AbstractIn this study, we integrated geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains to investigate substrate-attached filamentous microbial biofilms at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. At this site, the venting gases are mainly composed of CO2 and H2S and the temperature at the emissions is the same as that of the surrounding water. To investigate the composition of the total and active fraction of the Tor Caldara biofilm communities, we collected established and newly formed filaments and we sequenced the 16S rRNA genes (DNA) and the 16S rRNA transcripts (cDNA). Chemoautotrophic sulfur-oxidizing members of the Gammaproteobacteria (predominantly Thiotrichales) dominate the active fraction of the established microbial filaments, while Epsilonproteobacteria (predominantly Sulfurovum spp.) are more prevalent in the young filaments. This indicates a succession of the two communities, possibly in response to age, sulfide and oxygen concentrations. Growth experiments with representative laboratory strains in sulfide gradient medium revealed that Sulfurovum riftiae (Epsilonproteobacteria) grew closer to the sulfide source than Thiomicrospirasp. (Gammaproteobacteria, Thiotrichales). Overall, our findings show that sulfur-oxidizing Epsilonproteobacteria are the dominant pioneer colonizers of the Tor Caldara biofilm communities and that Gammaproteobacteria become prevalent once the community is established. This succession pattern appears to be driven - among other factors - by the adaptation of Epsilon- and Gammaproteobacteria to different sulfide concentrations.
AbstractMarine shallow-water hydrothermal vents are defined as occurring at less than ~ 200 m below sea level, and are often found off the coasts of island arc volcanoes, which provide the necessary heat source to drive circulation. Recent research suggests that marine shallow-water hydrothermal vents, also known as “shallow-sea” vents (SHVs), are abundant across the Earth. While they have many similarities to deep-sea hydrothermal vents (DHVs), they also have many important differences, primarily due to their occurrence at shallower depths. Here we introduce SHVs and describe some of the processes which influence their geochemistry. This information is summarized from Price and Giovannelli (2017), and is complementary to Giovannelli and Price (2018), which describes the microbiology of shallow-sea vents.
AbstractThe reduction of elemental sulfur is an important energy‐conserving pathway in prokaryotes inhabiting geothermal environments, where sulfur respiration contributes to sulfur biogeochemical cycling. Despite this, the pathways through which elemental sulfur is reduced to hydrogen sulfide remain unclear in most microorganisms. We integrated growth experiments using Thermovibrio ammonificans, a deep‐sea vent thermophile that conserves energy from the oxidation of hydrogen and reduction of both nitrate and elemental sulfur, with comparative transcriptomic and proteomic approaches, coupled with scanning electron microscopy. Our results revealed that two members of the FAD‐dependent pyridine nucleotide disulfide reductase family, similar to sulfide‐quinone reductase and to NADH‐dependent sulfur reductase (NSR), respectively, are over‐expressed during sulfur respiration. Scanning electron micrographs and sulfur sequestration experiments indicated that direct access of T. ammonificans to sulfur particles strongly promoted growth. The sulfur metabolism of T. ammonificans appears to require abiotic transition from bulk elemental sulfur to polysulfide to nanoparticulate sulfur at an acidic pH, coupled to biological hydrogen oxidation. A coupled biotic‐abiotic mechanism for sulfur respiration is put forward, mediated by an NSR‐like protein as the terminal reductase.
Since its inception, the Deep Carbon Observatory (DCO) has coalesced a multidisciplinary and international group of researchers focused on understanding and quantifying Earth's deep carbon budget. Carbon is the fourth most abundant element in the universe, and understanding carbon chemistry under a variety of environmental conditions impacts all aspects of planetary sciences. DCO recognizes that contributions of early career scientists are integral to the advancement of knowledge regarding the quantities, movements, origins, and forms of Earth's deep carbon. This research topic highlights the contributions of the DCO Early Career Scientist community.
AbstractAn 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-stain-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 % (w/v) NaCl (optimum 3.0 %) and at 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 as a sole terminal electron acceptor. The predominant fatty acids were C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone 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 relatives were Sulfurovum lithotrophicum 42BKTT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7 % sequence similarity, respectively). DNA–DNA relatedness between strain 1812ET and the type strain of 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 novel species within the genus Sulfurovum , for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812ET (=DSM 101780T=JCM 30810T).
AbstractAt 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 67.3 µM) 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 (0.3–2.9 µM), 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.
AbstractSedimenticola 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. selenatireducensstrain AK4OH1T.
AbstractAll 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.
AbstractPockmarks 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.
AbstractThe 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.
AbstractMarine 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.
AbstractAnaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO2fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.
|Project Title||Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere|
|Acronym||Deep Biosphere Energy Limitation|
|Created||August 15, 2016|
|Modified||August 15, 2016|
Despite being the largest ecosystem on earth, the deep biosphere is considered to be energy limited. Chemoautotrophy is an important source of organic carbon in the deep biosphere, and significantly contributes to the deep carbon cycle. The Wood-Ljungdahl (WL) pathway of carbon fixation is common to both acetogenic and methanogenic prokaryotes and, together with the reverse Tricarboxylic Acid cycle (rTCA), is the most widely distributed carbon fixation pathway in subsurface organisms. Recent genomic studies suggested that hybrid strategies of carbon fixation may be functioning in several organisms. The simultaneous presence of different carbon fixation strategies might give an ecological and evolutionary advantage to organisms living in the energy limited subsurface. Despite this, our comprehension of alternative carbon fixation strategies under energy limiting conditions is scarce. Here I propose to investigate the use of carbon fixation pathways in T. ammonificans under energy limiting conditions, exploring the ecological and evolutionary implications associated with the co-occurrence of different carbon fixation pathways. The results will increase our understanding of the functioning of subseafloor habitats.
|Donato Giovannelli||Rutgers University (Rutgers IMCS)||Lead Principal Investigator|