Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent campylobacteria

Author Posting. © American Society for Microbiology, 2022. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 88(2),(2022): e02083-21, https://doi.org/10.1128/AEM.02083-21.Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, Arcobacter, Sulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances.This research was funded by the U.S. National Science Foundation grants OCE-1131095 (S.M.S.) and OCE-1136727 (S.M.S., J.S.S.). Further support was provided by the WHOI Investment in Science Fund (S.M.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office

Dissolved organic carbon compounds in deep-sea hydrothermal vent fluids from the East Pacific Rise at 9°50′N

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 125 (2018): 41-49, doi:10.1016/j.orggeochem.2018.08.004.Deep-sea hydrothermal vents are unique ecosystems that may release chemically distinct dissolved organic matter to the deep ocean. Here, we describe the composition and concentrations of polar dissolved organic compounds observed in low and high temperature hydrothermal vent fluids at 9°50’N on the East Pacific Rise. The concentration of dissolved organic carbon was 46 μM in the low temperature hydrothermal fluids and 14 μM in the high temperature hydrothermal fluids. In the low temperature vent fluids, quantifiable dissolved organic compounds were dominated by water-soluble vitamins and amino acids. Derivatives of benzoic acid and the organic sulfur compound 2,3-dihydroxypropane-1-sulfonate (DHPS) were also present in low and high temperature hydrothermal fluids. The low temperature vent fluids contain organic compounds that are central to biological processes, suggesting that they are a by-product of biological activity in the subseafloor. These compounds may fuel heterotrophic and other metabolic processes at deep-sea hydrothermal vents and beyond.This project was funded by a grant from WHOI’s Deep Ocean Exploration Institute and WHOI’s Ocean Ridge Initiative (to EBK and SMS) and by NSF OCE-1154320 (to EBK and KL), OCE- 1136727 (to SMS and JSS), and OCE 1131095 (to SMS)

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hou, J., Sievert, S. M., Wang, Y., Seewald, J. S., Natarajan, V. P., Wang, F., & Xiao, X. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome, 8(1), (2020): 102, doi:10.1186/s40168-020-00851-8.Background Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys. Results Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9–10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased. Conclusions This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a “fluid-shaped” microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a “mineral-shaped” community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years.This work was supported by the China Ocean Mineral Resources R&D Association (grant No. DY135-B2-12), the Natural Science Foundation of China (grant No. 41530967, 41921006, 91751205), the Senior User Project of RV KEXUE (KEXUE2019GZ06), and by the US National Science Foundation grant OCE-1136727 and the WHOI Investment in Science Fund to S.M.S

Primary productivity below the seafloor at deep-sea hot springs

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 6756–6761, doi:10.1073/pnas.1804351115.The existence of a chemosynthetic subseafloor biosphere was immediately recognized when deep-sea hot springs were discovered in 1977. However, quantifying how much new carbon is fixed in this environment has remained elusive. In this study, we incubated natural subseafloor communities under in situ pressure/temperature and measured their chemosynthetic growth efficiency and metabolic rates. Combining these data with fluid flux and in situ chemical measurements, we derived empirical constraints on chemosynthetic activity in the natural environment. Our study shows subseafloor microorganisms are highly productive (up to 1.4 Tg C produced yearly), fast-growing (turning over every 17–41 hours), and physiologically diverse. These estimates place deep-sea hot springs in a quantitative framework and allow us to assess their importance for global biogeochemical cycles.This research was funded by a grant of the Dimensions of Biodiversity program of the US National Science Foundation (NSF-OCE-1136727 to S.M.S. and J.S.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office

Full-thickness resection device (FTRD) for treatment of upper gastrointestinal tract lesions: the first international experience.

