scholarly journals Microbial Predation Accelerates Granulation and Modulates Microbial Community Composition

2021 ◽  
Author(s):  
Siew Herng Chan ◽  
Muhammad Hafiz Ismail ◽  
Chuan Hao Tan ◽  
Scott A. Rice ◽  
Diane McDougald
Keyword(s):  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Extracellular Dna ◽  
Biological Nutrient Removal ◽  
Strong Positive Correlation ◽  
Bacterial Cells ◽  
Dominant Group ◽  
Granule Formation ◽  
Structural Formation ◽  
Granulation Process

Abstract BackgroundBacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.ResultsFour independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of ‘Candidatus Accmulibacter’ was positively correlated with the formation of compact aggregates and granules.ConclusionPredation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of Candidatus Accumulibacter was necessary for the formation of granules in the absence of protozoa.

scholarly journals Microbial predation accelerates granulation and modulates microbial community composition

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siew Herng Chan ◽  
Muhammad Hafiz Ismail ◽  
Chuan Hao Tan ◽  
Scott A. Rice ◽  
Diane McDougald
Keyword(s):  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Extracellular Dna ◽  
Biological Nutrient Removal ◽  
Strong Positive Correlation ◽  
Bacterial Cells ◽  
Dominant Group ◽  
Granule Formation ◽  
Structural Formation ◽  
Granulation Process

Abstract Background Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge. Results Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of ‘Candidatus Accumulibacter’ was positively correlated with the formation of compact aggregates and granules. Conclusion Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of ‘Candidatus Accumulibacter’ was necessary for the formation of granules in the absence of protozoa.

Bacterial presence in polar regions associated with environment modification by chemical compounds including contaminants

2017 ◽  
Vol 25 (4) ◽  
pp. 481-491 ◽  
Author(s):  
Klaudia Kosek ◽  
Katarzyna Jankowska ◽  
Żaneta Polkowska
Keyword(s):  
Bacterial Communities ◽  
Chemical Compounds ◽  
Freshwater Ecosystems ◽  
Trophic Levels ◽  
Polar Regions ◽  
Bacterial Cells ◽  
Chemical Contamination ◽  
Climate Conditions ◽  
Biological Communities ◽  
Long Time

Microbes are omnipresent and diverse members of all biological communities. In marine and freshwater ecosystems, microorganisms form the base of the food chain supporting higher trophic levels. Even though microbes are generally thought to live in warm regions of Earth, many of them develop in cold climates. Polar regions remain relatively protected from widespread anthropogenic disturbances, which is a consequence of thier remoteness and extreme climate conditions. For a long time these regions were considered to be free from chemical contamination until scientists discovered a presence of pollutants there. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. Xenobiotics including persistent organic pollutants are transported thousands of kilometers by the air and ocean currents, and they are deposed in high-latitude regions and accumulate in all elements of the environment including bacterial communities. It is important to determine their concentration levels in bacterial cells to assess the possibility of contaminants becoming transferred to higher trophic levels; however, some species of bacteria are capable of metabolizing xenobiotics, which makes them less toxic or even removes them from the environment.

Pseudomonas aeruginosa Oligoribonuclease Controls Susceptibility to Polymyxin B by Regulating Pel Exopolysaccharide Production

2022 ◽  
Author(s):  
Baopeng Yang ◽  
Yujun Jiang ◽  
Yongxin Jin ◽  
Fang Bai ◽  
Zhihui Cheng ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Resistance ◽  
Defense Mechanism ◽  
Extracellular Polysaccharide ◽  
Opportunistic Pathogen ◽  
Polymyxin B ◽  
Guanosine Monophosphate ◽  
Extracellular Dna ◽  
Bacterial Cells ◽  
Bacterial Survival

Polymyxins are considered as the last resort antibiotics to treat infections caused by multidrug-resistant Gram negative pathogens. Pseudomonas aeruginosa is an opportunistic pathogen that causes various infections in humans. Proteins involved in lipopolysaccharide modification and maintaining inner and outer membrane integrities have been found to contribute to the bacterial resistance to polymyxins. Oligoribonuclease (Orn) is an exonuclease that regulates the homeostasis of intracellular (3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), thereby regulating the production of extracellular polysaccharide in P. aeruginosa . Previously, we demonstrated that Orn affects the bacterial resistance to fluoroquinolone, β-lactam and aminoglycoside antibiotics. In this study, we found that mutation of orn increased the bacterial survival following polymyxin B treatment in a wild type P. aeruginosa strain PA14. Overexpression of c-di-GMP degradation enzymes in the orn mutant reduced the bacterial survival. By using a fluorescence labeled polymyxin B, we found that mutation of orn increased the bacterial surface bound polymyxin B. Deletion of the Pel synthesis genes or treatment with a Pel hydrolase reduced the surface bound polymyxin B and bacterial survival. We further demonstrated that Pel binds to extracellular DNA (eDNA), which traps polymyxin B and thus protects the bacterial cells. Collectively, our results revealed a novel defense mechanism against polymyxin in P. aeruginosa .

