Vetriani
Costantino
Vetriani
Costantino
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ArticleSingle cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system(Frontiers Media, 2019-06-12) Labonté, Jessica M. ; Pachiadaki, Maria G. ; Fergusson, Elizabeth ; McNichol, Jesse C. ; Grosche, Ashley ; Gulmann, Lara K. ; Vetriani, Costantino ; Sievert, Stefan M. ; Stepanauskas, RamunasPhage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.
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ArticleDiversity and distribution of prokaryotes within a shallow-water pockmark field(Frontiers Media, 2016-06-17) Giovannelli, Donato ; d'Errico, Giuseppe ; Fiorentino, Federica ; Fattorini, Daniele ; Regoli, Francesco ; Angeletti, Lorenzo ; Bakran-Petricioli, Tatjana ; Vetriani, Costantino ; Yucel, Mustafa ; Taviani, Marco ; Manini, ElenaPockmarks 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.
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ArticleHydrothermal vent mussel habitat chemistry, pre- and post-eruption at 9°50′North on the East Pacific Rise(National Shellfisheries Association, 2008-03) Nees, Heather A. ; Moore, Tommy S. ; Mullaugh, Katherine M. ; Holyoke, Rebecca R. ; Janzen, Christopher P. ; Ma, Shufen ; Metzger, Edouard ; Waite, Tim J. ; Yucel, Mustafa ; Lutz, Richard A. ; Shank, Timothy M. ; Vetriani, Costantino ; Nuzzio, Donald B. ; Luther, George W.Between October 2005 and March 2006, a seafloor volcanic eruption occurred at 9°50′N East Pacific Rise (EPR), establishing a “time zero” for characterizing newly-formed hydrothermal vent habitats and comparing them to pre-eruption habitats. Before the eruption, mussels (Bathymodiolus thermophilus) formed large aggregates between 9°49.6′ and 9°50.3′N. After the eruption, the few mussels remaining were in sparsely-distributed individuals and clumps, seemingly transported via lava flows or from mass wasting of the walls of the axial trough. In situ voltammetry with solid state gold-amalgam microelectrodes was used to characterize the chemistry of vent fluids in mussel habitats from 2004 to 2007, providing data sets for comparison of oxygen, sulfide, and temperature. Posteruption fluids contained higher sulfide-to-temperature ratios (i.e., slopes of linear regressions) (10.86 μM °C−1) compared with pre-eruption values in 2004 and 2005 (2.79 μM °C−1 and −0.063 μM °C−1, respectively). These chemical differences can be attributed to the difference in geographic location in which mussels were living and physical factors arising from posteruptive fluid emissions.
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ArticleInsight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans(eLife, 2017-04-24) Giovannelli, Donato ; Sievert, Stefan M. ; Hugler, Michael ; Markert, Stephanie ; Becher, Dorte ; Schweder, Thomas ; Vetriani, CostantinoAnaerobic 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 pathway for CO2 fixation. 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.
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ArticleInterrelationships between vent fluid chemistry, temperature, seismic activity, and biological community structure at a mussel-dominated, deep-sea hydrothermal vent along the East Pacific Rise(National Shellfisheries Association, 2008-03) Lutz, Richard A. ; Shank, Timothy M. ; Luther, George W. ; Vetriani, Costantino ; Tolstoy, Maya ; Nuzzio, Donald B. ; Moore, Tommy S. ; Waldhauser, Felix ; Crespo-Medina, Melitza ; Chatziefthimiou, Aspassia D. ; Annis, Eric R. ; Reed, Andrew J.In April 1991, submarine volcanic eruptions initiated the formation of numerous hydrothermal vents between 9°45′ and 9°52′N along the crest of the East Pacific Rise (EPR). Dramatic changes in biological community structure and vent fluid chemistry have been documented throughout this region since the eruptive event. By April 2004, mussels (Bathymodiolus thermophilus) dominated the faunal assemblages at several of the vent sites formed during of after the 1991 eruptions, whereas other habitats within the region were dominated by the vestimentiferan Riftia pachyptila. In the present paper, we build upon the extensive data sets obtained at these sites over the past decade and describe a manipulative experiment (conducted at 9°49.94′N; 104°14.43′W on the EPR) designed to assess interrelationships between vent fluid chemistry, temperature, biological community structure, and seismic activity. To this end, in situ voltammetric systems and thermal probes were used to measure H2S/HS− and temperature over time in a denuded region of an extensive mussel bed in which an exclusion cage was placed to inhibit the subsequent migration of mussels into the denuded area. Fluid samples were taken from the same locations to characterize the associated microbial constituents. Basalt blocks, which were placed in the cage in April 2004 and subsequently recovered in April 2005, were colonized by more than 25 different species of invertebrates, including numerous vestimentiferans and remarkably few mussels. Recorded temporal changes in vent fluid chemistry and temperature regimes, when coupled with microbiological characterization of the vent fluids and seismic activity data obtained from ocean bottom seismometers, shed considerable light on factors controlling biological community structure in these hydrothermal ecosystems.
