Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum.

BACKGROUND: Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS: Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS: This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

Surgical management of spontaneous bowel perforation and fascial dehiscence in a patient on bevacizumab and pembrolizumab in the setting of active Clostridium difficile infection.

Immunotherapy such as bevacizumab and pembrolizumab is used to treat an increasing number of malignancies. These medications have been associated with poor wound healing and several gastrointestinal complications, including intestinal perforations in rare cases. We present a unique case of a patient with metastatic cervical cancer on pembrolizumab and recent bevacizumab therapy, presenting with a colonic perforation requiring urgent exploratory laparotomy, in the setting of active Clostridium difficile infection. She required a second laparotomy shortly after due to fascial dehiscence, where a synthetic absorbable mesh was used for fascial approximation. We review the factors that led to these events and describe the surgical technique used for safe abdominal closure.

Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L.

Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.

30-Day Postoperative Outcomes in Patients With Limited Mobility - A Propensity Score-Matched Comparative Analysis.

INTRODUCTION: There is limited data correlating preoperative mobility limitations with clinical outcomes in bariatric patients. This study uses propensity score matching (PSM) to compare 30-day outcomes between patients with preoperative limited mobility (LM) versus patients without (non-LM). METHODS: Using the 2016-2018 Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) database, patients undergoing primary laparoscopic sleeve gastrectomy or gastric bypass were identified. Two cohorts were defined using preoperative LM status. To adjust for confounders, 1:1 PSM was performed using 25 preoperative characteristics, and balance was assessed with standardized mean difference. Preoperative patient demographics and postoperative 30-day outcomes were compared in both matched and unmatched cohorts. RESULTS: 453,146 patients were identified, of which 6942 (1.47%) were LM and 464,555 were non-LM. 1:1 PSM matched 6624 LM to 6624 non-LM patients with good balance for all covariates. LM had higher rates of unplanned intubation (0.4% vs 0.7%, P < .01), unplanned admission to ICU (1.4% vs 2.5%, P < .01), readmissions (4.1% vs 4.9%, P = .036), unplanned reoperation (1.5% vs 2.0%, P = .02), and 30-day mortality (0.2% vs 0.5%, P = .02). Complications including acute renal failure, intra/postoperative myocardial infarction, venous thrombosis, and pulmonary embolism were not significantly different between the matched groups. CONCLUSION: After adjusting for confounders, patients with preoperative limited mobility have higher rates of intubation, ICU admission, reoperation, readmission, and mortality. Prudent pre-operative candidate selection, counseling, and risk mitigation strategies are needed when a patient with limited mobility status is being considered for bariatric surgery.

Risks of therapeutic versus prophylactic neurectomies.

INTRODUCTION: Neuralgia due to a peripheral nerve injury may result in chronic pain, requiring a therapeutic surgical neurectomy. Meanwhile, some neurectomies are performed prophylactically, such as during inguinal mesh removal. Outcomes and risks associated with neurectomies are largely unknown despite consensus panels recommending them. METHODS: All patients who underwent neurectomy 2013-2020 were analyzed. Data collection included demographics, preoperative symptoms, and postoperative outcomes. Indications for neurectomy were categorized as "therapeutic" if the patient had preoperative neuralgia or "prophylactic" if neurectomy was deemed necessary intra-operatively. RESULTS: 66 patients underwent 80 operations and a total of 122 neurectomies. On average, 1.5 neurectomies were performed per operation. Therapeutic neurectomies were performed in 42 (64%) patients and prophylactic in 34 (52%). The most commonly transected nerve was the ilioinguinal nerve. Average preoperative pain score was 5.8/10. On paired analysis, there was a significant reduction in pain after prophylactic neurectomy (2.5 points, p = 0.002) but not after therapeutic neurectomy. None of the nerves transected prophylactically had postoperative neuralgia, whereas 35% of the nerves transected therapeutically resulted in persistent or recurrent neuralgia (p < 0.001). To treat this, 21% required only nerve blocks and 9% required ablation or reoperative neurectomy. Three patients had complex regional pain syndrome (CRPS), a severe complication; all three were diagnosed with chronic pain syndrome pre-operatively. DISCUSSION: We demonstrate that prophylactic neurectomy is largely safe. In contrast, a therapeutic neurectomy had a 35% risk of persistent or recurrent neuralgia, 9% required additional ablative or reoperative neurectomy. Three patients advanced from chronic pain syndrome to CRPS. We recommend the decision to perform a neurectomy be judicious and selective, especially in patients with known chronic pain syndrome. Prior to planning surgical neurectomy, other less invasive modalities should be exhausted and patients should be aware of its risks.

Outcomes from laparoscopic versus robotic mesh removal after inguinal hernia repair.

INTRODUCTION: Preperitoneally placed mesh for inguinal hernia repair may require removal to address hernia recurrence, mesh reaction, meshoma, or other chronic pain. These are best approached either laparoscopically or robotically, but there is no consensus on which is the best approach for mesh removal nor are there any studies to evaluate and compare their outcomes. METHODS: All patients who underwent inguinal mesh removal via laparoscopic and robotic approaches from 2011 to 2020 were analyzed. Data regarding demographics, preoperative, intraoperative, and postoperative outcomes were collected. RESULTS: Over 9 years, 62 patients underwent 24 laparoscopic and 50 robotic operations. Laparoscopic cases had a shorter operative time by a mean of 55 min (p = 0.02). There were no differences in intraoperative complications or postoperative outcomes between the two groups. Patients in both groups showed significant improvement after mesh removal (p = 0.02, p < 0.01) within 2 weeks postoperatively and at long-term follow up (p < 0.01, p < 0.01). CONCLUSION: It is our experience that both laparoscopic and robotic approaches are viable options for removal of retroperitoneally placed inguinal mesh. Operative time with the laparoscopic approach was significantly shorter than the robotic approach. Patients on average had significant reduction in their preoperative pain, regardless of the approach. Minimally invasive mesh removal is a technically challenging operation, with risk of vascular and nerve injuries regardless of the approach. These findings demonstrate that both modalities are safe and effective with experienced surgeons.

Routine Versus Selective Liver Biopsy During Bariatric Surgery: Postoperative Outcomes and Preoperative Predictors of NASH.

BACKGROUND: Nonalcoholic steatohepatitis (NASH) is common in patients with obesity. Liver biopsy (LB) can be routinely or selectively performed during bariatric surgery to identify patients with NASH. METHODS: Patients undergoing bariatric surgery between 2016 and 2020 at our institution were identified. Chart review identified patients undergoing concurrent LB. LB results were compared between patients undergoing routine LB and selective LB. Patient demographics and postoperative outcomes were compared between those who received LB and those who did not (non-LB). In the LB cohort, preoperative characteristics of patients with NASH were compared to those without NASH, and multivariable regression was used to identify predictors of NASH. RESULTS: Two thousand three hundred ninety-three patients were identified, of which 400 (16.7%) had liver biopsies (LB) and 1,993 (83.3%) did not (non-LB). Three hundred thirty LB were performed routinely, and 70 were selective. Compared to selective LB, routine LB identified significantly higher rates of steatosis (83.6% vs. 4.5%, p < 0.01), periportal inflammation (67.0% vs. 3.2%, p < 0.01), fibrosis (65.8% vs. 2.1%, p < 0.01), and NASH (10.9% vs. 1.5%, p < 0.01). There were no differences in postoperative complications, blood transfusions, readmissions, or reoperations between LB and non-LB. On multivariable regression, highest BMI > 40 (OR 2.85, 95% CI 1.43-5.67) and insulin-dependent diabetes (OR 4.83, 95% CI 1.70-13.69) were associated with a higher odds of NASH, while Black race was associated with lower odds (OR 0.25, 95% CI 0.09-0.65). CONCLUSIONS: Routine liver biopsies during bariatric surgery identify higher rates of advanced NAFLD compared to selective biopsies, and can be safely performed without an increased risk of postoperative complications.

Management of Postoperative Complications Following Bariatric and Metabolic Procedures.

Bariatric and metabolic surgery is a safe and effective treatment of morbid obesity, a disease that continues to increase in prevalence in the United States and worldwide. The two most commonly performed operations are the sleeve gastrectomy and the gastric bypass. Early and late complications can occur, and although referral to a bariatric surgeon or center is ideal, emergency management of acute problems is relevant to all general surgeons. Bariatric surgery can have surgical and metabolic consequences. An understanding of the altered anatomy and physiology helps to guide management of morbidities. This article discusses surgical postoperative complications and metabolic complications.

Management of Postcholecystectomy Complications.

Cholecystectomy is one of the most common general surgery procedures performed worldwide. Complications include bile duct injury, strictures, bleeding, infection/abscess, retained gallstones, hernias, and postcholecystectomy syndrome. Obtaining a critical view of safety and following the other tenets of the Safe Cholecystectomy Task Force will aid in the prevention of bile duct injury and other morbidity associated with cholecystectomy.

