Silurian trace fossils in carbonate turbidites from the Alexander arc of southeastern Alaska

Early to Late Silurian (Llandovery‐Ludlow) body and trace fossils from the Heceta Formation of southeastern Alaska are preserved in the oldest widespread carbonates in the Alexander terrane. These fossils represent the earliest benthos to inhabit diverse shallow and deep subtidal environments in the region and are important indicators of early stages in benthic community development within the evolving Alexander arc. The ichnofossils are particularly significant because they add to a small but growing body of knowledge about trace fossils in deep‐water carbonates of Paleozoic age.

Carbonate turbidites that originated along a deep marine slope within the arc yield a low‐diversity suite of trace fossils consisting of five distinct biogenic forms. Simple burrows (Planolites, two forms), ramifying tunnels (Chondrites), and tiny cylindrical burrows (?Chondrites) represent the feeding activities (fodinichnia) of pre‐turbidite animals that burrowed in the lime mud before the influx of coarser sediment deposited by turbidity currents. These trace fossils are associated locally with cross‐cutting burrows created as domichnia (Palaeophycus). Rarer hypichnial burrows and endichnial traces were created by post‐turbidite animals that fed soon after the deposition of coarse detritus from turbidity flows.

Trace fossils in these deposits reflect much lower diversity levels than in Paleozoic siliciclastic turbidites. This difference may represent unfavorable environmental conditions for infaunas, differential preservation, or significant paleogeographic isolation of the Alexander terrane during the Silurian. Greater utilization of trace fossils in terrane analysis may help to resolve this issue and provide new data for reconstructing the paleogeography of circum‐Pacific terranes.     

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite‐associated sediment profiles

The emplacement of subaqueous gravity‐driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro‐organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate‐reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite‐induced changes to the geochemical environment. Species‐level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1‐cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low‐energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.     

Lower Miocene bathyal and submarine canyon ichnocoenoses from Northland, New Zealand

Thalassinidean crustacean remains ( Callianassa ) are recorded from lower Miocene burrow networks belonging to the ichnogenus Thalassinoides . They were produced at mid bathyal depths of 1000–3000 m. Mid to lower bathyal basinal sediments and inferred outer neritic to upper bathyal submarine canyon sediments contain sparse ichnocoenoses composed entirely of feeding and dwelling structures, produced by burrowing polychaetes, echinoids and possibly sipunculoids and also by bivalves escaping burial during rapid sedimentation. These two ichnocoenoses are similar to those of proximal turbidite sequences, and this is considered a response to similar rates of sedimentation, water agitation and coarseness of sediment rather than a similarity in depth. An outer neritic to upper bathyal canyon wall ichnocoenosis was developed in semi-consolidated lutites and arenites by burrowing polychaetes, decapod Crustacea (shrimps and crabs) and possibly amphipods and other organisms. Inclined, but randomly oriented Rhizocorallium occur in the canyon wall, and their presence at these depths is explained by inferred abnormally high water turbulence and abundant suspended food matter as well as a favourable semi-consolidated lutite substrate.     

The Ichnofossils of the Triassic Hope Bay Formation,Trinity Peninsula Group,Antarctic Peninsula

The Triassic Hope Bay Formation (Trinity Peninsula Group) includes a diverse ichnocoenosis in the Puerto Moro succession (Hope Bay, Antarctic Peninsula). The Hope Bay Formation is a thick turbidite succession with a minimum vertical exposure of 533 meters along the Hope Bay coast. The rocks are locally affected by contact metamorphism related to later arc magmatism. The ichnofossils are found mainly in thick- and thin-bedded sandstone-mudstone facies composed of a monotonous repetition of sandstone-mudstone cycles. The sandstones are usually medium grained, massive or parallel laminated; the mudstones are massive and rarely laminated. In the fine-grained rocks, mainly the mudstones, there are distinct densities of bioturbation, and at least six patterns were observed. The following ichnogenera were recognized: Arenicolites Salter 1857, Lophoctenium Richter 1850, Taenidium Heer 1877, Palaeophycus Hall 1847, Phycosiphon von Fischer-Ooster 1858 and Rhizocorallium Zenker 1836. All appear to be feeding-traces. The trace fossil assemblages occur mainly in black mudstones rich in organic material that suggest a low oxygen environment. The stratigraphic interval in which they occur is interpreted as progradational supra-fan lobes with channel fill and levee deposits. The thin-bedded turbidite and mudstone lithofacies, where the ichnofossils are abundant, is interpreted as a distal fan turbidite or levee deposit related to a long-term channel fill. This study is the first significant report of trace fossils in the Hope Bay Formation.     

