Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.

Introduction: Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities. Methods: To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2. Results and discussion: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.

Length of the Remnant Cystic Duct and Bile Duct Stone Recurrence: a Case‒Control Study.

BACKGROUND: Since the introduction of the Critical View of Safety approach in laparoscopic cholecystectomy, exposure of the common bile duct, and common hepatic duct is not recommended, therefore, the length of the cystic duct remnant is no longer controlled. The aim of this case‒control study is to evaluate the relationship between the length of the cystic duct remnant and the risk for bile duct stone recurrence after cholecystectomy. METHODS: All MRIs with dedicated sequences of the biliary tract taken between 2010 and 2020 from patients who underwent prior cholecystectomy were reviewed. The length of the cystic duct remnant was measured and compared between the patients with and without bile duct stones using multivariate logistic regression analysis. RESULTS: A total of 362 patients were included in this study, 23.5% of whom had bile duct stones on MRI. The cystic duct remnant was significantly longer in the patients with stones than in the control group (median 31 mm versus 18 mm, P < 0.001). In the MRIs performed > 2 years after cholecystectomy, the cystic duct remnant was also significantly longer in the patients with bile duct stones (median 32 mm versus 21 mm, P < 0.001). A cystic duct remnant ≥ 15 mm in length increased the odds of stones (OR = 2.3, P = 0.001). Overall, the odds of bile duct stones increased with an increasing cystic duct remnant length (≥ 45 mm, OR = 5.0, P < 0.001). CONCLUSIONS: An excessive cystic duct remnant length increases the odds of recurrent bile duct stones after cholecystectomy.

Limitations and prospects in the management of IPMN: a retrospective, single-center observational study.

BACKGROUND: With increasing use and enhanced accuracy of cross-sectional imaging, the diagnosis of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas has increased over the last few decades. The extent to which malignant transformation occurs remains unclear, making the management of IPMNs controversial. The aim of this study was to evaluate the progression rate and outcome of follow-up in patients with IPMNs. METHODS: A database of all patients diagnosed with IPMN at the Cantonal Hospital HFR Fribourg, Switzerland, between January 2006 and December 2019 with a follow-up of at least 6 months was analyzed retrospectively. Descriptive statistics were performed on patient demographics, IPMN characteristics, and follow-up data. RESULTS: A total of 56 patients were included in this study. Ten patients underwent primary surgery, 46 were enrolled in a surveillance program.21.7% (n = 5) of patients under surveillance presented with worrisome features of IPMN; progression rates were significantly higher in these patients (p = 0.043). Most progression occurred in the early follow-up period. Five patients underwent surgery due to progression, of which 2 presented high-grade dysplasia and 2 malignancy on postoperative histology. CONCLUSIONS: The limited predictive value of current guidelines may lead to surgical overtreatment, and the decision to proceed with surgical resection should be made with caution. Further prospective analyses and the development of novel biomarkers are needed to better understand the natural history of IPMN and improve diagnostic precision.

Metagenome-Assembled Genome of a Putative Methanogenic Methanosarcina sp. Strain Enriched from Terrestrial High-CO2 Subsurface Sediments.

A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.

Circular Metagenome-Assembled Genome of Methanobacterium sp. Strain ERen5, a Putative Methanogenic, H2-Utilizing Terrestrial Subsurface Archaeon.

A circular, single-contig Methanobacterium sp. metagenome-assembled genome (MAG) was recovered from high-CO2 enrichments inoculated with drill core material from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered MAG highlighted putative methanogenesis genes, providing valuable information on archaeal activity in the deep biosphere.

Neurogenic appendicopathy: an underestimated disease-systematic review of the literature.

PURPOSE: Appendectomy is one of the most frequently performed surgeries worldwide, but neurogenic appendicopathy (NA) remains a poorly understood disease with controversial clinical management. The aim of this review was to obtain a clear definition of the disease and summarize its management. METHODS: We performed a systematic review of the literature on NA in PubMed, EMBASE, Web of Science, and Cochrane databases from inception to 19/01/2021 according to PRISMA statement standards. Eligibility criteria were original articles examining histopathology, clinical management, and/or follow-up of patients with NA. The literature review is complemented by a clinical case. RESULTS: In 40 articles, the estimated incidence of NA among appendectomies performed in patients with a suspicion of acute appendicitis (AA) was 10.4% (N = 740, range 1.8-32%). NA more frequently causes recurrent and longer lasting pain compared to AA; however, these diseases are usually not clinically or radiologically distinguishable. Based on our analysis, NA is defined as the presence of three criteria: (1) clinical presentation of AA, (2) absence of acute inflammation on histopathology, and (3) presence of S-100-positive spindle cells or proliferation of Schwann cells. Laparoscopic appendectomy has been shown to be a safe and successful treatment. CONCLUSIONS: NA is a poorly known disease, which may clinically appear as AA but is often related to recurrent and longer lasting abdominal pain. Patients with NA may suffer for years before diagnosis. In cases of typical symptoms, appendectomy should be performed even in cases of macroscopically and radiologically normal-appearing appendices with normal laboratory results.

Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.