QIC: A Pilot Quality Improvement Curriculum Utilizing Interactive, Team-based Workshops.

BACKGROUND: Incorporation of quality improvement (QI) training is essential to meet the milestones set forth by the Accreditation Council for Graduate Medical Education. However, there is no standardized curriculum. OBJECTIVE: We aimed to create a QI curriculum through the integration of didactics and team-based learning via the completion of resident-led QI projects. METHODS: An institutional review board-approved QI curriculum consisting of four interactive workshops was developed. The workshops introduced the various components of QI, with a focus on Plan-Do-Study-Act. Anonymous and voluntary precurriculum and postcurriculum surveys were administered during the study period in 2018. RESULTS: Fifty surgical residents participated in the curriculum, and four QI projects were completed, with 23 residents completing both precurriculum and postcurriculum surveys. Following the curriculum, residents were more confident in their ability to design a QI project (5.7 ± 2.6 versus 7.1 ± 1.9, P = 0.02), write a problem statement (6.7 ± 2.5 versus 7.8 ± 1.1, P = 0.04), and write an aim statement (6.7 ± 2.6 versus 7.8 ± 1.2, P = 0.04). Residents also improved in perceived ability to lead a QI project (5.6 ± 2.9 versus 6.9 ± 1.9, P = 0.05), knowing the steps to complete a QI project (6.0 ± 2.8 versus 7.4 ± 1.7, P = 0.04), and familiarity with QI terminology (5.6 ± 2.6 versus 7.0 ± 1.9, P = 0.03). CONCLUSIONS: We found that the curriculum was a success and was well received. In addition, there was an improvement in perceived competency and confidence surrounding some of the steps necessary to complete a QI endeavor.

Comparative Analysis of the MADS-Box Genes Revealed Their Potential Functions for Flower and Fruit Development in Longan (Dimocarpus longan).

Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mß, Mγ) and type II (MIKC*, MIKC C ) groups, and MIKC C genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKC C genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKC C genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.

How safe is bariatric surgery in patients with class I obesity (body mass index 30-35 kg/m2)?

BACKGROUND: The safety profile of bariatric surgery in patients with class I obesity, or body mass index ≥30 and <35 kg/m2, is a matter of concern among patients and physicians. OBJECTIVE: To assess the safety profile of bariatric surgery in patients with class I obesity. SETTING: The Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) data set. METHODS: The Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program 2015 to 2016 data sets were queried for class I obesity patients who underwent primary bariatric procedures. The 30-day postoperative safety profile, predictors of adverse events, and comparison between Roux-en-Y gastric bypass (RYGB) versus sleeve gastrectomy (SG) were studied. RESULTS: A total of 8628 cases with a mean preoperative body mass index of 33.7 ± 1.1 kg/m2 were analyzed: 1838 (21.3%) underwent RYGB, 6243 (72.4%) underwent SG, 530 (6.1%) underwent gastric banding, and 17 (.2%) underwent duodenal switch; 33.9% had diabetes and 75% had hypertension. The composite morbidity rate (defined as presence of any of 24 postoperative adverse events) for the entire cohort was 3.8%, and the serious morbidity rate (presence of any of 9 serious complications) was .7%. The 30-day mortality rate was .05% (4 cases). Presence of chronic kidney disease was found to be associated with higher composite and serious morbidity (composite morbidity: odds ratio 5.1, 95% confidence interval 2.22-11.71; serious morbidity: odds ratio 5.66, 95% confidence interval 1.52-21.14). SG patients had significantly better short-term safety outcomes than RYGB patients. CONCLUSION: Findings from this study, the largest series to date, indicate that bariatric surgery is safe in patients with class I obesity, with very low risk of morbidity and mortality.

Utilization of Quality Improvement Methodology to Standardize Communication of Outside Hospital Transfers in a General Surgery Program.