Colonization of sulfide‐oxygen interfaces on hot spring tufa by Thermothrix thiopara

Cream‐colored streamers of Thermothrix thiopara were found at the sulfide‐oxygen interfaces of active tufa mounds where reducing geothermal groundwaters mixed with the oxidizing atmosphere. In the Jemez hot springs, the molar ratio of sulfide to oxygen was 0.3 to 0.8 at streamer locations within the interface. This corresponded to the optimum stoichiometric proportion (0.5) necessary for sulfur metabolism. The mechanism of cell positioning at the interface was studied by shifting the interface location with a plastic cover to extend reducing conditions from the mouth of the spring to the edge of the plastic. Macroscopically visible streamers of filamentous cells became established at the new interface within a period of eight days. They could then be reestablished at the original interface by removing the cover.

Calcite crystals, pyrite crystals, and membrane enrichment vials were incubated on both sides of the interface and the kinetics of colonization determined. The preferential attachment of rod‐shaped cells to pyrite appeared to be the mechanism by which cells located themselves where pyrite occurred in situ, upstream from the interface. The formation of filamentous cells from rod‐shaped cells was induced by oxygen‐limited growth conditions. This moved the cells slightly downstream and directly within the interface.     

Intrastratal trace fossil zonation,Cretaceous flysch of northern California

Dissection of fine‐grained turbidites within the Franciscan complex at Trinidad Harbor reveals intrastratal zonation of biogenic structures. The pre‐depositional association comprises only three ichnotaxa (preserved in convex hyporelief) and is less diverse than the tiered post‐depositional association (comprised by at least seven ichnotaxa preserved in full relief). The latter association is dominated by Melatercichnus (n. ichnogen.). Post‐depositional trace‐makers exploited abundant plant detritus deposited with the turbidite sand. Temporal alternation of trace fossil associations resulted from the infrequent, but catastrophic, disturbance of pre‐turbidite communities and local replacement by assemblies of opportunistic organisms. Although probably short‐lived at specific sites, the post‐turbidite infauna was tiered, enabling a variety of deposit feeders to harvest phytodetritus of varied size or density simultaneously at different depths within newly deposited turbidite sand layers.     

First Record of Graphoglyptids in Cyprus: Indicative Presence of Turbidite Deposits at the Pakhna Formation

Abstract

Ichnological analysis at the Pakhna Formation (Miocene, Cyprus) reveals, for the first time, the presence of graphoglyptid structures. The Pakhna Formation is dominated by pelagic/hemipelagic sediments, together with contourite, reworked turbidite and turbidite facies. Thus, a complex interaction between pelagic, bottom-current and gravitational sedimentation is envisaged. The discernment of facies is sometimes difficult, based principally on stratigraphic and microfacies features. The record of Helminthorhaphe as a component of the graphoglytid group supports the presence of turbidites, facilitating their differentiation from the other facies. Nereites ichnofacies, punctuating a dominant/background Zoophycos ichnofacies, would reflect changes in paleoenvironmental conditions. This record offers significant perspectives to advance in the study of bottom-current and gravitational processes through outcrop examples.     

Microaerobic conditions enhance type III secretion and adherence of enterohaemorrhagic Escherichia coli to polarized human intestinal epithelial cells

Advances in the understanding of the pathogenesis of enterohaemorrhagic Escherichia coli (EHEC) have greatly benefited from the use of human epithelial cell lines under aerobic conditions. However, in the target site of EHEC infection, the human intestine, conditions are microaerobic. In our study we used polarized human colon carcinoma cells in a vertical diffusion chamber system to investigate the influence of reduced apical oxygen levels on EHEC colonization. While apical microaerobiosis did not affect cell integrity and barrier function, numbers of adherent bacteria were significantly increased under low compared with high apical oxygen concentrations. In addition, expression and translocation of EHEC type III secreted (T3S) effector proteins was considerably enhanced under microaerobic conditions and dependent on the presence of host cells. Increased colonization was mainly mediated via EspA as adherence levels of an isogenic deletion mutant were not influenced by low oxygen levels. Other potential adherence factors (E. coli common pilus and flagella) were only minimally expressed under high and low oxygen levels. Addition of nitrate and trimethylamine N‐oxide as terminal electron acceptors for anaerobic respiration failed to further increase bacterial colonization or T3S under microaerobiosis. This study indicates that EHEC T3S and colonization are enhanced by the microaerobic environment in the gut and therefore might be underestimated in conventional aerobic cell culture systems.     

