Donato Giovannelli

Donato GiovannelliTokyo Institute of Technology | TITech · Earth-Life Science Institute

· PhD Ecology and Microbiology
  • About
    My current research is focuses on two major theme, linked to each other: 1) the metabolic and taxonomic diversity of prokaryotes in different geothermally influenced marine ecosystems; and 2) the emergence and evolution of early metabolism. To carry out my research I combine of classic microbiology techniques with molecular tools and bioinformatic. For more information visit my website at
    Current Institution
    Earth-Life Science Institute
    Current position
    Research Fellow
    Research items
    Research Experience
    Jun 2013 - May 2016
    Postdoctoral Fellow
    Rutgers, The State University of New Jersey · Institute of Marine and Coastal Sciences
    New Brunswick, USA
    Jan 2012
    Associate Scientist
    National Research Council · Institute of Marine Science ISMAR
    Ancona, Italy
    Mar 2010 - Feb 2013
    PhD Student
    University of Naples Federico II · Department of Structural and Functional Biology
    Napoli, Italy
    Mar 2010 - Feb 2013
    University of Naples Federico II
    Microbiology of Extreme environments
    Sep 2005 - Jul 2007
    Università Politecnica delle Marche
    Microbial Ecology
    Sep 2004 - Jun 2005
    University of Plymouth
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    Marco Sigovini
    Marcello Liotta
    Mihaela Glamoclija
    Caterina Bergami
    Alberto Zanetti
    Luca Bolognini
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    Irene Guarneri
    Fabrizio Bernardi Aubry
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    Marco Sigovini
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    Aldo Marchetto
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    Fernando Rubino
    Marco Abbiati
    Carlo Pipitone
    Awards & Achievements (6)
    Dec 2015
    Deep Carbon Observatory Emerging Leader Award
    Oct 2011
    PNRA (National Antarctic Research Program of Italy) Young Researcher Project
    Jul 2011
    InterRidge Student and Postdoctoral Fellowships
    Mar 2011
    eCapital Business plan competition first prize
    Jul 2010
    ADISU Puglia International Exchange Student Scholarship
    Research Items (75)
    Marine shallow-water vents are ubiquitous but poorly studied geothermal environments located worldwide between the intertidal zone and 212 m depth. Important factors differentiating them from their deep-sea counterparts include sunlight, tidal/wave pumping, meteoric water sources, terrigenous inputs, elevated metal concentrations, and abundant free gas. Mixing of vent fluids with oxidized seawater generates multiple redox disequilibria readily exploited by microbes. Although highly diverse, two major groups include an Epsilonprotebacteria-dominated community sharing similarities with deep-sea analogs, and a community dominated by Gammaproteobacteria/Firmicutes. The distribution of different microbial taxa within each vent is primarily controlled by temperature and availability of suitable electron donors and acceptors. However, the coexistence of phototrophs, chemolithoautotrophs, and a high abundance of aerobic and anaerobic heterotrophs, suggests the presence of sunlight and high organic carbon loads define unique microbial habitats that are transitionary between terrestrial and deep-sea vents. We summarize here the current knowledge of shallow-sea vents worldwide, highlighting gaps on our understanding of these unique environments.
    Hydrothermal vent systems are inhabited by dense benthic communities adapted to extreme conditions such as high temperature, hydrogen sulphide (H2S) and elevated fluxes of metals. In the present work, a wide range of trace elements (Ag, Al, As, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sb, Se, V and Zn) were measured in tissues of three tube dwelling annelids, Alvinella pompejana, Alvinella caudata and Riftia pachyptila, which colonize distinct habitats of the East Pacific Rise (EPR) at 2500 m depth. Metals concentrations in alvinellids were often 2–4 orders of magnitude higher than those commonly found in marine organisms, while much lower values were observed in the vestimentiferan polychaete. Mobility of trace elements was further characterized in tissues of A. pompejana where metals appeared mostly in insoluble forms, i.e. associated with hydrated oxides and sulphides. Arsenic was mainly present in a weakly insoluble form and with concentrations in the branchial tentacles of alvinellids, approximately 5–15 fold higher than those measured in the thorax. Chemical speciation of this element in tissues of the three polychaete species revealed a major contribution of methylated arsenic compounds, like dimethylarsinate (DMA) and, to a lower extent, monomethylarsonate (MMA) and trimethylarsine oxide (TMAO). Although the biotransformation of inorganic arsenic might represent a detoxification mechanism in polychaetes from hydrothermal vents, the elevated levels of methylated forms of arsenic in branchial tissues also suggest an ecological role of this element as an antipredatory strategy for more vulnerable tissues toward generalist consumers.
    Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron–sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.
    The global scale of the biodiversity crisis has stimulated research into the relationship between biodiversity and ecosystem functioning (BEF). Even though the deep sea is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scant. Moreover, the small number of recent studies, which mostly focus on meiobenthic nematodes, report conflicting results that range from a very clear positive relationship to none at all. In this BEF study, the deep-sea macrofauna were used as a model to investigate the structural and functional diversity of macrofauna assemblages at three depths (1,200, 1,900, and 3,000 m) in seven open-slope systems from the North-Eastern Atlantic Ocean to the Central-Eastern Mediterranean Sea. The presence and nature of BEF relationships were studied considering two spatial scales, the large and the basin scale, in different environmental settings. Total benthic biomass and macrofaunal predator biomass were used as proxies to assess ecosystem functioning. Ecosystem efficiency was expressed as macrofaunal biomass to biopolymeric carbon content ratio, macrofaunal biomass to prokaryotic biomass ratio, macrofaunal biomass to meiofaunal biomass ratio, and meiofaunal biomass to prokaryotic biomass ratio. On both large and basin spatial scales, some significant relationships between macrofaunal diversity and ecosystem functioning and efficiency were reported. When significant, the nature of BEF relations was positive and exponential or linear supporting the general idea that a higher diversity can enhance ecosystem functioning. Other BEF relationships were explained by the effect of environmental variables. More data from different deep-sea systems are needed, to better elucidate the consequences of biodiversity loss on the ocean floor.
    The report includes and examines the list of taxonomists from IAMC (Institute for Coastal Marine Environment), IGG (Institute of Geosciences and Earth Resources), ISE (Institute of Ecosystem Study), and ISMAR (Institute of Marine Sciences), who responded to the Taxonomy Census 2016, their scientific publications and the number of taxa described new for the science in the last 50 years. Every paper is reported with keywords, helping the reader to understand taxon/taxa of each publication and the focal habitat. This analysis becomes the basis for the future steps to resurrect taxonomy within CNR, from common project proposals to the protection of past and present knowledge gained to date in this area.
    List of the proteins identified in the proteome of T. ammonificans grown under nitrate reducing conditions.DOI:
    Accession number of the ATP citrate lyase sequences used for the reconstruction of the phylogenetic history of the enzyme presented in Figure 2 in the main text.DOI:
    Geological, geochemical, and biological processes drive the cycling of carbon on Earth, both in surface and subsurface environments. Subduction represents a critical link between the shallow and deep carbon cycles where crustal carbon is transported into the mantle. Along the Costa Rican convergent margin, the Cocos Plate actively subducts beneath the Caribbean Plate, where shallow dewatering processes allow for carbon-containing fluids to be released into the overlying fore-arc, much of which is subaerial. These shallow subduction fluids may transport microbes from oceanic sediments to the fore-arc under non-lethal conditions to some extremophiles. While extensive research has been invested in quantifying abiotic volcanic carbon fluxes, the influence of biological processes on the deep carbon budget is not well understood. In February 2017, an expedition to sites along the fore-arc and the volcanic arc of Costa Rica allowed for the collection of biological samples from 25 geochemically diverse sites including hot springs, mud pools, and volcanic lakes in parallel with geochemical and gas flux measurements along the convergent margin. Water and sediment samples will be analyzed for methane, sulfate, and sulfide and other major and minor components to characterize biologically relevant geochemical properties of these sites in parallel with biological measurements. Single cell amplified genome (SAG) analysis will allow for determination of individual organisms present in these environments to complement metagenomic and metatranscriptomic data generated by our collaborators. Through the synthesis of the aforementioned biological parameters with geological and gas flux analyses, we can begin to tease apart the biological and abiotic processes driving carbon cycling and gain a more holistic understanding of deep carbon on Earth.