Background and study aims The Full-Thickness Resection Device (FTRD) provides a novel treatment option for lesions not amenable to conventional endoscopic resection techniques. There are limited data on the efficacy and safety of FTRD for resection of upper gastrointestinal tract (GIT) lesions. Patients and methods This was an international multicenter retrospective study, including patients who had an endoscopic resection of an upper GIT lesion using the FTRD between January 2017 and February 2019. Results Fifty-six patients from 13 centers were included. The most common lesions were mesenchymal neoplasms (n = 23, 41 %), adenomas (n = 7, 13 %), and hamartomas (n = 6, 11 %). Eighty-four percent of lesions were located in the stomach, and 14 % in the duodenum. The average size of lesions was 14 mm (range 3 to 33 mm). Deployment of the FTRD was technically successful in 93 % of patients (n = 52) leading to complete and partial resection in 43 (77 %) and 9 (16 %) patients, respectively. Overall, the FTRD led to negative histological margins (R0 resection) in 38 (68 %) of patients. A total of 12 (21 %) mild or moderate adverse events (AEs) were reported. Follow-up endoscopy was performed in 31 patients (55 %), on average 88 days after the procedure (IQR 68-138 days). Of these, 30 patients (97 %) did not have any residual or recurrent lesion on endoscopic examination and biopsy, with residual adenoma in one patient (3 %). Conclusions Our results suggest a high technical success rate and an acceptable histologically complete resection rate, with a low risk of AEs and early recurrence for FTRD resection of upper GIT lesions

Diagnostic strategy and timing of intervention in infected necrotizing pancreatitis: an international expert survey and case vignette study

AbstractBackgroundThe optimal diagnostic strategy and timing of intervention in infected necrotizing pancreatitis is subject to debate. We performed a survey on these topics amongst a group of international expert pancreatologists.MethodsAn online survey including case vignettes was sent to 118 international pancreatologists. We evaluated the use and timing of fine needle aspiration (FNA), antibiotics, catheter drainage and (minimally invasive) necrosectomy.ResultsThe response rate was 74% (N = 87). None of the respondents use FNA routinely, 85% selectively and 15% never. Most respondents (87%) use a step-up approach in patients with infected necrosis. Walled-off necrosis (WON) is considered a prerequisite for endoscopic drainage and percutaneous drainage by 66% and 12%, respectively. After diagnosing infected necrosis, 55% routinely postpone invasive interventions, whereas 45% proceed immediately to intervention. Lack of consensus about timing of intervention was apparent on day 14 with proven infected necrosis (58% intervention vs. 42% non-invasive) as well as on day 20 with only clinically suspected infected necrosis (59% intervention vs. 41% non-invasive).DiscussionThe step-up approach is the preferred treatment strategy in infected necrotizing pancreatitis amongst expert pancreatologists. There is no uniformity regarding the use of FNA and timing of intervention in the first 2–3 weeks of infected necrotizing pancreatitis

Diagnosis and treatment of pancreatic duct disruption or disconnection: an international expert survey and case vignette study

Background: Pancreatic duct disruption or disconnection is a potentially severe complication of necrotizing pancreatitis. With no existing treatment guidelines, it is unclear whether there is any consensus among experts in clinical practice. We evaluated current expert opinion regarding the diagnosis and treatment of pancreatic duct disruption and disconnection in an international case vignette study. Methods: An online case vignette survey was sent to 110 international expert pancreatologists. Expert selection was based on publications in the last 5 years and/or participation in development of IAP/APA and ESGE guidelines on acute pancreatitis. Consensus was defined as agreement by at least 75% of the experts. Results: The response rate was 51% (n = 56). Forty-four experts (79%) obtained a MRI/MRCP and 52 experts (93%) measured amylase levels in percutaneous drain fluid to evaluate pancreatic duct integrity. The majority of experts favored endoscopic transluminal drainage for infected (peri)pancreatic necrosis and pancreatic duct disruption (84%, n = 45) or disconnection (88%, n = 43). Consensus was lacking regarding the treatment of patients with persistent percutaneous drain production, and with persistent sterile necrosis. Conclusion: This international survey of experts demonstrates that there are many areas for which no consensus existed, providing clear focus for future investigation

Sample log from Jason-II dives for Sievert collected from the R/V Atlantis (AT26-10) in the East Pacific Rise, Pacific Ocean (Microbial Communities at Deep-Sea Vents project)

Dataset: Jason-II sample log AT26-10This dataset is a sample log of samples collected by ROV Jason II at the 9ºN deep-sea hydrothermal vent field on the East Pacific Rise, Pacific Ocean, January 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/559780NSF Division of Ocean Sciences (NSF OCE) OCE-113672

The influence of near-surface sediment hydrothermalism on the TEX86 tetraether-lipid-based proxy and a new correction for ocean bottom lipid overprinting

