Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate

Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources. After several growth cycles, cell growth stabilized at the maximum level and exhibited a reproducible growth profile. The specific growth rates measured for benzoate (1.01 ± 0.11 h-1) and citrate (1.11 ± 0.12 h-1) were similar, while a higher yield was observed for benzoate (0.6 and 0.3 g cell mass per g of benzoate and citrate, respectively), reflecting the different degrees of carbon reduction in the two substrates. Comparative proteomic analysis revealed an enrichment of several oxygenases/dehydrogenases in benzoate-grown cells, indicative of the higher carbon reduction of benzoate. Moreover, the upregulation of all 14 proteins implicated in benzoate degradation via the catechol ortho-cleavage pathway was observed, while several stress-response proteins were increased to aid cells to cope with benzoate toxicity. Unexpectedly, citrate posed more challenges than benzoate in the maintenance of pH homeostasis, as indicated by the enhancement of the Na+/H+ antiporter and carbonic anhydrase. The study provides important mechanistic insights into Pseudomonas adaptation to varying carbon sources that are of great relevance to bioremediation efforts

Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)

Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth\u27s subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2‐saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications

Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece)

Studies of submarine hydrothermal systems in Mediterranean Sea are limited to the southern Italian volcanism, while are totally missing in the Aegean. Here, we report on the geochemistry of high-temperature fluids (up to 220°C) venting at 500 m b.s.l. from the floor of Kolumbo submarine volcano (Hellenic Volcanic Arc, Greece), which is located 7 km northeast of Santorini Island. Despite the recent unrest at Santorini, Kolumbo submarine volcano is considered more active due to a higher seismicity. Rizzo et al. (2016) investigated the He-isotope composition of gases collected from seven chimneys and showed that are dominated by CO2 (>97%), with only a small air contamination. Here we provide more-complete chemical data and isotopic compositions of CO2 and CH4, and Hg(0) concentration. We show that the gases emitted from different vents are fractionated by the partial dissolution of CO2 in water. Fractionation is also evident in the C-isotope composition (δ13CCO2), which varies between -0.04 and 1.15‰. We modeled this process to reconstruct the chemistry and δ13CCO2 of intact magmatic gases before fractionation. We argue that the CO2 prior to CO2 dissolution in water had δ13C ∼-0.4‰ and CO2/3He ∼1 × 1010. This model reveals that the gases emitted from Kolumbo originate from a homogeneous mantle contaminated with CO2, probably due to decarbonation of subducting limestone, which is similar to other Mediterranean arc volcanoes (e.g., Stromboli, Italy). The isotopic signature of CH4 (δ13C ∼-18‰ and δD ∼-117‰) is within a range of values typically observed for hydrothermal gases (e.g., Panarea and Campi Flegrei, Italy), which is suggestive of mixing between thermogenic and abiotic CH4. We report that the concentrations of Hg(0) in Kolumbo fluids are particularly high (∼61 to 1300 ng m-3) when compared to land-based fumaroles located on Santorini and worldwide aerial volcanic emissions. This finding may represent further evidence for the high level of magmatic activity at Kolumbo. Based on the geo-indicators of temperature and pressure, we calculate that the magmatic gases equilibrate within the Kolumbo hydrothermal system at about 270°C and at a depth of ∼1 km b.s.l

Isotopic characterization of aerosol organic carbon components over the eastern United States

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): D13303, doi:10.1029/2011JD017153.Carbon isotopic signatures (δ13C, Δ14C) of aerosol particulate matter total organic carbon (TOC) and operationally defined organic carbon (OC) components were measured in samples from two background sites in the eastern U.S. TOC and water-soluble OC (WSOC) δ13C values (−27 to −24‰) indicated predominantly terrestrial C3 plant and fossil derived sources. Total solvent extracts (TSE) and their aliphatic, aromatic, and polar OC components were depleted in δ13C (−30 to −26‰) relative to TOC and WSOC. Δ14C signatures of aerosol TOC and TSE (−476 to +25‰) suggest variable fossil contributions (~5–50%) to these components. Aliphatic OC while comprising a small portion of the TOC (<1%), was dominated by fossil-derived carbon (86 ± 3%), indicating its potential utility as a tracer for fossil aerosol OC inputs. In contrast, aromatic OC contributions (<1.5%) contained approximately equal portions contemporary (52 ± 8%) and fossil (48 ± 8%) OC. The quantitatively significant polar OC fraction (6–25% of TOC) had fossil contributions (30 ± 12%) similar to TOC (26 ± 7%) and TSE (28 ± 9%). Thus, much of both of the fossil and contemporary OC is deduced to be oxidized, polar material. Aerosol WSOC consistently showed low fossil content (<8%) relative to the TOC (5–50%) indicating that the majority of fossil OC in aerosol particulates is insoluble. Therefore, on the basis of solubility and polarity, aerosols are predicted to partition differently once deposited to watersheds, and these chemically distinct components are predicted to contribute in quantitatively and qualitatively different ways to watershed carbon biogeochemistry and cycling.ASW was partially supported by a Graduate Fellowship from the Hudson River Foundation during the course of this study. Additional funding for this work came from a NOSAMS student internship award, a fellowship award from Sun Trust Bank administered through the VIMS Foundation, a student research grant from VIMS, and the following NSF awards: DEB Ecosystems grant DEB-0234533, Chemical Oceanography grant OCE-0327423, and Integrated Carbon Cycle Research Program grant EAR-0403949 to JEB; and Chemical Oceanography grant OCE-0727575 to RMD and JEB.2013-01-0

The essentials of marine biotechnology.

Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs