Earthworm Cast Formation and Development: A Shift From Plant Litter to Mineral Associated Organic Matter

Earthworms play a major role in litter decomposition, in processing soil organic matter and driving soil structure formation. Earthworm casts represent hot spots for carbon turnover and formation of biogeochemical interfaces in soils. Due to the complex microscale architecture of casts, understanding the mechanisms of cast formation and development at a process relevant scale, i.e., within microaggregates and at the interface between plant residues, microorganisms and mineral particles, remains challenging. We used stable isotope enrichment to trace the fate of shoot and root litter in intact earthworm cast samples. Surface casts produced by epi-anecic earthworms (Lumbricus terrestris) were collected after 8 and 54 weeks of soil incubation in mesocosms, in the presence of 13C-labeled Ryegrass shoot or root litter deposited onto the soil surface. To study the alteration in the chemical composition from initial litter to particulate organic matter (POM) and mineral-associated organic matter (MOM) in cast samples, we used solid-state 13C Nuclear Magnetic Resonance spectroscopy (13C-CPMAS-NMR) and isotopic ratio mass spectrometry (EA-IRMS). We used spectromicroscopic approach to identify plant tissues and microorganisms involved in plant decomposition within casts. A combination of transmission electron microscopy (TEM) and nano-scale secondary ion mass spectrometry (NanoSIMS) was used to obtain the distribution of organic carbon and δ13C within intact cast sample structures. We clearly demonstrate a different fate of shoot- and root-derived organic carbon in earthworm casts, with a higher abundance of less degraded root residues recovered as particulate organic matter on the short-term (8 weeks) (73 mg·g−1 in Cast-Root vs. 44 mg·g−1 in Cast-Shoot). At the early stages of litter decomposition, the chemical composition of the initial litter was the main factor controlling the composition and distribution of soil organic matter within casts. At later stages, we can demonstrate a clear reduction of structural and chemical differences in root and shoot-derived organic products. After 1 year, MOM clearly dominated the casts (more than 85% of the total OC in the MOM fraction). We were able to highlight the shift from a system dominated by free plant residues to a system dominated by MOM during cast formation and development

From rhizosphere to detritusphere – Soil structure formation driven by plant roots and the interactions with soil biota

Roots and the associated soil directly affected by root activity, termed the rhizosphere, have both been extensively studied and recognized for their crucial role in soil functioning. The formation of the rhizosphere is primarily driven by the effect of roots on shaping the physical structure of the soil, which in turn has direct feedbacks on the interactions between physical, biological and chemical processes. As a result, the rhizosphere is a hot spot for microbial activity, cycling of nutrients and turnover of organic matter. Despite the pivotal role of soil structure in controlling rhizosphere processes, we still lack a quantitative description and understanding of the interrelationships of root-systems and soil in the creation and stabilization of soil structure. We provide a comprehensive review of current knowledge and novel insights into processes that drive the formation and stabilization of soil structure in the rhizosphere. These processes are regulated by multiple indirect and direct pathways, involving root growth, the production of rhizodeposits and root hairs, as well as the activity of soil microorganisms and fauna. Further, we highlight that rhizosphere processes may persist and evolve after root death to an extent currently largely unknown. Finally, we identify five pertinent challenges that should be addressed to fully apprehend rhizosphere processes and thus harness the potential resilience of plant-soil interactions. These challenges include refining structural assessment and sampling of rhizosheaths, examining the rhizosphere in-situ and bridging the gap between solid phase and pore scale research. In our view, overcoming these obstacles can be accomplished by combining the power of imaging and isotopic approaches, especially at the field scale, encompassing diverse soils and plant species. The ultimate objective of future research should be to upscale rhizosphere processes by conducting more field experiments in concert with modeling efforts, under the umbrella of collaborative interdisciplinary research

Dead wood gathering among Neanderthal groups: Charcoal evidence from Abric del Pastor and El Salt (Eastern Iberia)

We present here a new approach combining the microscopic characterization of fungal decay features and the fragmentation degree of the charcoal remains from Middle Palaeolithic combustion structures: features H4 and H11 from Abric del Pastor, unit IV (>75 ka BP) and features H50 and H57 from El Salt, unit Xb (ca. 52 ka BP), Eastern Iberia. The observation of wood degradation patterns that occurred prior to charring followed by their quantitative analysis according to previous experimental studies revealed differences between the alteration degrees of the firewood used in the hearths, highlighting the existence of firewood acquisition criteria based on dead wood gathering and also suggesting smoke-related functions. Coupled with fragmentation analyses, this method highlighted possible post-depositional processes affecting the higher degraded charcoals. These results lead us to propose a quantitative analysis of the fungal decay patterns on Middle Palaeolithic charcoal reinforcing the previous hypotheses about dead wood gathering among Neanderthal groups as an accessible and available resource in the surroundings. These data have significant implications for the interpretation of firewood use and management by Palaeolithic hunter-gatherers which was traditionally defined as an opportunistic activity according to the absence of selection criteria based on specific taxa

