bluuebunny/crossref_metadata_2025 huggingface dataset:
Benthic Foraminiferal Response to the Millennial-Scale Variations in Monsoon-Driven Productivity and Deep-Water Oxygenation in the Western Bay of Bengal During the Last 45 ka
Authors: Verma Komal , Singh Harshit , Singh Arun Deo , Singh Pradyumna , Satpathy Rajeev Kumar , Naidu Pothuri Divakar
Published: September 2021

In this study, we presented a high-resolution benthic foraminiferal assemblage record from the western Bay of Bengal (BoB) (off Krishna–Godavari Basin) showing millennial-scale variations during the last 45 ka. We studied temporal variations in benthic foraminiferal assemblages (relative abundances of ecologically sensitive groups/species, microhabitat categories, and morphogroups) to infer past changes in sea bottom environment and to understand how monsoon induced primary productivity-driven organic matter export flux and externally sourced deep-water masses impacted the deep-sea environment at the core site. Our records reveal a strong coupling between surface productivity and benthic environment on glacial/interglacial and millennial scale in concert with Northern Hemisphere climate events. Faunal data suggest a relatively oxic environment when the organic matter flux to the sea floor was low due to low primary production during intensified summer monsoon attributing surface water stratification and less nutrient availability in the mixed layer. Furthermore, records of oxygen-sensitive benthic taxa (low-oxygen vs. high-oxygen benthics) indicate that changes in deep-water circulation combined with the primary productivity-driven organic matter flux modulated the sea bottom oxygen condition over the last 45 ka. We suggest that the bottom water at the core site was well-ventilated during the Holocene (except for the period since 3 ka) compared with the late glacial period. At the millennial timescale, our faunal proxy records suggest relatively oxygen-poor condition at the sea floor during the intervals corresponding to the cold stadials and North Atlantic Heinrich events (H1, H2, H3, and H4) compared with the Dansgaard/Oeschger (D-O) warm interstadials. The study further reveals oxygen-poor bottom waters during the last glacial maximum (LGM, 19–22 ka) which is more pronounced during 21–22 ka. A major shift in sea bottom condition from an oxygenated bottom water during the warm Bølling–Allerød (B/A) (between 13 and 15 ka) to the oxygen-depleted condition during the cold Younger Dryas (YD) period (between 10.5 and 13 ka) is noticed. It is likely that the enhanced inflow of North Atlantic Deep Water (NADW) to BoB would have ventilated bottom waters at the core site during the Holocene, B/A event, and probably during the D-O interstadials of marine isotope stage (MIS) 3.
Physiological and Transcriptional Responses to Acute and Chronic Thermal Stress in the Ark Shell Scapharca subcrenata
Authors: Zou Desheng , Ning Junhao , Lu Xia , Wang Xia , Chen Min , Liu Bo , Fang Jun , Wang Chunde
Published: September 2021

Ark shells (Scapharca subcrenata) grown on the tidal flats are often exposed to high temperature stresses in summer. In order to better understand their adaption to extreme or natural high temperature, we first determined the 96-h upper lethal temperature of ark shell and then investigated their physiological and transcriptional responses to acute or chronic thermal stress at the 96-h upper median lethal temperature (32°C). A significantly higher cumulative mortality (52% in 96 h) was observed in the acute heating treatment (AHT) group than that (22% in 7 days) in the chronic heating treatment (CHT) group. The apoptosis and necrosis rates of hemocytes were increased significantly in a time-dependent manner under both thermal stress strategies. Activities of antioxidant enzymes [superoxide dismutase (SOD) and catalase (CAT)] increased dramatically in a short time followed by a quick decline and reached to a lower level within 12 h in the AHT group, but maintain relatively high levels over a long period in the CHT group. The contents of malondialdehyde (MDA) were increased significantly firstly and restored to the original later in both acute and chronic thermal stress. Moreover, expression of the genes related to heat shock proteins (HSPs; HSP90, HSP70, HSP20, and sHSP), apoptosis [TNF receptor-associated factor 6 (TRAF6), glucose regulated protein 78 kD (GRP78), and caspase-3 (Casp-3)] and antioxidant responses [glutathione S-transferase (GST) and multidrug resistance protein (MRP)] could be induced and up-regulated significantly by thermal stress, however, expression of regucalcin (RGN), metallothionein (MT), and peroxiredoxin (PRX) was down-regulated dramatically under the two heating treatments. These results suggested that anti-apoptotic system, antioxidant defense system and HSPs could play important roles in thermal tolerance of ark shells, and the heat-resistant ark shell strains could be selected continuously by properly chronic thermal stress.
A Hotspot in the Romanian Black Sea: Eelgrass Beds Drive Local Biodiversity in Surrounding Bare Sediments
Authors: Surugiu Victor , Teacă Adrian , Şvedu Ilie , Quijón Pedro A.
Published: September 2021