Trace fossils in middle to late triassic fluvial redbeds,pranhita‐godavari valley,south India

Several morphological varieties of trace fossils abound in Middle and Late Triassic fluvial redbeds in the Pranhita‐Godavari Valley, south India, including Skolithos, Palaeophycus, Taenidium, escape burrows, and a type of trace very similar to ‘small stuffed burrows’ from the Triassic of Greenland. Burrow morphology was influenced by local hydrodynamic conditions. The distribution of burrows was facies controlled; some forms are restricted to channel deposits whereas others occur only in floodplains. Vertical dwelling burrows (Skolithos) occur in both channel and floodplain deposits. Horizontal structures representing deposit feeding (Taenidium) are confined to nondepositional surfaces within parallel‐laminated sandstones having parting lineations that represent catastrophically emplaced sand‐sheets in channels and proximal floodplains. Vertical escape burrows are confined to what were slowly but continually accreting parallel‐laminated sands of channel bars. Horizontal dwelling burrows (Palaeophycus) and ‘small stuffed burrows’ are virtually restricted to the smaller sandsheets of floodplain drainage systems.

The burrow assemblages do not occur as recurrent associations throughout the redbed sequence, and variations in different stratigraphic levels seem to be controlled by minor differences within a broadly similar environment. The entire assemblage has components of both the Scoyenia and Rusophycus ichnocoenoses reported from East Greenland but may be considered as the Scoyenia ichnofacies characteristic of redbeds deposited in extensive floodplains dissected by small streams, even though no Scoyenia individuals are present.     

The influence of environmental factors on the rate and extent of stainless steel ennoblement mediated by manganese‐oxidizing biofilms

The increase in the open circuit potential of passive metals in natural waters due to biofilm formation at the metal surface, termed ennoblement, has been reported for nearly 30 years. Although its occurrence is undoubtedly associated with microbial colonization, the underlying mechanism of ennoblement remains controversial. Recent work produced in the authors’ laboratory has provided convincing experimental evidence that ennoblement can be caused by deposition of biomineralized manganese produced by manganese‐oxidizing biofilms. The purpose of this study was to determine the effects of environmental factors on the rate and extent of ennoblement of 316L stainless steel exposed to natural waters. This was accomplished by exposing corrosion coupons to four freshwater systems over a 4‐yearperiod. The rate and extent of ennoblement observed in these locations was correlated with dissolved manganese concentrations, the mass of accumulated manganese oxides, organic carbon concentration, dissolved oxygen concentration, flow, conditions, temperature, and pH in these environments.     

Tolerance to oxidative stress is required for maximal xylem colonization by the xylem‐limited bacterial phytopathogen,Xylella fastidiosa

Bacterial plant pathogens often encounter reactive oxygen species (ROS) during host invasion. In foliar bacterial pathogens, multiple regulatory proteins are involved in the sensing of oxidative stress and the activation of the expression of antioxidant genes. However, it is unclear whether xylem‐limited bacteria, such as Xylella fastidiosa, experience oxidative stress during the colonization of plants. Examination of the X. fastidiosa genome uncovered only one homologue of oxidative stress regulatory proteins, OxyR. Here, a knockout mutation in the X. fastidiosa oxyR gene was constructed; the resulting strain was significantly more sensitive to hydrogen peroxide (H₂O₂) relative to the wild‐type. In addition, during early stages of grapevine infection, the survival rate was 1000‐fold lower for the oxyR mutant than for the wild‐type. This supports the hypothesis that grapevine xylem represents an oxidative environment and that X. fastidiosa must overcome this challenge to achieve maximal xylem colonization. Finally, the oxyR mutant exhibited reduced surface attachment and cell–cell aggregation and was defective in biofilm maturation, suggesting that ROS could be a potential environmental cue stimulating biofilm development during the early stages of host colonization.     

Cinnamic,myristic and fumaric acids in tobacco root exudates induce the infection of plants by Ralstonia solanacearum

Aim

The secretion of allelochemicals from plant roots plays a key role in soil sickness and soil-borne disease. The goal of this study was to investigate the role of allelopathic chemicals in Ralstonia solanacearum-infected tobacco roots.

Methods

The organic acids investigated in the present study are major components of tobacco root exudates. Through a swarming assay, we assessed the chemotaxis and colonization of R. solanacearum in response to organic acids.