scholarly journals MiSiC, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Swapnesh Panigrahi ◽  
Dorothée Murat ◽  
Antoine Le Gall ◽  
Eugénie Martineau ◽  
Kelly Goldlust ◽  
...  
Keyword(s):  
Deep Learning ◽  
Bacterial Communities ◽  
Cell Biology ◽  
Imaging Modality ◽  
Interaction Model ◽  
Cell Segmentation ◽  
Bacterial Cells ◽  
Interspecies Interactions ◽  
Prey Interaction ◽  
Simple Implementation

Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based 2D segmentation method that automatically segments single bacteria in complex images of interacting bacterial communities with very little parameter adjustment, independent of the microscopy settings and imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.

scholarly journals Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China

2020 ◽  
Vol 10 ◽  
Author(s):  
Xun Kang ◽  
Yanhong Wang ◽  
Siping Li ◽  
Xiaomei Sun ◽  
Xiangyang Lu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Disease Control ◽  
Bacterial Communities ◽  
Mosquito Species ◽  
Microbial Community Composition ◽  
Variable Region ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Quality Filtering ◽  
And Function

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

scholarly journals Neutrophils in Deep Venous Thrombosis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. SCI-29-SCI-29
Author(s):  
Thomas W. Wakefield
Keyword(s):  
Venous Thrombosis ◽  
Deep Venous Thrombosis ◽  
Extracellular Dna ◽  
Strong Positive Correlation ◽  
Plasma Dna ◽  
Vein Wall ◽  
Control Serum ◽  
Significant Difference ◽  
Wells Score

Abstract Neutrophils are involved in venous thrombogenesis, through P-selectin and neutrophil endothelial traps (NETS). In order to determine the importance of neutrophils to thrombogenesis, neutrophil depletion was performed in our rat model of stasis-induced deep venous thrombosis (DVT). Animals were treated with control serum or rabbit anti-rat PMN serum administered perioperatively and sacrificed at two and seven days. At two days, neutropenic rats had 1.6-fold larger thrombi (P = 0.04) and 1.4-fold higher femoral venous pressures by manometry (P = 0.008) without a difference in thrombus neovascularization. By seven days, DVT sizes were similar, but vein wall injury persisted in neutropenic rats with a two-fold increase in vein wall stiffness by microtensiometry (P < 0.05), as well as a 1.2-fold increased thickness (P = 0.04). Vein wall and intrathrombus uPA by Western immunoblotting, as well as intrathrombus MMP-9 gelatinase activity was significantly less in neutropenic rats than controls (P < 0.001). Conversely, MMP-2 was significantly elevated in neutropenic inferior vena cava (IVC) at two days after DVT.1 P-selectin inhibition has been found to limit venous thrombosis in mice. Animals with high circulating levels of sP-selectin (^CT) were compared to selectin gene-deleted animals (PKO, EPKO) and wild-type (WT) mice. ^CT mice showed a significant 50% increase in thrombosis in our IVC ligation model while EPKO mice had the smallest thrombi. A significant difference was noted between ^CT and EPKO for neutrophils, monocytes, and total inflammatory cells at day two. Microparticle (MP) analysis revealed that in the ^CT, WT and PKO mice, a mixed leukocyte (MAC-1) and platelet (CD41) MP population was present. EPKO mice (with the smallest thrombi) revealed primarily a platelet-derived MP population, suggesting the importance of leukocyte-derived MPs in venous thrombogenesis. Of interest, the ^CT mice with the highest TM showed an elevated level of mean channel fluorescence for MAC-1 antibody, indicative of leukocyte derived MPs.2 Through processes that also involve the initial activation of leukocytes and platelets, neutrophils initiate and amplify thrombosis through the formation of NETS, which are extracellular fragments of DNA containing histones and antimicrobial proteins.3,4 In vitro and in vivo, NETs provide a scaffold and stimulus for thrombus formation.5 In order to investigate if plasma DNA (surrogate for NETS) is elevated in patients with DVT and to determine correlations with other biomarkers of DVT, we studied patients presenting to our diagnostic vascular laboratory. From December 2008 to August 2010, patients were divided into three distinct groups: (1) DVT positive, patients symptomatic for DVT confirmed by ultrasound (n = 47); (2) DVT negative, patients with leg pain but negative by ultrasound (n = 28); and (3) control healthy non-pregnant volunteers without signs or symptoms of active or previous DVT (n = 19). Blood was collected for biomarkers and the Wells score risk of DVT was assessed. Results showed that circulating DNA was significantly elevated in DVT patients, compared with both DVT-negative patients (57.7 vs. 17.9 ng/mL; P < 0.01) and controls (57.7 vs. 23.9 ng/mL; P < 0.01). There was a strong positive correlation with C-reactive protein (P < 0.01), D-dimer (P < 0.01), VWF (P < 0.01), Wells score (P < 0.01) and MPO (P < 0.01), along with a strong negative correlation with ADAMTS13 (P < 0.01) and the ADAMTS13/VWF ratio. The logistic regression model showed a strong association between plasma DNA and the presence of DVT (ROC curve 0.814) suggesting a role for DNA in venous thrombogenesis.6 References: 1. Varma MR, Varga AJ, Knipp BS, Sukheepod P, Upchurch GR, Kunkel SL, Wakefield TW, Henke PK. Neutropenia impairs venous thrombosis resolution in the rat. J Vasc Surg. 2003;38:1090-1098 2. Myers DD, Hawley AE, Farris DM, Wrobleski SK, Thanaporn P, Schaub RG, Wagner DD, Kumar A, Wakefield TW. P-selectin and leukocyte microparticles are associated with venous thrombogenesis. J Vasc Surg.2003;38:1075-1089 3. Fuchs TA, Brill A, Duerschmied D, Schatzberg D, Monestier M, Myers DD, Wrobleski SK, Wakefield TW, Hartwig JH, Wagner DD. Extracellular DNA traps promote thrombosis. Proceedings of the National Academy of Sciences. 2010;107:15880-15885 4. von Brühl M-L, Stark K, Steinhart A, Chandraratne S, Konrad I, Lorenz M, Khandoga A, Tirniceriu A, Coletti R, Köllnberger M. Monocytes, neutrophils, and platelets cooperate to initiate and propagate venous thrombosis in mice in vivo. The Journal of Experimental Medicine. 2012;209:819-835 5. Massberg S, Grahl L, von Bruehl M-L, Manukyan D, Pfeiler S, Goosmann C, Brinkmann V, Lorenz M, Bidzhekov K, Khandagale AB. Reciprocal coupling of coagulation and innate immunity via neutrophil serine proteases. Nature Medicine. 2010;16:887-896 6. Diaz JA, Fuchs TA, Jackson TO, Kremer Hovinga JA, Lämmle B, Henke PK, Myers Jr DD, Wagner DD, Wakefield TW. Plasma DNA is elevated in patients with deep vein thrombosis. J Vasc Surg. 2013;1:341-348 Disclosures No relevant conflicts of interest to declare.