Ecosystem engineers create habitat and provide conditions otherwise unavailable for the development of diverse communities. In marine soft-bottoms in particular, the biodiversity sustained by a matrix of relatively uniform sediments can be drastically enhanced by the presence of ecosystem engineers such as seagrasses. Unfortunately, the influence of seagrass meadows on the diversity of surrounding sediments is often unrecognized in spite of its importance, especially in coastlines exposed to multiple sources of pollution. This study examined composition and diversity associated with a bed of Zostera noltei Hornemann, 1832, and its surrounding bare sediments in a highly urbanized coastal area of the Romanian Black Sea. Dissimilarity levels were quantified and key species driving the differences between uniform (bare) and complex (eelgrass) sedimentary habitats were identified. 48 taxa were collected and counted, with epifaunal and infaunal species each accounting for nearly half of that diversity. Abundance, richness and diversity were strikingly higher in eelgrass-associated sediments, a difference driven primarily by various species of snails, crustaceans, polychaetes and bivalves. Between-habitat differences remained significant even after the removal of epifaunal species and each dataset undergoing strong data transformation. These results suggest that even small eelgrass beds, located in the vicinity of multiple sources of stress, can act as hotspots and make a substantial contribution to local benthic diversity.
Fabrication, Microstructure and Properties of Nickel/Epoxy Resin Functionally Graded Materials With Magnetic-Field-Driving Method
Authors: Zhan Tongkang , Chang Jiasong , Li Jing
Published: September 2021

Functionally graded materials are attracting more attentions because of the continuously varying properties in different locations. How to design and fabricate FGMs has become a key and difficult point. In this paper, a magnetic-field-driving method is developed to prepare Ni/epoxy resin FGMs by moving a narrow magnetic field from one end of the sample to the other end with the moving direction perpendicular to the field direction. Ni follows the moving of the magnetic field, and a gradient distribution is obtained. The composition gradients are influenced by Ni content, moving velocity, and also cycle times. The results illustrate that this magnetic-field-driving method is an effective way to prepare FGMs, which is very promising into scientific and technological applications.
The Potential Role of Human Papillomavirus Infection in Bell's Palsy: A Hypothesis-Generating Study Based on a Nationwide Cohort
Authors: Li Kuan-Ying , Chou Mei-Chia , Chang Renin , Yip Hei-Tung , Hung Yao-Min , Wei James Cheng-Chung
Published: September 2021

Objective: Our purpose was to investigate whether people with a previous human papillomavirus (HPV) infection were associated with an increased risk of Bell's palsy (BP).

Methods: By using Taiwan population-based data, patients aged > 18 years with HPV infection (n = 22,260) from 2000 to 2012 were enrolled and compared with control subjects who had never been diagnosed with an HPV infection at a 1:4 ratio matched by sex, age, index date, and co-morbidities (n = 89,040). The index date was the first date of HPV diagnosis. All the patients were tracked until the occurrence of BP. Cox proportional hazards regression was applied to estimate the hazard ratios (HRs) for the development of BP in both groups.

Results: The HPV group had 1.25 [95% confidence interval (CI) = 1.03–1.51] times higher risk of BP compared with the non-HPV group after adjusting for sex, age, and co-morbidities. The association of HPV and BP was significant in the sensitivity analyses. In the subgroup analysis, the impact of HPV infection on the risk of BP was more pronounced in the elderly > 50 years [adjusted hazard ratio (aHR) =1.86; 95% CI = 1.37–2.52], hypertension (aHR = 1.65; 95% CI = 1.17–2.31), and chronic obstructive pulmonary disease (aHR = 2.14, 95% CI 1.333.43) subgroups.

Conclusions: Patients with HPV infection have a higher risk of subsequent BP compared with non-HPV patients. More rigorous studies are needed to confirm if and how specific HPV genotypes are associated with BP and the possible role of vaccines in disease prevention.
Gastrointestinal Symptoms and Irritable Bowel Syndrome Are Associated With Female Sex and Smoking in the General Population and With Unemployment in Men
Authors: Nilsson Daniel , Ohlsson Bodil
Published: September 2021

Background: The influence of daily life exposure on the gastrointestinal tract is not fully understood. This study aimed to examine associations between functional gastrointestinal symptoms and sociodemographic status and lifestyle habits in the general population.

Methods: The Malmö Offspring Study (MOS) included 2,648 participants from the general population who had answered a questionnaire about sociodemographic status, lifestyle habits, medical health, and self-reported irritable bowel syndrome (IBS). The visual analog scale for IBS (VAS-IBS) was completed to assess gastrointestinal symptoms the past 2 weeks. Subjects with organic gastrointestinal diseases were excluded. Presence of self-reported IBS and gastrointestinal symptoms the past 2 weeks were used as dependent variables to study the associations with age, sex, body mass index, education, occupation, marital status, smoking, snuff using, alcohol drinking frequency, alcohol amount per drinking occasion, physical activity at work, and physical activity during leisure time, using logistic regression and generalized linear model.