    All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena. Expected final online publication date for the Annual Review of Microbiology Volume 70 is September 08, 2016. Please see for revised estimates.
    Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    An anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812ET, was isolated from the vent polychaete, Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram staining-negative rods, measuring approximately 1.05 ± 0.11 µm by 0.40 ± 0.05 µm. Strain 1812ET grew at 25-45 °C (optimum 35 °C), with 1.5-4.0 % NaCl (optimum 3.0 %), and pH 5.0-8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812ET was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used a sole terminal electron acceptor. The predominant fatty acids were C16:1ω7c, C18:1ω7c and C16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The major respiratory quinone was MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812ET showed that the isolate belonged to the Epsilonproteobacteria, and its closest related species were Sulfurovum lithotrophicum 42BKT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7% sequence similarity respectively). DNA-DNA similarity between Strain 1812ET and S. lithotrophicum was 29.7%, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic, and physiological evidence, strain 1812ET represents a new species within the genus Sulfurovum, for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain of the species is 1812ET (=DSM 101780T =JCM 30810T).
    Second Deep Carbon Observatory Early Career Scientist Workshop; São Miguel, Azores, Portugal, 31 August to 5 September 2015
    The global scale of the biodiversity crisis has stimulated research on the relationship between biodiversity and ecosystem functioning (BEF) in several ecosystems of the world. Even though the deep-sea seafloor is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scarce. In addition, the few recent studies, mostly focus on meiobenthic nematodes, report quite different results spanning from a very clear positive relationship to none at all. If deep-sea BEF relationships are indeed so variable or have a more common nature is not established. In this first BEF study of deep-sea macrobenthic fauna, we investigated the structural and functional diversity of macrofauna assemblages at three depths (1200, 1900 and 3000 m) in seven different open slope systems in the NE Atlantic Ocean (n = 1) and Western (n = 3) and Central (n = 3) Mediterranean Sea. The results demonstrate a positive relationship between deep-sea macrobenthic diversity and ecosystem function, with some variability in its strength between slope areas and in relation to the spatial scale of investigation and environmental conditions. The macrofauna functional diversity did not appear to be more effective than structural diversity in influencing ecosystem processes. Rare macrofaunal species were seen to have a negligible effect on BEF relationship, suggesting a high ecological redundancy and a small role of rare species in providing community services.
    Sedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducens strain AK4OH1T.
    At deep-sea hydrothermal vents, reduced, super-heated hydrothermal fluids mix with cold, oxygenated seawater. This creates temperature and chemical gradients that support chemosynthetic primary production and a biomass-rich community of invertebrates. In late 2005/early 2006 an eruption occurred on the East Pacific Rise at 9°50'N, 104°17'W. Direct observations of the post-eruptive diffuse-flow vents indicated that the earliest colonizers were microbial biofilms. Two cruises in 2006 and 2007 allowed us to monitor and sample the early steps of ecosystem recovery. The main objective of this work was to characterize the composition of microbial biofilms in relation to the temperature and chemistry of the hydrothermal fluids and the observed patterns of megafaunal colonization. The area selected for this study had local seafloor habitats of active diffuse flow (in-flow) interrupted by adjacent habitats with no apparent expulsion of hydrothermal fluids (no-flow). The in-flow habitats were characterized by higher temperatures (1.6-25.2°C) and H2S concentrations (up to 67.3μM) than the no-flow habitats, and the microbial biofilms were dominated by chemosynthetic Epsilonproteobacteria. The no-flow habitats had much lower temperatures (1.2-5.2°C) and H2S concentrations (0.3-2.9μM), and Gammaproteobacteria dominated the biofilms. Siboglinid tubeworms colonized only in-flow habitats, while they were absent at the no-flow areas, suggesting a correlation between siboglinid tubeworm colonization, active hydrothermal flow, and the composition of chemosynthetic microbial biofilms.
