilled lakes provides a comprehensive framework to evaluate the potential and limitations of lacustrine ichnofaunas in sequence stratigraphy. Based on a number of case studies spanning the three lake-basin types, a model of trace-fossil distribution in overfilled, balanced-fill, and underfilled basins is proposed. Overfilled lake basins contain well-developed softground trace fossils ( Mermia and Skolithos ichnofacies, and the softground suite of the Scoyenia ichnofacies) that are useful to delineate parasequences and parasequence sets. Fluvial discharge into overfilled lakes usually generates density currents that oxygenate lake bottoms, allowing the establishment of epifaunal and infaunal communities. Additionally, these are freshwater lakes where no stress due to hypersalinity occurs, leading to the development of a relatively diverse benthos. Land–plant derived organic matter is the prime source of nutrients, favoring the development of a deposit-feeding benthic fauna in permanently subaqueous, low-energy zones. Firmground suites are rare because such large lakes usually do not experience desiccation. Abundant firmground trace-fossil suites of the Scoyenia ichnofacies occur in balanced-fill lakes, but softground assemblages are usually depauperate. Lowstand deposits contain abundant and widespread ichnofaunas, commonly meniscate trace fossils and arthropod trackways of the Scoyenia ichnofacies. Lake hydrology is closed during lowstands and salinity usually increases, imposing a stress factor on the lake biota and, therefore, softground ichnofaunas are depauperate. Ichnofaunas from turbidite systems in balanced-fill lakes are less abundant and diverse than those from overfilled lacustrine turbidites. Freshwater conditions are common during transgression, but dysaerobic conditions may prevail, imparting a stress factor on the benthic biota. In hydrologically closed lakes, the Scoyenia ichnofacies is widespread, but the Mermia ichnofacies is commonly absent or impoverished. The Scoyenia ichnofacies is associated with lowstand desiccated substrates in underfilled lakes. The density of arthropod trackways may be high, forming tracked omission surfaces. Some of these omission surfaces may represent sequence boundaries expressed by co-planar surfaces of lowstand and subsequent flooding. Rapid changes in depositional conditions reflecting desiccation during vertical aggradation can lead to the formation of composite ichnofabrics that reflect successive bioturbation events.

A generalized stochastic approach to particle dispersal in soils and sediments

We explore a generalized stochastic description for the dispersal of particles in soils and sediments. The model is based on the continuous-time random-walk (CTRW), which enables a very general description of particle mixing due to biological activity. A community of burrowing organisms is characterized by a bioturbation “fingerprint” that consists of two probability distributions. The jump-length distribution describes the distance a particle travels within a given bioturbation event. The waiting-time distribution describes the time interval a particle waits at a given location in between two bioturbation events. Our stochastic analysis provides insight on the applicability of the widely used biodiffusion model, which forms the asymptotic limit of the CTRW model. This asymptotic behaviour of diffusion is always reached, independent of the shape of bioturbation fingerprint, provided that the waiting-time distribution has a finite mean and the jump-length distribution has a finite variance. The biodiffusion coefficient can be decomposed as the variance of the jump-length distribution over the mean of the waiting-time distribution. Since the variance enables a squared weighing of the jump distance, long-range displacements will contribute more to the mixing intensity D b than short-range displacements. Therefore, large macrofauna will contribute disproportionately to the mixing intensity relative to their abundance, as they displace particles over longer distances than smaller organisms. Finally, we review the potential for bioturbation of so-called anomalous transport models where either the mean of the waiting-time distribution or the variance of the jump-length distribution becomes infinite.

A comparison of sediment reworking rates by the surface deposit-feeding bivalve Abra ovata during summertime and wintertime, with a comparison between two models of sediment reworking

Sediment reworking rates by the surface deposit-feeding bivalve Abra ovata were assessed in thin aquaria using an automated image analysis procedure for luminophore tracer particles. Experiments were carried in winter (10 °C) and summer (20 °C), and three food treatments were tested: no food addition (CF), low food addition (LF) and high food addition (HF). The rate of sediment reworking was characterized in four different ways: (1) the maximum penetration depth of luminophores (MPD), (2) the proportion of reworked sediment surface (PRS) from which individual rates of surface area reworking (IRSAR) were derived, (3) the fitting of the standard biodiffusion model resulting in a biodiffusion coefficient D b, and (4) the application of a new non-local bioturbation model that produced an alternative mixing intensity D b NL. In winter, sediment reworking was low and was not affected by food availability. In contrast, during summer, reworking activity was very high and significantly affected by food availability. This suggests that temperature and not food availability controls sediment reworking during wintertime. Although the biodiffusive and non-local models produced similar values for mixing intensities after 48 h, the non-local model gave markedly better fits during the initial stage of the experiment. This agrees nicely with theoretical predictions: over short-time scales the non-local model should provide a more accurate description of bioturbation, but as the number of bioturbation events increases, the non-local model should converge to the biodiffusion one. Yet, an additional advantage of the non-local model is that it allows constraining two crucial parameters characterizing A. ovata bioturbation: the average distance over which particles are displaced (2.1 mm) and the waiting time between two bioturbation events (5.39 h). Accordingly, reworking is characterized by highly frequent and small-scale particle displacement, which makes that A. ovata can be classified as a true biodiffuser.