Results: Self-reported IBS was associated with gastrointestinal symptoms the past 2 weeks (p < 0.001). There was an association between IBS and female sex (p < 0.001), former smoking (p < 0.001), present smoking (p < 0.001), and an inverse association with drinking 3–4 standard glasses per occasion (p = 0.038). Gastrointestinal symptoms were associated with age 50–59 years (p = 0.009), ≥60 years (p = 0.004), female sex (p < 0.001), studying (p = 0.036), unemployment (p = 0.009), former smoking (p = 0.001), and present smoking (p = 0.012). In men, IBS was associated with middle-age and both IBS and gastrointestinal symptoms were associated with unemployment (p < 0.001 and p = 0.001, respectively). In women, IBS was associated with present smoking (p = 0.022), and gastrointestinal symptoms were associated with former smoking and inversely associated with higher age (p = 0.006) and intermediate physical activity at work (p = 0.008). No associations were found with BMI, education, marital status, or snuff using.

Conclusion: Self-reported IBS in the general population shows strongest association with female sex and smoking, whereas gastrointestinal symptoms also are associated with unemployment and inversely associated with higher age. In men, both IBS and gastrointestinal symptoms are associated with unemployment. In women, both IBS and gastrointestinal symptoms are associated with smoking, whereas symptoms are inversely associated with higher age and intermediate physical activity.
Microcatheter-Assisted Trabeculotomy Combined With Deep Sclerectomy and Trabeculectomy in Young to Middle-Aged Adults With Advanced Primary Open-Angle Glaucoma: 1-Year Result
Authors: Zhang Hengli , Yan Xiaowei , Li Fan , Ma Lihua , Geng Yulei , Jiao Kexin , Tang Guangxian
Published: September 2021

Objective: We aimed to evaluate the safety and clinical efficacy of ab externo microcatheter-assisted trabeculotomy combined with deep sclerectomy and trabeculectomy (MATT-DS-Trab) in the surgical management of advanced primary open-angle glaucoma (POAG).

Methods: According to the inclusion criteria, we retrospectively collected and analyzed 37 POAG cases in advanced stage who received MATT-DS-Trab. The intraocular pressure (IOP), best corrected visual acuity (BCVA), use of anti-glaucoma drugs, shape of the filtering bleb, size of the scleral lake, complications, and the surgical success rate were recorded.

Results: The mean IOP was 37.50 ± 8.11 mmHg before the operation, while it depleted to 10.08 ± 2.01 and 11.43 ± 2.07 mmHg at 1 week and 12 months after the operation, respectively (both P < 0.001 compared to preoperative IOP). From none to two kinds of anti-glaucoma drugs were used 12 months after surgery on the patients, which were significantly reduced compared with that preoperatively (P < 0.001). An L-type filtering bleb was the main form at all time points after the operation. At 12 months following surgery, an F-type filtering bleb accounted for 5.41% and no E-type filtering bleb was recorded. The length and height of the scleral lake shrunk with time, but there was no statistical significance (P > 0.05). Also, there was no correlation between the size of the scleral pool and the IOP (P > 0.05). At 12 months after the operation, the complete success rates were 94.59, 83.78, and 72.97% according to standards A (≤18 mmHg), B (≤15 mmHg), and C (≤12 mmHg), respectively. Intraoperative complications were mainly anterior chamber hemorrhage, and no complications related to the filtration bleb were observed after the operation.

Conclusion: Based on multichannel mechanisms, MATT-DS-Trab is able to effectively reduce IOP in advanced POAG patients, with few serious complications and a high success rate.
Efficacy and Safety of Treatments for Patients With Portal Hypertension and Cirrhosis: A Systematic Review and Bayesian Network Meta-Analysis
Authors: Yao Qigu , Chen Wenyi , Yan Cuilin , Yu Jiong , Jiang Tian'an , Cao Hongcui
Published: September 2021

Background and Aims:Viral hepatitis are one of the main causes of liver cirrhosis. The treatment of portal hypertension caused by liver cirrhosis is difficult and diverse, and the therapeutic effect is unknown. Bayesian network meta-analysis was performed to compare the efficacy and safety of treatments for patients with portal hypertension and cirrhosis, including a transjugular intrahepatic portosystemic shunt (TIPS), endoscopic therapy, surgical therapy and medications.

Methods:Eligible articles were searched for in PubMed, Embase, Cochrane Library and Web of Science databases from their inception until June 2020. Using the “gemtc-0.8.4” package in R v.3.6.3 software and the Just Another Gibbs Sampler v.4.2.0 program, network meta-analysis was performed using a random effects model within a Bayesian framework. The odds ratios for all-cause rebleeding, bleeding-related mortality, overall survival (OS), treatment failure and hepatic encephalopathy were determined within the Bayesian framework.

Results:Forty randomized controlled trials were identified, including 4,006 adult patients and nine treatment strategies. Our results showed that distal splenorenal shunt and TIPS provided the best control of hemorrhage. Endoscopic variceal ligation with medication resulted in the highest OS rate. Medication alone resulted in poor OS and treatment failure.