    The West Antarctic Peninsula is one of the fastest warming regions on Earth. Faster glacier retreat and related calving events lead to more frequent iceberg scouring, fresh water input and higher sediment loads, which in turn affect shallow water benthic marine assemblages in coastal regions. In addition, ice retreat creates new benthic substrates for colonization. We investigated three size classes of benthic biota (microbenthos, meiofauna and macrofauna) at three sites in Potter Cove (King George Island, West Antarctic Peninsula) situated at similar water depths but experiencing different disturbance regimes related to glacier retreat. Our results revealed the presence of a patchy distribution of highly divergent benthic assemblages within a relatively small area (about 1 km2). In areas with frequent ice scouring and higher sediment accumulation rates, an assemblage mainly dominated by macrobenthic scavengers (such as the polychaete Barrukia cristata), vagile organisms and younger individuals of sessile species (such as the bivalve Yoldia eightsi) was found. Macrofauna were low in abundance and very patchily distributed in recently ice-free areas close to the glacier, whereas the pioneer nematode genus Microlaimus reached a higher relative abundance in these newly exposed sites. The most diverse and abundant macrofaunal assemblage was found in areas most remote from recent glacier influence. By contrast, the meiofauna showed relatively low densities in these areas. The three benthic size classes appeared to respond in different ways to disturbances likely related to ice retreat, suggesting that the capacity to adapt and colonize habitats is dependent on both body size and specific life traits. We predict that, under continued deglaciation, more diverse, but less patchy, benthic assemblages will become established in areas out of reach of glacier-related disturbance.
    Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.The ISME Journal advance online publication, 16 January 2014; doi:10.1038/ismej.2013.246.
    The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.
    Shallow-water hydrothermal vents are extreme environments that share many characteristics with their deep-sea analogs. However, despite ease of access, much less is known about the geochemical dynamics of these ecosystems. Here, we report on the spatial and temporal geochemical dynamics of a shallow-water vent system at Paleochori Bay, Milos Island, Greece. Our multi-analyte voltammetric profiles of dissolved O2 and hydrothermal tracers (e.g. Fe2+, FeSaq, Mn2+) on sediment cores taken along a transection in hydrothermally affected sediments indicate three different areas: the central vent area (highest temperature) with a deeper penetration of oxygen into the sediment, and a lack of dissolved Fe2+ and Mn2+; a middle area (0.5 m away) rich in dissolved Fe2+ and Mn2+ (exceeding 2 mM) and high free sulfide with potential for microbial sulfide oxidation as suggested by the presence of white mats at the sediment surface; and, finally, an outer rim area (1–1.5 m away) with lower concentrations of Fe2+ and Mn2+ and higher signals of FeSaq, indicating an aged hydrothermal fluid contribution. In addition, high-frequency temperature series and continuous in situ H2S measurements with voltammetric sensors over a 6-day time period at a distance 0.5 m away from the vent center showed substantial variability in temperature (31.6 to 46.4 °C) and total sulfide (488 to 1329 μM) in the upper sediment layer. The analysis of these data suggests that tidal and wind forcing, and abrupt geodynamic events generate intermittent mixing conditions lasting for several hours to days. Despite substantial variability, the concentration of sulfide available for chemoautotrophic microbes remained high. However, the availability of electron acceptors originating from seawater might be more intermittent, which in turn has an effect on the reestablishment of the white mats after wave-induced disturbances. Our results emphasize the importance of transient events in the development of chemoautotrophic communities in the hydrothermally influenced sediments of Paleochori Bay.
    Studies of shallow-water hydrothermal vents have been lagging behind their deep-sea counterparts. Hence, the importance of these systems and their contribution to the local and regional diversity and biogeochemistry is unclear. This study analyzes the bacterial community along a transect at the shallow-water hydrothermal vent system of Milos island, Greece. The abundance and biomass of the prokaryotic community is comparable to areas not affected by hydrothermal activity and was, on average, 1.34 × 10(8) cells g(-1). The abundance, biomass and diversity of the prokaryotic community increased with the distance from the center of the vent and appeared to be controlled by the temperature gradient rather than the trophic conditions. The retrieved 16S rRNA gene fragments matched sequences from a variety of geothermal environments, although the average similarity was low (94%), revealing previously undiscovered taxa. Epsilonproteobacteria constituted the majority of the population along the transect, with an average contribution to the total diversity of 60%. The larger cluster of 16S rRNA gene sequences was related to chemolithoautotrophic Sulfurovum spp., an Epsilonproteobacterium so far detected only at deep-sea hydrothermal vents. The presence of previously unknown lineages of Epsilonproteobacteria could be related to the abundance of organic matter in these systems, which may support alternative metabolic strategies to chemolithoautotrophy. The relative contribution of Gammaproteobacteria to the Milos microbial community increased along the transect as the distance from the center of the vent increased. Further attempts to isolate key species from these ecosystems will be critical to shed light on their evolution and ecology.