Results

Fumaric acid was detected, and the results showed that this acid could serve as a semiochemical for attracting R. solanacearum and inducing the formation of biofilms of this species. The results also revealed that cinnamic and myristic acids play significant roles on swarming motility and chemotaxis. In addition, cinnamic, myristic and fumaric acids could enhance the expression of chemotaxis- and motility-related genes in R. solanacearum cultured in minimal medium. Furthermore, these three acids promote R. solanacearum colonization and accelerate disease progression in tobacco.

Conclusion

Cinnamic, myristic and fumaric acids could serve as semiochemical attractants to induce the colonization and infection of R. solanacearum. The results of the present study enhance our understanding of the ecological effects of plant root exudates in plant-microbe interactions and help to reveal the relationship between tobacco bacterial wilt and the autotoxins and allelochemicals that accumulate from root exudates.

     

Fungal and Bacterial Colonization of Submerged Leaf Litter in a Mediterranean Stream

Microbial colonization dynamics of fungi and bacteria were analyzed in an intermittent Mediterranean forested stream using two different leaf substrata (Platanus acerifolia and Populus nigra). Results showed that fungal and bacterial biomass accumulation was stimulated on both leaves due to a flooding episode that increased dissolved inorganic nitrogen (DIN) and dissolved oxygen (DO) availability in the stream water. Leaf mass loss coincided with the parallel increase in microbial biomass and extracellular enzymatic activities after the flood event. Differences in litter quality favoured bacterial biomass accumulation and β‐glucosidase and cellobiohydrolase enzymatic activities in the soft Populus species. Microbial heterotrophs colonization of submerged leaf litter and organic matter use in Mediterranean‐type streams are modulated by environmental conditions, especially the hydrological variability. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The spread of the Collared Dove Streptopelia decaocto in Europe: colonization patterns in the west of the Iberian Peninsula

Capsule The pattern and timing of spread are examined, particularly in Extremadura, and theories on speed and extent of spread and possible competition with related species are discussed.

Aims To describe the present pattern of the spread of the Collared Dove in one of the few areas in Europe where the process is still active, in the light of the hypothesis of general expansion in Europe.

Methods Information was obtained from field data collected in 1996–97 and from responses by local observers to a questionnaire. We recorded data on the presence in localities, numbers of birds, extent of colonization, date the first birds were sighted, and confirmed nesting.

Results The first settlements in Extremadura were observed less than ten years ago. The timing indicates that the process of expansion in Extremadura is now at a stage of full development, enabling us to study the mechanism involved. The colonization shows a clear northwest–southeast direction to the interior from coastal areas of Iberia. The species first established itself in urban-areas, from which it slowly but steadily expanded towards rural areas.

Conclusions The expansion of the species has been very rapid, and is still active in Extremadura. The colonization pattern shows a clear directionality (northwest–southeast), beginning with urban nuclei, followed by expansion into rural areas.     

Cretaceous Nonmarine Trace Fossils from the Hasandong and Jinju Formations of the Namhae Area,Kyongsangnamdo, Southeast Korea

Nonmarine strata of the Cretaceous Hasandong and Jinju formations of the Sindong Group of the Namhae area, Kyongsangnamdo, southeast Korea, contain relatively diverse and abundant ichnofaunas including domichnia, fodinichnia, pascichnia, and repichnia. These ichnofaunas are systematically described herein and three ichnocoenoses, namely the Skolithos, Palaeophycus, and Chondrites ichnocoenoses, are defined based on their paleoenvironmental occurrence. The Skolithos ichnocoenose characterizes tabular laminated sandstone facies deposited on fluvial channel levées. It is dominated by infaunally produced ichnotaxa, particularly Skolithos magnus Howell, Planolites montanus Richter and Chondrites isp. type A, with reduced numbers of Skolithos verticalis (Hall) Taenidium barretti (Bradshaw) and rare examples of Circulichnus montanus (Vyalov), Cochlichnus anguineus Hitchcock, Helminthopsis abeli Ksi??kiewicz, Helimthopsis hieroglyphica Wetzel and Bromley, Laevicyclus isp., Planolites beverleyensis (Billings), Skolithos isp., Spirodesmos isp., Thalassinoides suevicus (Rieth), and rhizoliths. The Palaeophycus ichnocoenose characterizes floodplain environments and occurs in purple mudstones and associated massive sandstone facies of crevasse-splay deposits and dark gray to green shale facies of abandoned channels. Palaeophycus tubularis Hall and Planolites montanus Richter are the most characteristic ichnotaxa, while Beaconites coronus (Frey, Pemberton and Fagerstrom), Planolites annularius Walcott, Skolithos magnus Howell, Thalassinoides paradoxicus (Woodward), and sauropod and ornithopod tracks also occur but in reduced numbers. The Chondrites ichnocoenose occurs in dark gray to black mudstones deposited in marginal lacustrine environments. It is dominated by Chondrites isp. type B. with associated Beaconites antarcticus Vyalov, Helminthopsis hieroglyphica, Palaeophycus tubularis, Skolithos magnus, Taenidium barretti, and Torrowangea rosei Webby. The three ichnocoenoses recognized herein cannot be satisfactorily assigned to currently defined nonmarine ichnofacies, suggesting that existing models of such ichnofacies are in need of additional refinement.     