Conclusions:We performed a systematic comparison of diverse treatments for cirrhotic patients with portal hypertension. Our meta-analysis indicated that a TIPS and distal splenorenal shunt resulted in lower rates of rebleeding than did other therapies. Furthermore, drugs are more suitable for combination therapy than monotherapy.
Rat Hepatitis E Virus: Presence in Humans in South-Western France?
Authors: Parraud Delphine , Lhomme Sébastien , Péron Jean Marie , Da Silva Isabelle , Tavitian Suzanne , Kamar Nassim , Izopet Jacques , Abravanel Florence
Published: September 2021

Background: Hepatitis E Virus (HEV) is one of the most common causes of hepatitis worldwide, and South-Western France is a high HEV seroprevalence area. While most cases of HEV infection are associated with the species Orthohepevirus-A, several studies have reported a few cases of HEV infections due to Orthohepevirus-C (HEV-C) that usually infects rats. Most of these human cases have occurred in immunocompromised patients. We have screened for the presence of HEV-C in our region.

Methods and Results: We tested 224 sera, mostly from immunocompromised patients, for HEV-C RNA using an in-house real time RT-PCR. Liver function tests gave elevated results in 63% of patients: mean ALT was 159 IU/L (normal < 40 IU/L). Anti-HEV IgG (49%) and anti-HEV IgM (9.4%) were frequently present but none of the samples tested positive for HEV-C RNA.

Conclusion: HEV-C does not circulate in the human population of South-Western France, despite the high seroprevalence of anti-HEV IgG.
Optimal Positive End Expiratory Pressure Levels in Ventilated Patients Without Acute Respiratory Distress Syndrome: A Bayesian Network Meta-Analysis and Systematic Review of Randomized Controlled Trials
Authors: Zhou Jing , Lin Zhimin , Deng Xiumei , Liu Baiyun , Zhang Yu , Zheng Yongxin , Zheng Haichong , Wang Yingzhi , Lai Yan , Huang Weixiang , Liu Xiaoqing , He Weiqun , Xu Yuanda , Li Yimin , Huang Yongbo , Sang Ling
Published: September 2021

Background: To find the optimal positive end expiratory pressure (PEEP) in mechanical ventilated patients without Acute Respiratory Distress Syndrome (ARDS), we conducted a Bayesian network meta-analysis and systematic review of randomized controlled trials (RCTs) comparing different level of PEEP based on a novel classification of PEEP level: ZEEP group (PEEP = 0 cm H2O); lower PEEP group (PEEP = 1–6 cm H2O); intermediate PEEP group (PEEP = 7–10 cm H2O); higher PEEP group (PEEP > 10 cm H2O).

Result: Twenty eight eligible studies with 2,712 patients were included. There were no significant differences in the duration of mechanical ventilation between higher and intermediate PEEP (MD: 0.020, 95% CI: −0.14, 0.28), higher and lower PEEP (MD: −0.010, 95% CI: −0.23, 0.22), higher PEEP and ZEEP (MD: 0.010, 95% CI: −0.40, 0.22), intermediate and lower PEEP (MD: −0.040, 95% CI: −0.18, 0.040), intermediate PEEP and ZEEP (MD: −0.010, 95% CI: −0.42, 0.10), lower PEEP and ZEEP (MD: 0.020, 95% CI: −0.32, 0.13), respectively. Higher PEEP was associated with significantly higher PaO2/FiO2 ratio(PFR) when compared to ZEEP (MD: 73.24, 95% CI: 11.03, 130.7), and higher incidence of pneumothorax when compared to intermediate PEEP, lower PEEP and ZEEP (OR: 2.91e + 12, 95% CI: 40.3, 1.76e + 39; OR: 1.85e + 12, 95% CI: 29.2, 1.18e + 39; and OR: 1.44e + 12, 95% CI: 16.9, 8.70e + 38, respectively). There was no association between PEEP levels and other secondary outcomes.

Conclusion: We identified higher PEEP was associated with significantly higher PFR and higher incidence of pneumothorax. Nonetheless, in terms of other outcomes, no significant differences were detected among four levels of PEEP.

Systematic Review Registration: The study had registered on an international prospective register of systematic reviews, PROSPERO, on 09 April 2021, identifier: [CRD42021241745].
Technological Improvement Rates and Evolution of Energy-Based Therapeutics
Authors: Basnet Subarna , Magee Christopher L.
Published: September 2021

This paper examines the field of energy-based medical therapies based on the analysis of patents. We define the field as the use of external stimuli to achieve biomedical modifications to treat disease and to increase health. Based upon distinct sets of patents, the field is subdivided into sub-domains for each energy category used to achieve the stimulation: electrical, magnetic, microwave, ultrasound, and optical. Previously developed techniques are used to retrieve the relevant patents for each of the stimulation modes and to determine main paths along the trajectory followed by each sub-domain. The patent sets are analyzed to determine key assignees, number of patents, and dates of emergence of the sub-domains. The sub-domains are found to be largely independent as to patent assignees. Electrical and magnetic stimulation patents emerged earliest in the 1970s and microwave most recently around 1990. The annual rate of improvement of all sub-domains (12–85%) is found to be significantly higher than one we find for an aggregate pharmaceutical domain (5%). Overall, the results suggest an increasingly important role for energy-based therapies in the future of medicine.
Embracing Mechanobiology in Next Generation Organ-On-A-Chip Models of Bone Metastasis
Authors: Slay Ellen E. , Meldrum Fiona C. , Pensabene Virginia , Amer Mahetab H.
Published: September 2021