    Lagoons are often affected by eutrophication phenomena, due to their shallow nature, high productivity, weak hydrodynamism and anthropic exploitation. Bioremediation techniques have been widely used in the treatment of chemical pollution; however, no information is available on the use of bioremediation of organic-rich sediments. In the present study, we investigated the priming effects following compost addition to organic-rich lagoon sediments, and the effects of this compost addition on degradation and cycling of organic detritus, transfer of organic matter to higher trophic levels, and in situ prokaryotic community structure. There was a positive response to treatment, particularly during the first days after compost addition. The compost had a stimulating effect on degradation activity of the prokaryotic community. This occurred despite an increase in available organic matter, as the community was more efficient at removing it. These data are supported by the prokaryotic community structure analysis, which revealed no changes in the in situ community following compost addition. This priming effect enhancement through compost addition represents an efficient method to treat organic-rich sediments.
    type strain HB-1 is a thermophilic (T: 75°C), strictly anaerobic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO/H, using NO or S as electron acceptors, which are reduced to ammonium or hydrogen sulfide, respectively. is one of only three species within the genus , a member of the family , and it forms a deep branch within the phylum . Here we report the main features of the genome of strain HB-1 (DSM 15698).
    A mesophilic, strictly microaerophilic, chemosynthetic bacterium, designated strain P2DT, was isolated from the sediment of an active shallow water hydrothermal vent in Paleochori bay, Milos, Greece. The cells were Gram-negative rods approximately 0.8-1.3 µm in length and 0.4-0.5 µm in width. Strain P2DT grew between 20 and 50 °C (optimum 35 °C), 10 and 50 g l-1 NaCl (optimum 30 g l-1) and pH 4.5 and 8.0 (optimum pH 5.5). The generation time under optimal conditions was 1.1 h. Growth occurred under chemolithoautotrophic conditions with S2O32- and CO2 as the energy and carbon sources, respectively. Oxygen (5%) was used as sole terminal electron acceptor. No growth was observed in the presence of acetate, formate, lactate, tryptone, and peptone. Chemolithoheterotrophic growth occurred in the presence of D(+)-glucose and sucrose as alternative carbon sources. No organic compound was used as electron donor. The G + C content of the genomic DNA was 44.9 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the closest relatives to strain P2DT belonged to the genera Thiomicrospira and Thioalkalimicrobium, with a sequence identity of 92% and 91%, respectively. Phylogenetic, physiological and chemotaxonomic characteristics indicated that strain P2DT represents a novel genus within the Gammaproteobacteria (family Piscirickettsiaceae), for which the name Galenea microaerophila gen. nov., sp. nov. is proposed. The type strain is P2DT (= DSM 24963T = JCM 17795T).
    a b s t r a c t Despite the major influence of the marine sub-surface area in carbon cycling and global biogeochemistry, there is little known of prokaryotic distribution and community structure information of the marine sub-surface and the factors that influence sub-surface prokaryotic assemblages. We provide quantitative estimations of active Bacteria and Archaea down vertical profiles of sub-surface coastal sediments from the southern Adriatic Sea (Manfredonia Gulf). Prokaryotic biomass, carbon incorporation and the metabolically active fraction were compared with environmental, trophic, and predatory variables down 100-cm sediment cores sectioned into 21 layers. Multiple regression analysis was used to identify variables that can explain the variance of community compositions down vertical profiles. CARD-FISH analysis showed Bacteria dominance for the first 11 cm below sediment surface. The community then changed significantly at increasing depth, towards Archaea dominance. The models tested show that prokaryotic abundance in superficial marine sediments is controlled by organic trophic resources, while in sub-surface sediments, active prokaryotic abundance is driven by environmental factors and predatory pressure, suggesting that the shift in prokaryotic community structure could be coupled to a change in life-style of microbial assemblages.
