Exploring computed tomography in ichnological analysis of cores from modern marine sediments

Ichnological analysis is considered a very useful tool in several disciplines of Earth Sciences, including palaeoenvironmental studies and hydrocarbon exploration. Sediment cores provide excellent records, despite difficulties encountered during study runs due to specific core features. Previous studies using 2D images have proven the benefits of high-resolution image treatment in improving the visibility of ichnological features, but with limitations. 3D computed tomography (CT) techniques were applied to palaeoichnological studies in lithified cores and other disciplines of palaeontology to solve these limitations, but not used for ichnological studies in unconsolidated sediments due to the low density contrast between host sediment and trace fossils. In this study, a CT processing technique, previously tested in coral research, is applied to facilitate the characterisation of the ichnological signature of cores from modern marine soft sediments. This technique allows for the first time the isolation of burrows within these kinds of sediments and the differentiation of intervals based on burrow orientation. Data obtained from the technique are complemented with the ichnological information from conventional core description, thus providing a more complete characterisation of the trace fossil assemblage with additional ichnological properties such as burrow orientation and branching. This will improve palaeoenvironmental interpretations related to changes in energy or oxygenation, and the analysis of reservoir quality given the impact of burrows on porosity and permeability. Therefore, adopting CT to complement visual core description in the ichnological analysis of soft modern marine cores is a very informative approach.This work is supported by the Spanish Government [Project CGL2015-66835-P, Secretaría de Estado de I + D + I], Andalusian Government [Research Groups RNM-178 and RNM-276], and University of Granada [Scientific Excellence Unit UCE-2016-05]. The research of J.D. is financed by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant Agreement No. 792314 (ICON-SE)

Trace fossil characterization during Termination V and MIS 11 at the western Mediterranean: Connection between surface conditions and deep environment

This study was supported by the predoctoral FPU contract FPU17/03349 awarded to A. Gonzalez-Lanchas by the Spanish Ministry of Sci-ence, Innovation and Universities. The research by JD was funded through the Juan de la Cierva Program (IJC2019-038866-I) by the Spanish Ministry of Science and Innovation. Essential financial infra-structure was provided by the programs RTI2018-099489-B-100 of the Spanish Ministry of Science, Innovation and Universities granted to GGO (Grupo de Geociencias Oceanicas de la Universidad de Salamanca) and CGL2015-66835-P and PID2019-104625RB-100 of the Spanish Ministry of Science, Innovation and Universities and B-RNM-072-UGR18, P18-RT-4074 of the Andalusian Government granted to Ichnology and Palaeoenvironment RG (University of Granada) . We thank Alessandra Negri and the two anonymous reviewers, whose comments contributed to improve this manuscript.Trace fossil assemblages are studied at Ocean Discovery Program (ODP) Site 977 to characterize the response of the macrobenthic trace maker community to deep paleoenvironmental conditions during the Termination V (TV) and interglacial Marine Isotope Stage (MIS) 11 at the western Mediterranean Alboran Sea. An assemblage composed of Chondrites, Planolites, Scolicia, Thalassinoides and Zoophycos is identified, showing notable variations in ichnodiversity, abundance and Bioturbation Index, that were analyzed in detail. The integration of ichnological information with sediment color and high-resolution coccolithophore records from Site 977, evidenced that variations in macrobenthic trace maker community are primarily controlled by oxygen availability and surface organic productivity patterns. During TV, high surface organic productivity by intense Alboran Upwelling System enhanced the deep organic accumulation that, together with reduced deep-water removal, resulted in a decrease of bioturbation and the formation of an Organic Rich Layer. Moderate and stable surface production through MIS 11c reduced deep food availability, resulting in an oligotrophic and stable deep environment. This is reflected by relatively abundant trace fossils in lighter sediments. Intra-interglacial increase in surface organic production at ~405 ka is evidenced by increased organic matter preservation. Minor impact of western Mediterranean circulation on deep-water removal, but a plausible stronger control by Bernoulli aspiration intensities in the region, is, in overall, observed during these intervals. During the Heinrich-type (Ht) events 3 and 2, increased trace fossil diversity and ameliorated oxygenation is driven by limited surface organic production, but intense western Mediterranean deep-water circulation and enhanced regional deep-water removal.Spanish Government FPU17/03349Juan de la Cierva Program by the Spanish Ministry of Science and Innovation IJC2019-038866-ISpanish Government RTI2018-099489-B-100 CGL2015-66835-P PID2019-104625RB-100Andalusian Government B-RNM-072-UGR18 P18-RT-407

Introducing Fiji and ICY image processing techniques in ichnological research as a tool for sedimentary basin analysis

Some features of trace fossils are not easy to determine due to limited vissibility of trace fossils. Here, we applied two image processing techniques (Fiji and ICY) to ichnological studies and we compare them with the previously used high-resolution image treatment method. , discussing their usefulness for ichnological studies. Then, these are compared with a high resolution image treatment. These techniques are revealed as rapid alternatives for estimation of some ichnological features, being so useful for the first stages of research, when a detailed analysis is not needed

Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance

Indexación: Web of Science; Scopus.The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.http://journal.frontiersin.org/article/10.3389/fmicb.2017.00456/ful

The puzzling influence of Ophiomorpha (trace fossil) on reservoir porosity: X-ray microtomography analysis

Bioturbation can influence petrophysical properties (e.g., porosity, permeability) of sedimentary rocks and, in consequence, reservoir quality. The impact can be positive, negative, or neutral, requiring detailed ichnological analysis. Ophiomorpha, a branched cylindrical burrow with diagnostic peloidal wall, may be present in bioturbated reservoirs that exhibit properties of both superpermeability and reduced porosity/permeability. However, no mechanistic understanding of how Ophiomorpha positively or negatively impacts petrophysical properties has yet been established. This study presents highresolution X-ray microtomographic analysis of how the features of Ophiomorpha (i.e., peloidal wall vs. burrow fill) influence porosity distribution in deep-water deposits (Neogene Tabernas Basin, SE Spain). The results show that the peloidal burrow wall exhibits the lowest porosity (up to six orders of magnitude lower than burrow fill or host sediment), while surrounding sediment shows variable values. Abrupt porosity changes within the fill material likely relate to burrow-associated diagenesis. A refined understanding of the features of Ophiomorpha and their associated porosity distribution help to constrain understanding of their diverse impacts on reservoir properties.MCIN/AEI PID 2019-104625RB100FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento/Projects P18RT-4074 B-RNM-072-UGR18 A-RNM-368-UGR20 PPJIA2021-07Junta de Andalucia RNM-178Universidad de Granada UCE-2016-05 University of GranadaHumboldt Postdoctoral FellowshipMinistry of Science and Innovation, Spain (MICINN) IJC 2019038866-

Determinants of copper resistance in Acidithiobacillus ferrivorans ACH isolated from the Chilean altiplano

Indexación; Scopus.The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0–800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/2073-4425/11/8/84