<p><strong>Abstract.</strong> We studied asphalt deposits, oil seepage and gas venting during a multidisciplinary cruise in the Bay of Campeche, southern Gulf of Mexico. We conducted multibeam bathymetric mapping with an autonomous underwater vehicle and performed seafloor observations as well as sampling with a remotely operated vehicle. While previous studies concentrated on the asphalt volcano Chapopote Knoll, we confirmed that asphalt deposits at the seafloor occurred across numerous other knolls and ridges in water depths between 1230 and 3150 m; this is evidence that the outflow of heavy oil is a common component of hydrocarbon seepage of Campeche Knolls. The outflow of heavy oil either created whips or sheets floating in the water that subsequently descend and pile-up as meter high stacks at the seafloor over time or spread at the seafloor forming flows ranging from meters to tens of meters in diameter. Unlike seafloor-covering asphalts known from other continental margins, those in our study include relatively fresh material. Seafloor observations documented how chemosynthetic communities develop on the asphalts, with bacterial mats and juvenile vestimentiferan tubeworms colonizing the most recent flows. <br><br> Gas bubble emissions were an additional widespread component of hydrocarbon seepage at Campeche Knolls. The hydrocarbon gas had thermogenic origins, as indicated by the composition (C<sub>1</sub>/C<sub>2</sub>-ratio: 14 to 185) and stable carbon isotopic signature of methane (<i>&#948;</i><sup>13</sup>C-CH<sub>4</sub>: &#8722;45.1 to &#8722;49.8 &#8240;). Gas emissions were detected by multibeam echosounder at water depths as great as 3420 m over Tsanyao Yang Knoll. Gas emissions occurred at sites without large asphalt deposits (Tsanyao Yang Knoll) as well as through old, fragmented asphalts (Mictlan Knoll, Chapopote Knoll). The gas emissions feed gas hydrate deposits at shallow seafloor depth. Gas hydrate formed mounds that were ~ 10 m wide by several meters high in soft sediments and filled the space within fragmented asphalts. The largest gas hydrate mounds supported dense colonies of 1&#8211;2 m long tubeworms that covered areas > 100 m<sup>2</sup>. These tubesworms grow with their posterior tubes implanted in a 5 to 10 cm thick reaction zone composed of authigenic carbonates, detritus, and microbial mats that overlie gas hydrate layers that were at least 2 m thick in places. This association between gas hydrates and vestimentifera has been noted in gas seeps at lesser depths, but was developed to an unequaled extent in the Campeche Knolls. <br><br> Previous studies have documented oil slicks on the ocean surface across many sites in the region. This study found liquid oil emissions in diverse settings. Sites with oil seepage are characterized by oil-soaked sediments, chemosynthetic fauna with associated heterotrophs, and bacterial coatings. Gas bubble emissions and oil seepage occurred independent of asphalt deposits or through old, fragmented asphalts, indicating that presently active hydrocarbon seepage overprints older asphalt deposits. Campeche Knolls are unique in several aspects including the occurrence of recent flows of heavy oil, deep-water hydrocarbon seepage, with many species that are new to science.</p>
Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, co-existed within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow towards the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase. This electron bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.ImportancePrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome opens the possibility to study the potential benefits of having two pathways and the interplay between these pathways. Additionally, this will allow the investigation of the unusual, and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.
<p>Foraminifera are highly abundant marine unicellular eukaryotes. They are known for their important ecological role in most marine ecosystems, their major contribution to the carbon cycle, and their remarkable physiological plasticity. Many foraminiferal species have mixotrophic metabolism that is often based on partnerships with diverse algae, or in some cases, on harvesting diatom chloroplasts, known as kleptoplasty. To date, kleptoplasty was shown only in rotaliid lineages. Here, we report the first discovery of a diatom kleptoplasty in the <em>Hauerina diversa,</em> a tropical shallow-water miliolid that is an unexpected candidate for this life strategy. To elucidate this adaptation, we collected <em>H. diversa</em> specimens from the southeastern Mediterranean coast and visualized many intact chloroplasts in clustered structures within the foraminiferal cytoplasm using transmission electron microscopy. Preliminary genetic analyses confirmed that the harvested chloroplasts originated from diatoms. Primary production estimates using isotopically labeled NaH<sup>14</sup>CO<sub>3</sub> as a carbon source suggest photosynthetic activity of the &#8216;stolen&#8217; chloroplasts inside the host cell. This activity was found to be about two orders lower compared to the diatom-bearing species <em>Amphistegina lobifera</em>. We finally provide the first molecular phylogeny of <em>H. diversa </em>and its evolutionary relationship to ancient alveolind foraminifera. We thus demonstrate the first case of kleptoplasty in the ancient group of alveolind-miliolids, expanding the evolutionary range of kleptoplasty in foraminifera</p>
Background: Diverse microbes catalyze biogeochemical cycles in the terrestrial subsurface, yet the corresponding ecophysiology was only estimated in a limited number of subterrestrial, often shallow aquifers. Here, we detrained the productivity, diversity, and functions of active microbial communities in the Judea Group carbonate and the underlying deep (up to 1.5 km below ground) Kurnub Group Nubian sandstone aquifers. These pristine oligotrophic aquifers, recharged more than tens to hundreds of thousands years ago, contain fresh/brackish, hypoxic/anoxic, often hot (up to 60°) water and serve as habitats for key microbial producers. Results: We show that recent groundwater recharge, inorganic carbon and ammonium strongly influence chemosynthetic primary productivity in carbonate and sandstone aquifers (4.4-21.9 μg C d-1 L-1 and 1.2-2.7 μg C d-1 L-1, respectively). These high values indicate the possibility that the global aquifer productivity rates may be underestimated. Metagenome analysis revealed the prevalence of chemoautotrophic pathways, particularly the Calvin-Benson-Bassham cycle. The key chemosynthetic lineages in the carbonate aquifer were Halothiobacillales, whereas Burkholderiales and Rhizobiales occupied the sandstone aquifer. Most chemosynthetic microbes may oxidize sulfur compounds or ammonium, using oxygen or oxidized nitrogen as electron acceptors. Abundant sulfate reducers in the anoxic deeper aquifer have the potential to catabolize various organics, fix carbon via the Wood Ljungdahl pathway, and often possess nitrogenase, indicating diazotrophic capabilities. Our data suggest that connectivity between the aquifers and their exposure to energy inputs and surface water may play a key role in shaping these communities, altering physicochemical parameters and selecting taxa and functions. We highlight the metabolic versatility in the deep subsurface that underpins their efficient harnessing of carbon and energy from different sources.
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