Bone metastasis in breast cancer is associated with high mortality. Biomechanical cues presented by the extracellular matrix play a vital role in driving cancer metastasis. The lack of in vitro models that recapitulate the mechanical aspects of the in vivo microenvironment hinders the development of novel targeted therapies. Organ-on-a-chip (OOAC) platforms have recently emerged as a new generation of in vitro models that can mimic cell-cell interactions, enable control over fluid flow and allow the introduction of mechanical cues. Biomaterials used within OOAC platforms can determine the physical microenvironment that cells reside in and affect their behavior, adhesion, and localization. Refining the design of OOAC platforms to recreate microenvironmental regulation of metastasis and probe cell-matrix interactions will advance our understanding of breast cancer metastasis and support the development of next-generation metastasis-on-a-chip platforms. In this mini-review, we discuss the role of mechanobiology on the behavior of breast cancer and bone-residing cells, summarize the current capabilities of OOAC platforms for modeling breast cancer metastasis to bone, and highlight design opportunities offered by the incorporation of mechanobiological cues in these platforms.
VPsero: Rapid Serotyping of Vibrio parahaemolyticus Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data
Authors: Bian Shengzhe , Jia Yangyang , Zhan Qiuyao , Wong Nai-Kei , Hu Qinghua , Zhang Wenwei , Zhang Yongwei , Li Liqiang
Published: September 2021

Vibrio parahaemolyticus has emerged as a significant enteropathogen in human and marine habitats worldwide, notably in regions where aquaculture products constitute a major nutritional source. It is a growing cause of diseases including gastroenteritis, wound infections, and septicemia. Serotyping assays use commercially available antisera to identify V. parahaemolyticus strains, but this approach is limited by high costs, complicated procedures, cross-immunoreactivity, and often subjective interpretation. By leveraging high-throughput sequencing technologies, we developed an in silico method based on comparison of gene clusters for lipopolysaccharide (LPSgc) and capsular polysaccharide (CPSgc) by firstly using the unique-gene strategy. The algorithm, VPsero, which exploits serogroup-specific genes as markers, covers 43 K and all 12 O serogroups in serotyping assays. VPsero is capable of predicting serotypes from assembled draft genomes, outputting LPSgc/CPSgc sequences, and recognizing possible novel serogroups or populations. Our tool displays high specificity and sensitivity in prediction toward V. parahaemolyticus strains, with an average sensitivity in serogroup prediction of 0.910 for O and 0.961 for K serogroups and a corresponding average specificity of 0.990 for O and 0.998 for K serogroups.
Oenological Characteristics of Four Non-Saccharomyces Yeast Strains With β-Glycosidase Activity
Authors: Qin Tao , Liao Jing , Zheng Yingyuan , Zhang Wenxia , Zhang Xiuyan
Published: September 2021

Non-Saccharomyces yeast with β-glucosidase activity might positively contribute to the flavor and quality of wines. The contribution of four non-Saccharomyces yeast strains Issatchenkia terricola SLY-4, Pichia kudriavzevii F2-24, P. kudriavzevii F2-16, and Metschnikowia pulcherrima HX-13 with β-glucosidase activity to the flavor and quality of wine making was studied. Compared with those of S. cerevisiae single fermentation, the four non-Saccharomyces yeast strains could grow and consume sugar completely with longer fermentation periods, and with no significantly negative effect on chemical characteristics of wines. Moreover, they produced lower content of C6 compounds, benzene derivative, and fatty acid ethyl ester compounds and higher content of terpene, β-ionone, higher alcohol, and acetate compounds. Different yeast strains produced different aroma compounds profiles. In general, the sensory evaluation score of adding non-Saccharomyces yeast-fermented wine was better than that of S. cerevisiae, and I. terricola SLY-4 fermentation received the highest one, followed by P. kudriavzevii F2-24, P. kudriavzevii F2-16, and M. pulcherrima HX-13 from high to low. The research results provide a theoretical basis for the breeding of non-Saccharomyces yeast and its application in wine making.
Bioaugmented Mixed Culture by Clostridium aceticum to Manipulate Volatile Fatty Acids Composition From the Fermentation of Cheese Production Wastewater
Authors: Atasoy Merve , Cetecioglu Zeynep
Published: September 2021