scholarly journals Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhu ◽  
Xiang Sun ◽  
Qi-Yong Tang ◽  
Zhi-Dong Zhang
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
Northwest China ◽  
Community Diversity ◽  
Radiation Stress ◽  
Core Microbiome ◽  
Essential Components

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

scholarly journals Biofilm regulation in Clostridioides difficile: Novel systems linked to hypervirulence

2021 ◽  
Vol 17 (9) ◽  
pp. e1009817
Author(s):  
Megan G. Taggart ◽  
William J. Snelling ◽  
Patrick J. Naughton ◽  
Roberto M. La Ragione ◽  
James S. G. Dooley ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Gastrointestinal Disease ◽  
Regulatory System ◽  
Disease Recurrence ◽  
The United States ◽  
Extracellular Dna ◽  
Published Data ◽  
Bacterial Cells ◽  
Healthcare Associated Infection ◽  
Clostridioides Difficile

Clostridiodes difficile (C. difficile) was ranked an “urgent threat” by the Centers for Disease Control and Prevention (CDC) in 2019. C. difficile infection (CDI) is the most common healthcare-associated infection (HAI) in the United States of America as well as the leading cause of antibiotic-associated gastrointestinal disease. C. difficile is a gram-positive, rod-shaped, spore-forming, anaerobic bacterium that causes infection of the epithelial lining of the gut. CDI occurs most commonly after disruption of the human gut microflora following the prolonged use of broad-spectrum antibiotics. However, the recurrent nature of this disease has led to the hypothesis that biofilm formation may play a role in its pathogenesis. Biofilms are sessile communities of bacteria protected from extracellular stresses by a matrix of self-produced proteins, polysaccharides, and extracellular DNA. Biofilm regulation in C. difficile is still incompletely understood, and its role in disease recurrence has yet to be fully elucidated. However, many factors have been found to influence biofilm formation in C. difficile, including motility, adhesion, and hydrophobicity of the bacterial cells. Small changes in one of these systems can greatly influence biofilm formation. Therefore, the biofilm regulatory system would need to coordinate all these systems to create optimal biofilm-forming physiology under appropriate environmental conditions. The coordination of these systems is complex and multifactorial, and any analysis must take into consideration the influences of the stress response, quorum sensing (QS), and gene regulation by second messenger molecule cyclic diguanosine monophosphate (c-di-GMP). However, the differences in biofilm-forming ability between C. difficile strains such as 630 and the “hypervirulent” strain, R20291, make it difficult to assign a “one size fits all” mechanism to biofilm regulation in C. difficile. This review seeks to consolidate published data regarding the regulation of C. difficile biofilms in order to identify gaps in knowledge and propose directions for future study.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

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