Assessing the role of soil chemoautotrophs in carbon cycling: An investigation into isotopically labelled soil microorganisms

Recently observed increases in atmospheric CO2 have created great interest in carbon capture technologies and natural sinks of this major component of the carbon cycle. Humic substances are a large, operationally defined fraction of soil organic matter. It was thought that humic substances consist of cross-linked macromolecular structures forming a distinct class of compounds. However, it was recently concluded by members of my research group that the vast majority of humic material in soils, are a complex mixture of microbial/plant biopolymers and degradation products, and not a distinct chemical category. The postulation that microbial inputs to soil carbon are greatly underestimated was put forward by my research group in 2007. Therefore, I have attempted to demonstrate the inputs made by soil chemoautotrophic bacteria. A method was developed where soil samples were measured for chemoautotrophic activity by subjecting them to a suite of scientific techniques. A growth chamber was used to propagate extant soil chemoautotrophic bacteria from different soils and subjected to an array of chemical and biological analyses. The growth chamber was used to measure CO2 concentrations and introduce stable isotopic 13CO2. Estimations of CO2 sequestration were made using direct measurements for Irish soils and one Eurasian soil. Isotope labelled DNA was isolated using cesium chloride gradient ultracentrifugation. The dominant chemoautotrophic bacteria uncovered were Thiobacillus denitrificans and Thiobacillus thioparus. Labelled biomass was isolated and described using GCMS-IRMS and NMR, where an array of PLFAs, protein/peptide, carbohydrates and aliphatics were observed. Finally, an attempt to mimic common agricultural practice was performed to measure soil chemoautotrophic activity. This demonstrated the capability of this approach to benefit carbon flux estimations and hopefully in the future help to elucidate carbon flow into soils for the greater environment

Composition of dissolved organic matter within a lacustrine environment

Freshwater dissolved organic matter (DOM) is a complex mixture of chemical components that are central to many environmental processes, including carbon and nitrogen cycling. However, questions remain as to its chemical characteristics, sources and transformation mechanisms. Here, we employ 1- and 2-D nuclear magnetic resonance (NMR) spectroscopy to investigate the structural components of lacustrine DOM from Ireland, and how it varies within a lake system, as well as to assess potential sources. Major components found, such as carboxyl-rich alicyclic molecules (CRAM) are consistent with those recently identified in marine and freshwater DOM. Lignin-type markers and protein/peptides were identified and vary spatially. Phenylalanine was detected in lake areas influenced by agriculture, whereas it is not detectable where zebra mussels are prominent. The presence of peptidoglycan, lipoproteins, large polymeric carbo- hydrates and proteinaceous material supports the substantial contribution of material derived from microorganisms. Evidence is provided that peptidoglycan and silicate species may in part originate from soil microbes

Enhanced woody biomass production in a mature temperate forest under elevated CO₂

Enhanced CO2 assimilation by forests as atmospheric CO2 concentration rises could slow the rate of CO2 increase if the assimilated carbon is allocated to long-lived biomass. Experiments in young tree plantations support a CO2 fertilization effect as atmospheric CO2 continues to increase. Uncertainty exists, however, as to whether older, more mature forests retain the capacity to respond to elevated CO2. Here we show, aided by tree-ring analysis and canopy laser scanning, that a 180-year-old Quercus robur L. woodland in central England increased the production of woody biomass when exposed to free-air CO2 enrichment (FACE) for seven years. Further, elevated CO2 increased exudation of carbon from fine roots into the soil with likely effects on nutrient cycles. The increase in tree growth and allocation to long-lived woody biomass, demonstrated here, substantiates the major role for mature temperate forests in climate change mitigation

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

<p>Abstract</p> <p>Background</p> <p>Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented.</p> <p>Results</p> <p>A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations.</p> <p>Conclusions</p> <p>CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at <url>http://www.ptools.ua.ac.be/CytoSQL</url>.</p

Characteristics of free air carbon dioxide enrichment of a northern temperate mature forest

Tausz, M ORCiD: 0000-0001-8205-8561In 2017, the Birmingham Institute of Forest Research (BIFoR) began to conduct Free Air Carbon Dioxide Enrichment (FACE) within a mature broadleaf deciduous forest situated in the United Kingdom. BIFoR FACE employs large scale infrastructure, in the form of lattice towers, forming 'arrays' which encircle a forest plot of ~30 m diameter. BIFoR FACE consists of three treatment arrays to elevate local CO2 concentrations (e[CO2 ]) by +150 μmol mol-1 . In practice, acceptable operational enrichment (ambient [CO2 ] + e[CO2 ]) is ± 20% of the set-point 1-minute average target. There are a further three arrays that replicate the infrastructure and deliver ambient air as paired controls for the treatment arrays. For the first growing season with e[CO2 ] (April to November 2017), [CO2 ] measurements in treatment and control arrays show that the target concentration was successfully delivered, i.e.: +147 ± 21 μmol mol-1 (mean ± SD) or 98 ± 14% of set-point enrichment target. e[CO2 ] treatment was accomplished for 97.7% of the scheduled operation time, with the remaining time lost due to engineering faults (0.6% of the time), CO2 supply issues (0.6%), or adverse weather conditions (1.1%). CO2 demand in the facility was driven predominantly by wind speed and the formation of the deciduous canopy. Deviations greater than 10% from the ambient baseline CO2 occurred  80 μmol mol-1 (i.e., > 53% of the treatment increment) into control arrays accounted for < 0.1% of the enrichment period. The median [CO2 ] values in reconstructed 3-dimensional [CO2 ] fields show enrichment somewhat lower than the target but still well above ambient. The data presented here provide confidence in the facility setup and can be used to guide future next-generation forest FACE facilities built into tall and complex forest stands. This article is protected by copyright. All rights reserved