Production of targeted volatile fatty acid (VFA) composition by fermentation is a promising approach for upstream and post-stream VFA applications. In the current study, the bioaugmented mixed microbial culture by Clostridium aceticum was used to produce an acetic acid dominant VFA mixture. For this purpose, anaerobic sequencing batch reactors (bioaugmented and control) were operated under pH 10 and fed by cheese processing wastewater. The efficiency and stability of the bioaugmentation strategy were monitored using the production and composition of VFA, the quantity of C. aceticum (by qPCR), and bacterial community profile (16S rRNA Illumina Sequencing). The bioaugmented mixed culture significantly increased acetic acid concentration in the VFA mixture (from 1170 ± 18 to 122 ± 9 mgCOD/L) compared to the control reactor. Furthermore, the total VFA production (from 1254 ± 11 to 5493 ± 36 mgCOD/L) was also enhanced. Nevertheless, the bioaugmentation could not shift the propionic acid dominancy in the VFA mixture. The most significant effect of bioaugmentation on the bacterial community profile was seen in the relative abundance of the Thermoanaerobacterales Family III. Incertae sedis, its relative abundance increased simultaneously with the gene copy number of C. aceticum during bioaugmentation. These results suggest that there might be a syntropy between species of Thermoanaerobacterales Family III. Incertae sedis and C. aceticum. The cycle analysis showed that 6 h (instead of 24 h) was adequate retention time to achieve the same acetic acid and total VFA production efficiency. Biobased acetic acid production is widely applicable and economically competitive with petroleum-based production, and this study has the potential to enable a new approach as produced acetic acid dominant VFA can replace external carbon sources for different processes (such as denitrification) in WWTPs. In this way, the higher treatment efficiency for WWTPs can be obtained by recovered substrate from the waste streams that promote a circular economy approach.
Distribution of Soil Extracellular Enzymatic, Microbial, and Biological Functions in the C and N-Cycle Pathways Along a Forest Altitudinal Gradient
Authors: Bayranvand Mohammad , Akbarinia Moslem , Salehi Jouzani Gholamreza , Gharechahi Javad , Baldrian Petr
Published: September 2021

The diverse chemical, biological, and microbial properties of litter and organic matter (OM) in forest soil along an altitudinal gradient are potentially important for nutrient cycling. In the present study, we sought to evaluate soil chemical, biological, microbial, and enzymatic characteristics at four altitude levels (0, 500, 1,000, and 1,500 m) in northern Iran to characterize nutrient cycling in forest soils. The results showed that carbon (C) and nitrogen (N) turnover changed with altitude along with microbial properties and enzyme activity. At the lowest altitude with mixed forest and no beech trees, the higher content of N in litter and soil, higher pH and microbial biomass nitrogen (MBN), and the greater activities of aminopeptidases affected soil N cycling. At elevations above 1,000 m, where beech is the dominant tree species, the higher activities of cellobiohydrolase, arylsulfatase, β-xylosidase, β-galactosidase, endoglucanase, endoxylanase, and manganese peroxidase (MnP) coincided with higher basal respiration (BR), substrate-induced respiration (SIR), and microbial biomass carbon (MBC) and thus favored conditions for microbial entropy and C turnover. The low N content and high C/N ratio at 500-m altitude were associated with the lowest microbial and enzyme activities. Our results support the view that the plain forest with mixed trees (without beech) had higher litter quality and soil fertility, while forest dominated by beech trees had the potential to store higher C and can potentially better mitigate global warming.
The Type 9 Secretion System Is Required for Flavobacterium johnsoniae Biofilm Formation
Authors: Eckroat Todd J. , Greguske Camillus , Hunnicutt David W.
Published: September 2021

Flavobacterium johnsoniae forms biofilms in low nutrient conditions. Protein secretion and cell motility may have roles in biofilm formation. The F. johnsoniae type IX secretion system (T9SS) is important for both secretion and motility. To determine the roles of each process in biofilm formation, mutants defective in secretion, in motility, or in both processes were tested for their effects on biofilm production using a crystal violet microplate assay. All mutants that lacked both motility and T9SS-mediated secretion failed to produce biofilms. A porV deletion mutant, which was severely defective for secretion, but was competent for motility, also produced negligible biofilm. In contrast, mutants that retained secretion but had defects in gliding formed biofilms. An sprB mutant that is severely but incompletely defective in gliding motility but retains a fully functional T9SS was similar to the wild type in biofilm formation. Mutants with truncations of the gldJ gene that compromise motility but not secretion showed partial reduction in biofilm formation compared to wild type. Unlike the sprB mutant, these gldJ truncation mutants were essentially nonmotile. The results show that a functional T9SS is required for biofilm formation. Gliding motility, while not required for biofilm formation, also appears to contribute to formation of a robust biofilm.
Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats
Authors: Garber Arkadiy I. , Cohen Ashley B. , Nealson Kenneth H. , Ramírez Gustavo A. , Barco Roman A. , Enzingmüller-Bleyl Tristan C. , Gehringer Michelle M. , Merino Nancy
Published: September 2021

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.
Cultivation of Important Methanotrophs From Indian Rice Fields
Authors: Rahalkar Monali C. , Khatri Kumal , Pandit Pranitha , Bahulikar Rahul A. , Mohite Jyoti A.
Published: September 2021

Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10–6–10–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.
Development and Application of a Novel Rapid and Throughput Method for Broad-Spectrum Anti-Foodborne Norovirus Antibody Testing
Authors: Zuo Yueting , Xue Liang , Gao Junshan , Liao Yingyin , Jiang Yueting , Li Ying , Liang Yanhui , Wang Linping , Cai Weicheng , Cheng Tong , Wang Juan , Chen Moutong , Zhang Jumei , Ding Yu , Wu Qingping
Published: September 2021

Foodbone norovirus (NoV) is the leading cause of acute gastroenteritis worldwide. Candidate vaccines are being developed, however, no licensed vaccines are currently available for managing NoV infections. Screening for stimulated antibodies with broad-spectrum binding activities can be performed for the development of NoV polyvalent vaccines. In this study, we aimed to develop an indirect enzyme-linked immunosorbent assay (ELISA) for testing the broad spectrum of anti-NoV antibodies. Capsid P proteins from 28 representative NoV strains (GI.1–GI.9 and GII.1–GII.22 except GII.11, GII.18, and GII.19) were selected, prepared, and used as coating antigens on one microplate. Combined with incubation and the horseradish peroxidase chromogenic reaction, the entire process for testing the spectrum of unknown antibodies required 2 h for completion. The intra-assay and inter-assay coefficients of variation were less than 10%. The new method was successfully performed with monoclonal antibodies and polyclonal antibodies induced by multiple antigens. In conclusion, the indirect ELISA assay developed in this study had a good performance of reliability, convenience, and high-throughput screening for broad-spectrum antibodies.
A Rickettsiella Endosymbiont Is a Potential Source of Essential B-Vitamins for the Poultry Red Mite, Dermanyssus gallinae
Authors: Price Daniel R. G. , Bartley Kathryn , Blake Damer P. , Karp-Tatham Eleanor , Nunn Francesca , Burgess Stewart T. G. , Nisbet Alasdair J.
Published: September 2021

Many obligate blood-sucking arthropods rely on symbiotic bacteria to provision essential B vitamins that are either missing or at sub-optimal levels in their nutritionally challenging blood diet. The poultry red mite Dermanyssus gallinae, an obligate blood-feeding ectoparasite, is a serious threat to the hen egg industry. Poultry red mite infestation has a major impact on hen health and welfare and causes a significant reduction in both egg quality and production. Thus far, the identity and biological role of nutrient provisioning bacterial mutualists from D. gallinae are little understood. Here, we demonstrate that an obligate intracellular bacterium of the Rickettsiella genus is detected in D. gallinae mites collected from 63 sites (from 15 countries) across Europe. In addition, we report the genome sequence of Rickettsiella from D. gallinae (Rickettsiella – D. gallinae endosymbiont; Rickettsiella DGE). Rickettsiella DGE has a circular 1.89Mbp genome that encodes 1,973 proteins. Phylogenetic analysis confirms the placement of Rickettsiella DGE within the Rickettsiella genus, related to a facultative endosymbiont from the pea aphid and Coxiella-like endosymbionts (CLEs) from blood feeding ticks. Analysis of the Rickettsiella DGE genome reveals that many protein-coding sequences are either pseudogenized or lost, but Rickettsiella DGE has retained several B vitamin biosynthesis pathways, suggesting the importance of these pathways in evolution of a nutritional symbiosis with D. gallinae. In silico metabolic pathway reconstruction revealed that Rickettsiella DGE is unable to synthesize protein amino acids and, therefore, amino acids are potentially provisioned by the host. In contrast, Rickettsiella DGE retains biosynthetic pathways for B vitamins: thiamine (vitamin B1) via the salvage pathway; riboflavin (vitamin B2) and pyridoxine (vitamin B6) and the cofactors: flavin adenine dinucleotide (FAD) and coenzyme A (CoA) that likely provision these nutrients to the host.
Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital
Authors: Esposito Fernanda , Cardoso Brenda , Fontana Herrison , Fuga Bruna , Cardenas-Arias Adriana , Moura Quézia , Fuentes-Castillo Danny , Lincopan Nilton
Published: September 2021

The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.
Gut Microbiota Associated With Different Sea Lamprey (Petromyzon marinus) Life Stages
Authors: Mathai Prince P. , Byappanahalli Muruleedhara N. , Johnson Nicholas S. , Sadowsky Michael J.
Published: September 2021