OBJECTIVE: There is no standardized method of communication regarding the arrival of outside hospital (OSH) transfers at our institution. We utilized quality improvement methodologies to enhance sign-out, benefiting both resident workflow and patient care. DESIGN: A dynamic census log of pending OSH transfers was created. Total number of OSH transfers (with or without prior notification), time to admission orders, and resident self-reported preparedness in receiving/triaging OSH admissions were measured before and after implementation of the census log tool. SETTING: Quaternary referral hospital in Cleveland, Ohio. PARTICIPANTS: The census log was made available to General Surgery residents on receiving surgical teams. After the data collection period, it was made available to all residents in the program. RESULTS: A total of 93 patients were transferred to receiving surgical teams during our 13-week study period. Resident notification of the OSH transfer prior to patient's arrival increased from 44.7% pre- to 70.3% postimplementation of the tool (p = 0.03). When residents received prior notification of pending transfers, time to place admission orders decreased from 81.2 ± 79.9 minutes to 40.4 ± 36.8 minutes (p = 0.0029). Junior residents' self-reported preparedness in admitting an OSH transfer did not significantly differ when they received prior notification versus when they did not. In contrast, senior residents' self-reported higher levels of preparedness in the instances where they received prior notification of a pending transfer. CONCLUSIONS: In light of the recent Clinical Learning Environment Review program set forth by the Accreditation Council for Graduate Medical Education, trainees are expected to engage in improvement processes as it relates to patient safety and transitions of care. The development and implementation of our tool demonstrate that quality improvement methodologies can be effectively applied to resident workflow challenges, improving both trainee education and patient care.

Characteristics of benign and malignant thyroid disease in familial adenomatous polyposis patients and recommendations for disease surveillance.

BACKGROUND: Familial adenomatous polyposis (FAP) is a hereditary colon cancer syndrome that involves multiple extracolonic organs, including the thyroid. Several studies have estimated the rate of thyroid cancer in FAP to occur at five times the rate of the general population, but no current consensus defines screening for thyroid cancer in this cohort. This study seeks to define the features of benign and malignant thyroid disease in FAP patients, to compare thyroid cancer cases found through screening with those found incidentally, and to propose disease surveillance recommendations. METHODS: Prospective screening for early thyroid cancer detection with thyroid ultrasound (US) was performed on FAP patients at the time of annual colonoscopy since November 2008. Clinical and US data were reviewed to characterize the observed thyroid nodules. Nonscreening-detected cases (NSD) were found through review of the colon cancer registry database. RESULTS: Eighteen NSD were found, compared with 15 screening-detected (SD) cases, out of 205 total patients screened (Mage=42 years; 55% female). The mean tumor size was larger in the NSD group than the SD group (p=0.04), and they tended to demonstrate more positive lymph nodes and more complications than the SD group. In the screened cohort, at least one thyroid nodule was detected in 106 (51.7%) patients, with 90% of these seen on initial exam. A total of 40/106 (37.7%) patients required fine-needle aspiration biopsy of a dominant nodule (Msize=14 mm), and 28/40 (70%) of these were performed at the first US visit. Suspicious US features were present in 16/40 (40%) patients, including five sub-centimeter nodules. Cytology and/or nodule US was abnormal in 15/205 screened patients, leading to surgery and revealing 14 papillary and one medullary thyroid cancer. CONCLUSIONS: Given the age and sex distribution of the screened cohort, this study reveals a higher-than-expected prevalence of both benign and malignant thyroid disease in the FAP population. Additionally, SD cases seemed to consist of smaller-sized cancers that required less radical therapy compared to NSD cases. Since it was found that the initial US in the screening program accounted for the majority of detected nodules (90%) and biopsies (70%), baseline and subsequent thyroid US surveillance is recommended in all FAP patients.

A multi-institutional international study of risk factors for hematoma after thyroidectomy.

BACKGROUND: Cervical hematoma can be a potentially fatal complication after thyroidectomy, but its risk factors and timing remain poorly understood. METHODS: We conducted a retrospective, case-control study identifying 207 patients from 15 institutions in 3 countries who developed a hematoma requiring return to the operating room (OR) after thyroidectomy. RESULTS: Forty-seven percent of hematoma patients returned to the OR within 6 hours and 79% within 24 hours of their thyroidectomy. On univariate analysis, hematoma patients were older, more likely to be male, smokers, on active antiplatelet/anticoagulation medications, have Graves' disease, a bilateral thyroidectomy, a drain placed, a concurrent parathyroidectomy, and benign pathology. Hematoma patients also had more blood loss, larger thyroids, lower temperatures, and higher blood pressures postoperatively. On multivariate analysis, independent associations with hematoma were use of a drain (odds ratio, 2.79), Graves' disease (odds ratio, 2.43), benign pathology (odds ratio, 2.22), antiplatelet/anticoagulation medications (odds ratio, 2.12), use of a hemostatic agent (odds ratio, 1.97), and increased thyroid mass (odds ratio, 1.01). CONCLUSION: A significant number of patients with a postoperative hematoma present >6 hours after thyroidectomy. Hematoma is associated with patients who have a drain or hemostatic agent, have Graves' disease, are actively using antiplatelet/anticoagulation medications or have large thyroids. Surgeons should consider these factors when individualizing patient disposition after thyroidectomy.