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bentley, J. N., Ventura, G. T., Walters, C. C., Sievert, S. M., & Seewald, J. S. The influence of near-surface sediment hydrothermalism on the TEX86 tetraether-lipid-based proxy and a new correction for ocean bottom lipid overprinting. Biogeosciences, 19(18), (2022): 4459–4477, https://doi.org/10.5194/bg-19-4459-2022.The diversity and relative abundances of tetraether lipids produced by archaea and bacteria in soils and sediments are increasingly used to assess environmental change. For instance, the TetraEther indeX of 86 carbon atoms (TEX86), based on archaeal isoprenoidal glycerol dialkyl glycerol tetraether (iGDGT) lipids, is frequently applied to reconstruct past sea-surface temperatures (SSTs). Yet, it is unknown how the ratio fully responds to environmental and/or geochemical variations and if the produced signals are largely the adaptive response by Thaumarchaeota to oceanographic effects associated with climate or seasonal temperature changes in the upper water column. We present the results of a four push-core transect study of surface sediments collected along an environmental gradient at the Cathedral Hill hydrothermal-vent system in Guaymas Basin, Gulf of California. The transect crosses a region where advecting hydrothermal fluids reach 155 ∘C within the upper 21 cm below the seafloor (cm b.s.f.) close to the vent center to near-ambient conditions at the vent periphery. The recovered iGDGTs closest to the vent center experienced high rates of turnover with up to 94 % of the lipid pool being lost within the upper 21 cm b.s.f. Here, we show that the turnover is non-selective across TEX86 GDGT lipids and does not affect the ratio independently. However, as evident by TEX86 ratios being highly correlated to the Cathedral Hill vent sediment porewater temperatures (R2=0.84), the ratio can be strongly impacted by the combination of severe lipid loss coupled with the addition of in situ iGDGT production from archaeal communities living in the vent sediments. The resulting overprint produces absolute temperature offsets of up to 4 ∘C based on the TEX calibration relative to modern climate records of the region. The overprint is also striking given the flux of iGDGTs from the upper water column is estimated to be ∼ 93 % of the combined intact polar lipid (IPL) and core GDGT lipid pool initially deposited on the seafloor. A model to correct the overprint signal using IPLs is therefore presented that can similarly be applied to all near-surface marine sediment systems where calibration models or climate reconstructions are made based on the TEX86 measure.This research has been supported by the Natural Sciences and Engineering Research Council of Canada (grant no. RGPIN-2018-06147; NSERC), NSERC Canada Research Chairs (CRC) program, Canada Foundation for Innovation (CFI; JELF–CRC, John R. Evans Leaders Fund), NSERC Discovery Grants program (application no. RGPIN-2017-05822), Woods Hole Oceanographic Institution (WHOI) Deep Ocean Exploration Initiative 2008, and Natural Science Foundation (grant no. MCB-0702677 to Jeffrey S. Seewald and Stefan M. Sievert; NSF)

Salvage endoscopic resection after definitive chemoradiotherapy for esophageal cancer: a Western experience.

Definitive chemoradiotherapy (CRT) is increasingly used as a nonsurgical treatment for esophageal cancer. In Japanese studies, salvage endoscopic resection (ER) has emerged as a promising strategy for local failure after definitive CRT. We aimed to evaluate the safety and efficacy of salvage ER in a Western setting. Gastroenterologists from Europe and the United States were invited to submit their experience with salvage endoscopic submucosal dissection (ESD) or endoscopic mucosal resection (EMR) after definitive CRT. Participating gastroenterologists completed an anonymized database, including patient demographics, clinicopathologic variables, and follow-up on survival and recurrence. Gastroenterologists from 10 endoscopic units in 6 European countries submitted information on 25 patients. A total of 35 salvage ER procedures were performed, of which 69% were ESD and 31% EMR. Most patients had squamous cell carcinoma (64%) of the middle or lower esophagus (68%) staged as cT2-3 (68%) and cN+ (52%) before definitive CRT. The median time from end of definitive CRT to ER was 22 months (interquartile range, 6-47). The en-bloc resection rate was 92% for ESD and 46% for EMR. During a median of 24 months (interquartile range, 12-59) of follow-up after salvage ER, 52% developed a recurrence (11 locoregional, 2 distant). The 5-year recurrence-free survival, overall survival, and disease-specific survival were 36%, 52%, and 79%, respectively. No major intra- or postprocedural adverse events, such as bleeding or perforation, were reported. In carefully selected esophageal cancer patients, salvage ER is technically feasible after definitive CRT. Further prospective research is recommended to validate the safety and effectivity of salvage ER for the management of local failure