Sea lamprey (SL; Petromyzon marinus), one of the oldest living vertebrates, have a complex metamorphic life cycle. Following hatching, SL transition into a microphagous, sediment burrowing larval stage, and after 2–10+ years, the larvae undergo a dramatic metamorphosis, transforming into parasitic juveniles that feed on blood and bodily fluids of fishes; adult lamprey cease feeding, spawn, and die. Since gut microbiota are critical for the overall health of all animals, we examined the microbiota associated with SLs in each life history stage. We show that there were significant differences in the gut bacterial communities associated with the larval, parasitic juvenile, and adult life stages. The transition from larval to the parasitic juvenile stage was marked with a significant shift in bacterial community structure and reduction in alpha diversity. The most abundant SL-associated phyla were Proteobacteria, Fusobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Firmicutes, with their relative abundances varying among the stages. Moreover, while larval SL were enriched with unclassified Fusobacteriaceae, unclassified Verrucomicrobiales and Cetobacterium, members of the genera with fastidious nutritional requirements, such as Streptococcus, Haemophilus, Cutibacterium, Veillonella, and Massilia, were three to four orders of magnitude greater in juveniles than in larvae. In contrast, adult SLs were enriched with Aeromonas, Iodobacter, Shewanella, and Flavobacterium. Collectively, our findings show that bacterial communities in the SL gut are dramatically different among its life stages. Understanding how these communities change over time within and among SL life stages may shed more light on the role that these gut microbes play in host growth and fitness.
Endophytes of Brazilian Medicinal Plants With Activity Against Phytopathogens
Authors: Iantas Jucélia , Savi Daiani Cristina , Schibelbein Renata da Silva , Noriler Sandriele Aparecida , Assad Beatriz Marques , Dilarri Guilherme , Ferreira Henrique , Rohr Jürgen , Thorson Jon S. , Shaaban Khaled A. , Glienke Chirlei
Published: September 2021

Plant diseases caused by phytopathogens are responsible for significant crop losses worldwide. Resistance induction and biological control have been exploited in agriculture due to their enormous potential. In this study, we investigated the antimicrobial potential of endophytic fungi of leaves and petioles of medicinal plants Vochysia divergens and Stryphnodendron adstringens located in two regions of high diversity in Brazil, Pantanal, and Cerrado, respectively. We recovered 1,304 fungal isolates and based on the characteristics of the culture, were assigned to 159 phenotypes. One isolate was selected as representative of each phenotype and studied for antimicrobial activity against phytopathogens. Isolates with better biological activities were identified based on DNA sequences and phylogenetic analyzes. Among the 159 representative isolates, extracts from 12 endophytes that inhibited the mycelial growth (IG) of Colletotrichum abscissum (≥40%) were selected to expand the antimicrobial analysis. The minimum inhibitory concentrations (MIC) of the extracts were determined against citrus pathogens, C. abscissum, Phyllosticta citricarpa and Xanthomonas citri subsp. citri and the maize pathogen Fusarium graminearum. The highest activity against C. abscissum were from extracts of Pseudofusicoccum stromaticum CMRP4328 (IG: 83% and MIC: 40 μg/mL) and Diaporthe vochysiae CMRP4322 (IG: 75% and MIC: 1 μg/mL), both extracts also inhibited the development of post-bloom fruit drop symptoms in citrus flowers. The extracts were promising in inhibiting the mycelial growth of P. citricarpa and reducing the production of pycnidia in citrus leaves. Among the isolates that showed activity, the genus Diaporthe was the most common, including the new species D. cerradensis described in this study. In addition, high performance liquid chromatography, UV detection, and mass spectrometry and thin layer chromatography analyzes of extracts produced by endophytes that showed high activity, indicated D. vochysiae CMRP4322 and P. stromaticum CMRP4328 as promising strains that produce new bioactive natural products. We report here the capacity of endophytic fungi of medicinal plants to produce secondary metabolites with biological activities against phytopathogenic fungi and bacteria. The description of the new species D. cerradensis, reinforces the ability of medicinal plants found in Brazil to host a diverse group of fungi with biotechnological potential.
Disinfection Performance of a Drinking Water Bottle System With a UV Subtype C LED Cap Against Waterborne Pathogens and Heterotrophic Contaminants
Authors: Mariita Richard M. , Blumenstein Sébastien A. , Beckert Christian M. , Gombas Thomas , Randive Rajul V.
Published: September 2021

The purgaty One systems (cap+bottle) are portable stainless-steel water bottles with UV subtype C (UVC) disinfection capability. This study examines the bottle design, verifies disinfection performance against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae, and heterotrophic contaminants, and addresses the public health relevance of heterotrophic bacteria. Bottles were inoculated with deliberately contaminated potable water and disinfection efficacy examined using colony forming unit (CFU) assay for each bacterial strain. The heterotrophic plate count (HPC) method was used to determine the disinfection performance against environmental contaminants at day 0 and after 3days of water in stationary condition without prior UVC exposure. All UVC irradiation experiments were performed under stationary conditions to confirm that the preset application cycle of 55s offers the desired disinfection performance under-tested conditions. To determine effectiveness of purgaty One systems (cap+bottle) in disinfection, inactivation efficacy or log reduction value (LRV) was determined using bacteria concentration between UVC ON condition and controls (UVC OFF). The study utilized the 16S ribosomal RNA (rRNA) gene for characterization of isolates by identifying HPC bacteria to confirm if they belong to groups that are of public health concern. Purgaty One systems fitted with Klaran UVC LEDs achieved 99.99% inactivation (LRV4) efficacy against E. coli and 99.9% inactivation (LRV3) against P. aeruginosa, V. cholerae, and heterotrophic contaminants. Based on the 16S rRNA gene analyses, the study determined that the identified HPC isolates from UVC irradiated water are of rare public health concern. The bottles satisfactorily inactivated the target pathogenic bacteria and HPC contaminants even after 3days of water in stationary condition.