    While ecological roles, ecosystem services and economic values of coral reefs worldwide are threatened by increasing anthropogenic and environmental pressures, the best management tools currently employed to offset reefs degradation do not achieve conservation objectives. There is therefore an urgent need to develop alternative instruments, focused on active management acts. In this study the applicability of an in situ coral intensive farming was tested, as first step of an active reef rehabilitation strategy, in the reefs of Singapore (China Sea, Western Pacific Ocean) that suffer from extreme sedimentation loads. About 3000 nubbins obtained from 13 coral species were farmed for 14 months in situ in two nurseries, one placed close to fish-farm pens and the other located away from the direct influence of the fish-farm effluents. After one year of mariculture, average of coral survival rates was low (34%). Survivorship (loss resulted primarily from coral detachment, not coral death) significantly differed among species, and, within each species, be-tween nurseries. Despite the adversities imposed by the rough environmental conditions, the survived nub-bins showed high growth rates. Growth and 3D architectures of farmed colonies significantly varied among coral species and nursery locations. Results reported here indicate that the first step of the coral gardening is feasible also in reefs impacted by high sedimentation rates and support the idea that future integrated coastal management programs can successfully include in situ coral mariculture.
    Caminibacter mediatlanticus strain TB-2(T) [1], is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge and the type strain of the species. C. mediatlanticus is a Gram-negative member of the Epsilonproteobacteria (order Nautiliales) that grows chemolithoautotrophically with H(2) as the energy source and CO(2) as the carbon source. Nitrate or sulfur is used as the terminal electron acceptor, with resulting production of ammonium and hydrogen sulfide, respectively. In view of the widespread distribution, importance and physiological characteristics of thermophilic Epsilonproteobacteria in deep-sea geothermal environments, it is likely that these organisms provide a relevant contribution to both primary productivity and the biogeochemical cycling of carbon, nitrogen and sulfur at hydrothermal vents. Here we report the main features of the genome of C. mediatlanticus strain TB-2(T).
    Coral bleaching (i.e., the release of coral symbiotic zooxanthellae) has negative impacts on biodiversity and functioning of reef ecosystems and their production of goods and services. This increasing world-wide phenomenon is associated with temperature anomalies, high irradiance, pollution, and bacterial diseases. Recently, it has been demonstrated that personal care products, including sunscreens, have an impact on aquatic organisms similar to that of other contaminants. Our goal was to evaluate the potential impact of sunscreen ingredients on hard corals and their symbiotic algae. In situ and laboratory experiments were conducted in several tropical regions (the Atlantic, Indian, and Pacific Oceans, and the Red Sea) by supplementing coral branches with aliquots of sunscreens and common ultraviolet filters contained in sunscreen formula. Zooxanthellae were checked for viral infection by epifluorescence and transmission electron microscopy analyses. Sunscreens cause the rapid and complete bleaching of hard corals, even at extremely low concentrations. The effect of sunscreens is due to organic ultraviolet filters, which are able to induce the lytic viral cycle in symbiotic zooxanthellae with latent infections. We conclude that sunscreens, by promoting viral infection, potentially play an important role in coral bleaching in areas prone to high levels of recreational use by humans.
    Undergraduate degree programs in the biosciences almost always include elements of biochemistry. In the United Kingdom, biosciences programs often have optional pathways to accommodate students of diverse interests. These programs rarely require students to demonstrate any school-level chemistry knowledge, and many students find biochemistry difficult and irrelevant to their primary areas of interest. We have developed laboratory practical work that is used with more than 200 first year (Level 1) students, over 100 second year (Level 2) students, and about 30 final year (Level 3, Honors) students on pathways within a biosciences scheme ranging from Human Biosciences through Plant Sciences and Marine Biology to Environmental Biology. The practical work is based on haloperoxidase enzymes and is modified easily for different student groups and levels. The wide biological distribution of these enzymes and their important biological roles allow students with a wide spectrum of interests to engage with the practical work, and through it with biochemistry. Attempts to align the laboratory work with other aspects of the curriculum were confounded by organizational aspects of the student experience on a complex modular degree scheme.
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