Short‐term effect of hypoxia on ammonia excretion and respiration rates in the crab carcinus maenas

The metabolic response of the crab Carcinus maenas to short‐term hypoxia (60% and 35% saturated seawater) was studied at 17.5°C in fed, 3 day‐unfed and 6 day‐unfed crabs.

Ammonia excretion rate decreased under hypoxia: a 40% and 45% decrease in the normoxic rate was observed in fed crabs at 35% saturation and in 3 day‐unfed crabs at both hypoxic levels respectively. In the 6 day‐unfed crabs, the effect of hypoxia was concealed by the effect of starvation.

Oxygen consumption rate was directly related to the external O₂ tension irrespective of the crab's nutritional state. Stressed crabs behaved as a whole, as oxygen‐conformers.

A strong relationship was observed between ammonia excretion and oxygen consumption rates in fed crabs under hypoxia but not in starved crabs.     

Salicylic acid prevents Trichoderma harzianum from entering the vascular system of roots

Trichoderma is a soil‐borne fungal genus that includes species with a significant impact on agriculture and industrial processes. Some Trichoderma strains exert beneficial effects in plants through root colonization, although little is known about how this interaction takes place. To better understand this process, the root colonization of wild‐type Arabidopsis and the salicylic acid (SA)‐impaired mutant sid2 by a green fluorescent protein (GFP)‐marked Trichoderma harzianum strain was followed under confocal microscopy. Trichoderma harzianum GFP22 was able to penetrate the vascular tissue of the sid2 mutant because of the absence of callose deposition in the cell wall of root cells. In addition, a higher colonization of sid2 roots by GFP22 compared with that in Arabidopsis wild‐type roots was detected by real‐time polymerase chain reaction. These results, together with differences in the expression levels of plant defence genes in the roots of both interactions, support a key role for SA in Trichoderma early root colonization stages. We observed that, without the support of SA, plants were unable to prevent the arrival of the fungus in the vascular system and its spread into aerial parts, leading to later collapse.     

Calcite and dolomite dissolution rates in the context of microbe–mineral surface interactions

Although microbes have been shown to alter the dissolution rate of carbonate minerals, a mechanistic understanding of the consequences of microbial surface colonization on carbonate dissolution has yet to be achieved. Here we report the use of vertical scanning interferometry (VSI) to study the effect of Shewanella oneidensis MR‐1 surface colonization on the dissolution rates of calcite (CaCO₃) and dolomite (CaMg(CO₃)₂) through qualitative analysis of etch pit development and quantitative measurements of surface‐normal dissolution rates. By quantifying and comparing the significant processes occurring at the microbe–mineral interface, the dominant mechanism of mineral dissolution during surface colonization was determined. MR‐1 attachment under aerobic conditions was found to influence carbonate dissolution through two distinct mechanistic pathways: (1) inhibition of carbonate dissolution through interference with etch pit development and (2) excavation of carbonate material at the cell–mineral interface during irreversible attachment to the mineral surface. The relative importance of these two competing effects was found to vary with the solubility of the carbonate mineral studied. For the faster‐dissolving calcite substrates, inhibition of dissolution by attachment and subsequent extracellular polysaccharide (EPS) production was the dominant effect associated with MR‐1 surface colonization. This interference with etch pit development resulted in a 40–70% decrease in the surface normal dissolution rate relative to cell‐free controls, depending primarily on the concentration of cells in solution. However, in the case of the slower‐dissolving dolomite substrates, carbonate material displaced during the entrenchment of cells on the surface far outweighed the abiotic dissolution rate. Therefore, during the initial stages of surface colonization, dolomite dissolution rates were actually enhanced by MR‐1 attachment. This study demonstrates the dynamic and competitive relationship between microbial surface colonization and mineral dissolution that may be expected to occur in natural environments.