[Comparison of nitrifying populations between a lab-scale system and an industrial system treating coking wastewater].

Molecular analysis of community structure can help diagnose problems in malfunctioning full-scale wastewater treatment system. A lab-scale A1-A2-O fixed biofilm system with highly efficient nitrification (NH3-N removal at 95. 2%) was set up as a reference for an industrial system with poor performance of nitrification (NH3-N removal efficiency at -106%) for treating coking wastewater. Composition of nitrifying bacteria of biofilm samples in aerobic reactors of the two systems was compared by 16S rDNA clone library analysis. The composition of clone library of the lab-scale system indicate Nitrosomonas europaea-Nitrosoccus mobilis cluster and sublineage I of Nitrospira genus are dominant ammonia and nitrite oxidizers in this process respectively. However, there were no clones related to nitrifying bacteria in clone library of the industrial system which suggested low abundance of nitrifying bacteria in this system. Further, Real-Time PCR with Taqman probe revealed that 16S rDNA copy number of Nitrospira in aerobic reactor of the lab-scale system was 3.4 x 10(6)/microg DNA of biofilm which is 300 times higher than that in the industrial system. The absence of Nitrosomonas and Nitrospira in the industrial system leads to poor performance of nitrification. Building up of a high population level of Nitrosomonas and Nitrospira in aerobic reactor is the key to improve efficiency of nitrification of the industrial system.

Cloning of environmental genomic fragments as physical markers for monitoring microbial populations in coking wastewater treatment system.

The association between community functional shift and dynamics of genomic DNA composition can be used to identify functionally relevant populations as indicator organisms for systems monitoring. In this work, fingerprinting-based community DNA hybridization was used to monitor community structural dynamics and identify genomic fragments whose abundance shifts were concomitant to changes in COD removal capacity in a reactor. A laboratory-scale anaerobic-anoxic-oxic fixed biofilm system treating coking wastewater was operated with (LR mode) or without effluent recirculation (LNR mode). The contribution to total chemical oxygen demand (COD) removal by the anoxic reactor increased from 4% in LNR mode to 26% in LR mode. Long primer RAPD (randomly amplified polymorphic DNA) community fingerprints of the anoxic reactor also changed most significantly from the one similar to the anaerobic reactor to one similar to the oxic reactor. DNA hybridization revealed one signature band of 2.1 kb shared by the anoxic and oxic reactors in LR, but not LNR mode. Clone library profiling of this band resulted in one predominant 2.1-kb genomic fragment (B3) with no homologous sequences in GenBank. Real-time polymerase chain reaction indicated that copy numbers of B3 in the anoxic reactor under LR mode were 69 times higher than that under LNR mode, concomitant to a significant increase in COD removal capacity in this reactor. The different patterns of distribution of B3 in the laboratory system and a comparable malfunctioning industrial system demonstrated the potential of this genomic fragment as physical markers in systems monitoring. In addition, this genomic fragment may allow sequence-guided isolation of the host microbe.

Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison.

Structural shifts associated with functional dynamics in a bacterial community may provide clues for identifying the most valuable members in an ecosystem. A laboratory-scale denitrifying reactor was adapted from use of non-efficient seeding sludge and was utilized to degrade quinoline and remove the chemical oxygen demand. Stable removal efficiencies were achieved after an adaptation period of six weeks. Both denaturing gradient gel electrophoresis profiling of the 16S rRNA gene V3 region and comparison of the 16S rRNA gene sequence clone libraries (LIBSHUFF analysis) demonstrated that microbial communities in the denitrifying reactor and seeding sludge were significantly distinct. The percentage of the clones affiliated with the genera Thauera and Azoarcus was 74% in the denitrifying reactor and 4% in the seeding sludge. Real-time quantitative PCR also indicated that species of the genera Thauera and Azoarcus increased in abundance by about one order of magnitude during the period of adaptation. The greater abundance of Thauera and Azoarcus in association with higher efficiency after adaptation suggested that these phylotypes might play an important role for quinoline and chemical oxygen demand removal under denitrifying conditions.