In situ quantification of bioturbation using time-lapse fluorescent sediment profile imaging (f-SPI), luminophore tracers and model simulation

In order to link actual biological data on bioturbation to the abstract parameters in bioturbation models, high-resolution data on the frequency and lengths of particle displacements are required. The temporal variation in bioturbation for a subtidal macrofaunal assemblage was studied non-invasively and in situ using an optically modified fluorescence sensitive time-lapse sediment profile imaging camera (f-SPI), fluorescent-dyed sediment particles (luminophores) and mathematical modelling. This combined approach allowed tracer particles to be non-invasively tracked and their displacements monitored at an unprecedented spatial (78 µm) and temporal (every 10 min) resolution for extended periods of time (16 h). The redistribution of luminophores was digitally acquired from sequential images and compared to model predictions, with particle transport modelled as (1) a diffusive process, allowing the biodiffusion coefficient, Db, to be estimated, and (2) a non-local process, allowing a reworking activity constant, a, to be calculated. Model predictions of luminophore particle transport for the final image of the f-SPI sequence gave: Db = 1.26 × 102 cm2 yr-1; a = 5.23 × 10-2 cm-1 yr-1. Discrete values of a fluctuated widely throughout the sequence and allowed discrete bioturbation events to be identified. Time-lapse movie sequences revealed that most of the bioturbation observed during the deployment could be directly attributed to the behaviour of the brachyuran crab Hyas araneus. Our findings demonstrate that f-SPI provides a rapid and non-invasive means to visualise and quantify, in situ, the extent and influence of discrete infaunal bioturbation events on particle mixing. This technique provides detailed information on the spatial and temporal resolution of such bioturbation events, which could significantly improve existing models of bioturbation.

OSL ages and possible bioturbation signals at the Upper Paleolithic site of Lagoa do Bordoal, Algarve, Portugal

Three sediment samples were collected from a soil profile at the Lagoa do Bordoal site, Algarve, Portugal. Quartz extracted from soil horizons within the profile, was optically dated using the single-aliquot regenerative-dose (SAR) protocol outlined by Murray and Wintle (Radiation Measurements 5 (2000) 523). The optically stimulated luminescence (OSL) emitted by quartz within the 90–150 μm size range was measured using three aliquot sizes. The equivalent doses ( D E) that were obtained show an asymmetric distribution. As the numbers of grains in each aliquot are reduced, the distribution of doses is clearly shifted to lower D E values including zero doses on single grain aliquots. This shift is accompanied by an increase in the asymmetry of the distribution. These patterns indicate that as the aliquot size decreases, the distributions are increasingly characterized by aliquots with lower D E's. With respect to the present day modern surface, this shift is most evident in the sample collected from a depth of 37 cm, within an ancient B-horizon. It is least evident in the sample located only 10 cm below it, within a sand unit. An asymmetric distribution of D E's can be a result of a large number of grains that were well bleached at burial being mixed with a small number of grains that were partially bleached at that time (Radiation Measurements 30 (1999) 207). However, the shift in D E's that is seen in the Lagoa East samples is most likely due to the postburial downward movement of fully and partially bleached grains from the surface, with possible contributions from the downward movement of grains that received low doses while buried in overlying horizons. The simplest explanation for our results is that grains carrying zero or small D E's have been moved downward during bioturbation events. These results suggest that downward bioturbation in ancient soil profiles can be identified based on the OSL characteristics of quartz grains. We are also able to provide a minimum age of 24.4±3.2 ka for the Upper Palaeolithic lithic assemblage at the site.

Bioturbated oxygenation-event beds in siliceous facies: Monterey Formation (Miocene), California

Predominatly laminated marine diatomaceous sequences deposited in oxygen-deficient Neogene basins typically contain bioturbated intervals that reflect episodes of improved benthic oxygenation. Excellent exposures of the siliceous facies of the Miocene Monterey Formation near Lompoc, central California, provided an opportunity to assess the ichnology and sedimentology of ≈200 such event beds in their general paleogeographic, paleoclimatic and sea-level context and, hence, to evaluate the character and causes of associated oxygenation episodes. Four recurring event-bed types (type I–IV) are distinguished on the basis of ichnologic characteristics. These types fall into two general groups delineated on the basis of sedimentologic attributes, primarily texture. Group 1 beds (type I only) have (1) homogeneous, bioturbate primary strata that are more clastic rich and much coarser than surrounding laminated diatomites, and (2) vertically extensive piped zones characterized by firmground Thalassinoides paradoxicus ( Glossifungites ichnofacies). These characteristics indicate that Group 1 events involve coincident increases in bottom-current intensity, clastic input, and benthic oxygenation. Some Group 1 beds may be the product of turbidity-current transport of sediments, trauma-resistant crustaceans, and allochtonous waters. However, most Group 1 beds more likely record climate- and sea-level-mediated migratio of incipient bank-top conditions down the flank of a submergent topographic high. Group 2 beds (types II, III, and IV) are characterized by primary strata that are only slightly coarser and more clastic-rich than surrounding laminites. Ichnofabrics and trace fossil assemblages, which are dominated by burrows of deposit feeders ( Thalassinoides suevicus, meniscate backfilled structures, and Chondrites, reflect normal softground substrates and quiet-water, pelagic deposition ( Zoophycos ichnofacies). Differences in ichnologic parameters (bed thickness adn presence, diversity, size and vertical extent of discrete burrows in primary strata and/or piped zones) among the bed types within this group reflect differences in magnitude, duration and, to a lesser extent, frequency of oxygenationepisodes. Coincident increases in oxygenation and clastic content recorded by Group 2 beds are attributed to E1 Niño-like climatic events. Gross temporal patterns in the intensity and frequency of these climatic events appear to be linked to the phases of a third-order sea-level cycle, whereas shorter-term variations (100–120 ka) may have been mediated by Milankovitch cyclicity. Relationships established between bioturbation events and relative water depth are of potential use in reconstructing basin paleogeography and/or recognizing the signal of sea-level change in the Monterey Formation and other Neogene siliceous sequences.