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PreprintCulture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes : a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge( 2008-04) Voordeckers, James W. ; Do, My H. ; Hugler, Michael ; Ko, Vivian ; Sievert, Stefan M. ; Vetriani, CostantinoThe bacterial and archaeal communities of three deep-sea hydrothermal vent systems located on the Mid-Atlantic Ridge (MAR; Rainbow, Logatchev and Broken Spur) were investigated using an integrated culture-dependent and independent approach. Comparative molecular phylogenetic analyses, using the 16S rRNA gene and the deduced amino acid sequences of the alpha and beta subunits of the ATP citrate lyase encoding genes were carried out on natural microbial communities, on an enrichment culture obtained from the Broken Spur chimney, and on novel chemolithoautotrophic bacteria and reference strains originally isolated from several different deep-sea vents. Our data showed that the three MAR hydrothermal vent chimneys investigated in this study host very different microbial assemblages. The microbial community of the Rainbow chimney was dominated by thermophilic, autotrophic, hydrogen-oxidizing, sulfur- and nitrate reducing Epsilonproteobacteria related to the genus Caminibacter. The detection of sequences related to sulfur-reducing bacteria and archaea (Archaeoglobus) indicated that thermophilic sulfate reduction might also be occurring at this site. The Logatchev bacterial community included several sequences related to mesophilic sulfur-oxidizing bacteria, while the archaeal component of this chimney was dominated by sequences related to the ANME-2 lineage, suggesting that anaerobic oxidation of methane may be occurring at this site. Comparative analyses of the ATP citrate lyase encoding genes from natural microbial communities suggested that Epsilonproteobacteria were the dominant primary producers using the reverse TCA cycle (rTCA) at Rainbow, while Aquificales of the genera Desulfurobacterium and Persephonella were prevalent in the Broken Spur chimney.
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ArticleChemoautotrophy at deep-sea vents : past, present, and future(The Oceanography Society, 2012-03) Sievert, Stefan M. ; Vetriani, CostantinoChemolithoautotrophic microorganisms are at the nexus of hydrothermal systems by effectively transferring the energy from the geothermal source to the higher trophic levels. While the validity of this conceptual framework is well established at this point, there are still significant gaps in our understanding of the microbiology and biogeochemistry of deep-sea hydrothermal systems. Important questions in this regard are: (1) How much, at what rates, and where in the system is organic carbon being produced? (2) What are the dominant autotrophs, where do they reside, and what is the relative importance of free-swimming, biofilm-forming, and symbiotic microbes? (3) Which metabolic pathways are they using to conserve energy and to fix carbon? (4) How does community-wide gene expression in fluid and biofilm communities compare? and (5) How efficiently is the energy being utilized, transformed into biomass, and transferred to higher trophic levels? In particular, there is currently a notable lack of process-oriented studies that would allow an assessment of the larger role of these ecosystems in global biogeochemical cycles. By combining the presently available powerful "omic" and single-cell tools with thermodynamic modeling, experimental approaches, and new in situ instrumentation to measure rates and concentrations, it is now possible to bring our understanding of these truly fascinating ecosystems to a new level and to place them in a quantitative framework and thus a larger global context.
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ArticleMapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy(Frontiers Media, 2023-08-10) Barosa, Bernardo ; Ferrillo, Alessandra ; Selci, Matteo ; Giardina, Marco ; Bastianoni, Alessia ; Correggia, Monica ; Iorio, Luciano di ; Bernardi, Giulia ; Cascone, Martina ; Capuozzo, Rosaria ; Intoccia, Michele ; Price, Roy ; Vetriani, Costantino ; Cordone, Angelina ; Giovannelli, DonatoShallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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ArticleFaunal colonists, including mussel settlers, respond to microbial biofilms at deep-sea hydrothermal vents(Elsevier, 2024-04-29) Ladd, Tanika M. ; Selci, Matteo ; Davis, Dexter J. ; Cannon, Olivia ; Plowman, Caitlin Q. ; Schlegel, Ian ; Inaba, Aila ; Mills, Susan Wier ; Vetriani, Costantino ; Mullineaux, Lauren S. ; Arellano, Shawn M.Colonization processes at dynamic deep-sea hydrothermal vent ecosystems ultimately determine ecosystem structure, function, resilience, and recovery. Microbial biofilms form rapidly on surfaces near hydrothermal vents and are continuously exposed to the highly variable abiotic environment. Thus, biofilm microbes may provide a temporally integrated signal that can indicate whether the habitat is suitable for faunal colonists. This study explored the role of microbial biofilms in controlling faunal colonization through in-situ colonization experiments at Tica Vent in the 9°50’ N region of the East Pacific Rise (EPR). Short-term experiments (∼2 weeks) were conducted by deploying colonization surfaces (“sandwiches”) either with an established biofilm (developed for >1 year) or a fresh biofilm (developed throughout experiment) in zones characterized by different faunal assemblages. Differences in associated larval settlers, faunal immigrants, and microbial communities according to biofilm age across multiple biogenic zones were investigated. Faunal and microbial community compositions significantly differed according to whether the sandwiches had established or fresh biofilms as well as the biogenic zone they were deployed in. Several faunal colonists, including settlers such as the foundational chemosymbiotic mussel Bathymodiolus thermophilus and the nectochaete Archinome sp., were found associated more with established biofilms than fresh biofilms. Microbial biofilm communities were dominated by putative chemoautotrophic members of the Campylobacterota phylum and Gammaproteobacteria class and several microbial taxa were found to covary with faunal colonists. Overall, these findings show that microbial community composition plays a role in larval settlement and animal migration in hydrothermal vent systems and the detection of microbial and faunal interactions provides a starting point for identifying key microbial characteristics influencing colonization processes at hydrothermal vents.