Earliest evidence of pollution by heavy metals in archaeological sites

Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called "Anthropocene". According to its heavy metal concentration, these sediments meet the present-day standards of "contaminated soil". Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence.Francisco J. Jiménez Palacios and to the Analytical Chemistry Department (Sevilla University) are gratefully acknowledged for their help in the use of Carbolite electric oven. A.G.-A. was supported by a Marie Curie Intra-European Fellowship of the 7th Framework Programme for Research, Technological Development and Demonstration (European Commission). R.B. is a Beatriu de Pinós-A post-doctoral fellowship recipient (Generalitat de Catalunya and COFUND Marie Curie Actions, EU-FP7). This work also was partially financed by projects 19434/PI/14 Fundación Séneca, HARP2013-44269P, , CGL2012-38434-C03-03 and CGL2012-38358 Ministerio de Economía y Competitividad, 2014 SGR 900 and 2014/100573 Generalitat de Catalunya-AGAUR, RNM 432 Research Group 179 (Junta de Andalucia) and MEXT-Japan

Bypass and hyperbole in soil science:A perspective from the next generation of soil scientists

International audienceWe, the co‐authors of this letter, are an international group of soil scientists at early career stages, from PhD students to postdoctoral researchers, lecturers, and research fellows with permanent positions. Here, we present our collective musings on soil research challenges and opportunities and, in particular, the points raised by Philippe Baveye (Baveye, 2020a, 2020b) and Johan Bouma (Bouma, 2020) on bypass and hyperbole in soil science. Raising awareness about these issues is a first and necessary step. To this end, we would like to thank Philippe Baveye and Johan Bouma for initiating this debate.......

Earliest evidence of pollution by heavy metals in archaeological sites

Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called “Anthropocene”. According to its heavy metal concentration, these sediments meet the present-day standards of “contaminated soil”. Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence.Francisco J. Jiménez Palacios and to the Analytical Chemistry Department (Sevilla University) are gratefully acknowledged for their help in the use of Carbolite electric oven. A.G.-A. was supported by a Marie Curie Intra-European Fellowship of the 7th Framework Programme for Research, Technological Development and Demonstration (European Commission). R.B. is a Beatriu de Pinós-A post-doctoral fellowship recipient (Generalitat de Catalunya and COFUND Marie Curie Actions, EU-FP7). This work also was partially financed by projects 19434/PI/14 Fundación Séneca, HARP2013-44269P, CGL-BOS-2012-34717, CGL2012-38434-C03-03 and CGL2012-38358 Ministerio de Economía y Competitividad, 2014 SGR 900 and 2014/100573 Generalitat de Catalunya-AGAUR, RNM 432 Research Group 179 (Junta de Andalucia) and MEXT-Japan

Early atmospheric metal pollution provides evidence for Chalcolithic/Bronze Age mining and metallurgy in Southwestern Europe

Although archaeological research suggests that mining/metallurgy already started in the Chalcolithic (3rd millennium BC), the earliest atmospheric metal pollution in SW Europe has thus far been dated to ~ 3500–3200 cal. yr. BP in paleo-environmental archives. A low intensity, non-extensive mining/metallurgy and the lack of appropriately located archives may be responsible for this mismatch. We have analysed the older section (> 2100 cal. yr. BP) of a peat record from La Molina (Asturias, Spain), a mire located in the proximity (35–100 km) of mines which were exploited in the Chalcolithic/Bronze Age, with the aim of assessing evidence of this early mining/metallurgy. Analyses included the determination of C as a proxy for organic matter content, lithogenic elements (Si, Al, Ti) as markers of mineral matter, and trace metals (Cr, Cu, Zn, Pb) and stable Pb isotopes as tracers of atmospheric metal pollutionThis work was funded by the projects CGL2010-20672 and HAR2008-06477-C03-03/HIST (Plan Nacional I + D + i, Spanish Ministerio de Economía y Competitividad), 10PXIB200182PR (General Directorate of I + D, Xunta de Galicia), and CDS-TCP (CSD2007-00058, Programa Consolider-Ingenio 2010). We are grateful to José Antonio López-Sáez, Fernando Gil Sendino, Carmen Fernández Ochoa and Roberto Zapico for their collaboration and assistance during the fieldwork, to José Rodríguez Racedo for helping with the geochemical analyses, and to Suzanne Leroy for perceptive comments on an earlier draftS

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead