scholarly journals Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled byHalobacteriovoraxpredators

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3315 ◽  
Author(s):  
Rory M. Welsh ◽  
Stephanie M. Rosales ◽  
Jesse R. Zaneveld ◽  
Jérôme P. Payet ◽  
Ryan McMinds ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Community Dynamics ◽  
Structure Stability ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Coral Microbiome ◽  
Opportunistic Bacteria ◽  
Vibrio Coralliilyticus ◽  
Time Point

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria:Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, andHalobacteriovorax, a unique bacterial predator ofVibrioand other gram-negative bacteria. We challenged reef-building coral withV. coralliilyticusin the presence or absence ofHalobacteriovoraxpredators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series.Vibrio coralliilyticusinoculation increased the mean relative abundance ofVibriosby greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of theVibriochallenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase inVibrios,two lineages of bacteria (RhodobacteralesandCytophagales) increased in coral tissues, suggesting thatV. coralliilyticuschallenge opens niche space for these known opportunists.Rhodobacteralesincreased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point andCytophagalesfrom <0.001% to 3.656%.Halobacteriovoraxpredators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized thatHalobacteriovoraxpredators might help protect corals by consuming foreign or “alien” gram negative bacteria.Halobacteriovoraxinoculation also altered the microbiome but to a lesser degree thanV. coralliilyticus, andHalobacteriovoraxwere never detected after inoculation. Simultaneous challenge with bothV. coralliilyticusand predatoryHalobacteriovoraxeliminated the increase inV. coralliilyticus, ameliorated changes to the rest of the coral microbiome, and prevented the secondary blooms of opportunisticRhodobacteralesandCytophagalesseen in theV. coralliilyticuschallenge. These data suggest that, under certain circumstances, host-associated bacterial predators may mitigate the ability of other bacteria to destabilize the microbiome.

scholarly journals Alien vs. Predator: Pathogens open niche space for opportunists, unless controlled by predators

2015 ◽  
Author(s):  
Rory M Welsh ◽  
Stephanie M Rosales ◽  
Jesse R.R. Zaneveld ◽  
Jérôme P Payet ◽  
Ryan McMinds ◽  
...  
Keyword(s):  
Coral Tissue ◽  
Structure Stability ◽  
Niche Space ◽  
Gram Negative ◽  
Pathogen Invasion ◽  
Coral Microbiome ◽  
Opportunistic Bacteria ◽  
Pathogen Challenge ◽  
Vibrio Coralliilyticus ◽  
Coral Pathogen

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. Pathogens invading the coral microbiome encounter diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the overall structure, stability, and function of the microbiome during the course of pathogen challenge. We sought to test how coral microbiome dynamics were affected by interactions between two of its members: Vibrio coralliilyticus, a known temperature-dependent coral pathogen, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged specimens of the important reef-building coral Montastraea cavernosa with Vibrio coralliilyticus pathogens in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene time-series. In addition to its direct effects on corals, pathogen challenge reshaped coral microbiomes in ways that allowed for secondary blooms of opportunistic bacteria. As expected, Vibrio coralliilyticus addition increased the infiltration of Vibrio into coral tissues. This increase of Vibrios in coral tissue was accompanied by increased richness, and reduced stability (increased beta-diversity) of the rest of the microbiome, suggesting strong secondary effects of pathogen invasion on commensal and mutualistic coral bacteria. Moreover, after an initial increase in Vibrios, two opportunistic lineages (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that this pathogen opens niche space for opportunists. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming gram-negative pathogens. In keeping with a protective role, Halobacteriovorax addition alone had only minor effects on the microbiome, and no infiltration of Halobacteriovorax into coral tissues was detected in amplicon libraries. Simultaneous challenge with both pathogen and predator eliminated detectable V. corallyticus infiltration into coral tissue samples, ameliorated changes to the rest of the coral microbiome, and prevented secondary blooms of opportunistic Rhodobacterales and Cytophagales. Thus, we show that primary infection by a coral pathogen is sufficient to cause increases in opportunists, as seen in correlational studies. These data further provide a proof-of-principle demonstration that, under certain circumstances, host-associated bacterial predators can mitigate the ability of pathogens to infiltrate host tissue, and stabilize the microbiome against complex secondary changes that favor growth of opportunistic lineages.

scholarly journals Alien vs. Predator: Pathogens open niche space for opportunists, unless controlled by predators

2015 ◽  
Author(s):  
Rory M Welsh ◽  
Stephanie M Rosales ◽  
Jesse R.R. Zaneveld ◽  
Jérôme P Payet ◽  
Ryan McMinds ◽  
...  
Keyword(s):  
Coral Tissue ◽  
Structure Stability ◽  
Niche Space ◽  
Gram Negative ◽  
Pathogen Invasion ◽  
Coral Microbiome ◽  
Opportunistic Bacteria ◽  
Pathogen Challenge ◽  
Vibrio Coralliilyticus ◽  
Coral Pathogen

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. Pathogens invading the coral microbiome encounter diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the overall structure, stability, and function of the microbiome during the course of pathogen challenge. We sought to test how coral microbiome dynamics were affected by interactions between two of its members: Vibrio coralliilyticus, a known temperature-dependent coral pathogen, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged specimens of the important reef-building coral Montastraea cavernosa with Vibrio coralliilyticus pathogens in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene time-series. In addition to its direct effects on corals, pathogen challenge reshaped coral microbiomes in ways that allowed for secondary blooms of opportunistic bacteria. As expected, Vibrio coralliilyticus addition increased the infiltration of Vibrio into coral tissues. This increase of Vibrios in coral tissue was accompanied by increased richness, and reduced stability (increased beta-diversity) of the rest of the microbiome, suggesting strong secondary effects of pathogen invasion on commensal and mutualistic coral bacteria. Moreover, after an initial increase in Vibrios, two opportunistic lineages (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that this pathogen opens niche space for opportunists. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming gram-negative pathogens. In keeping with a protective role, Halobacteriovorax addition alone had only minor effects on the microbiome, and no infiltration of Halobacteriovorax into coral tissues was detected in amplicon libraries. Simultaneous challenge with both pathogen and predator eliminated detectable V. corallyticus infiltration into coral tissue samples, ameliorated changes to the rest of the coral microbiome, and prevented secondary blooms of opportunistic Rhodobacterales and Cytophagales. Thus, we show that primary infection by a coral pathogen is sufficient to cause increases in opportunists, as seen in correlational studies. These data further provide a proof-of-principle demonstration that, under certain circumstances, host-associated bacterial predators can mitigate the ability of pathogens to infiltrate host tissue, and stabilize the microbiome against complex secondary changes that favor growth of opportunistic lineages.

Tolerance to glyphosate and antibiotic resistance in gram-negative bacteria isolated from soils of different agricultural management systems in Ceará, Brazil

Gaia Scientia ◽  
2021 ◽  
Vol 15 (2) ◽  
Author(s):  
Raul Vítor Ferreira de Oliveira ◽  
Margareth Borges Coutinho Gallo ◽  
Oscarina Viana de Sousa ◽  
Álef Vasconcelos Ribeiro ◽  
Tatiana Salata Lima ◽  
...  
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Selective Pressure ◽  
Multidrug Resistant ◽  
Agricultural Management ◽  
Management Systems ◽  
Cross Resistance ◽  
Gram Negative Bacteria ◽  
Conventional Farming ◽  
Gram Negative ◽  
Opportunistic Bacteria

Brazil is among the world’s largest consumers of pesticides, with glyphosate (GLY) being the most commercialized herbicide in the country. Studies showed microorganisms suffer selective pressure when exposed to pesticides, developing tolerance to pesticides and resistance to antibiotics (ABs), in a phenomenon known as “cross-resistance”. The present work aimed to evaluate the occurrence of glyphosate-tolerance and AB-resistance in bacteria isolated from different agricultural management systems in Ceará State, Brazil. Gram-negative bacteria isolated from agroforestry (S1), conventional farming (S2) and uncultivated (S3) soils were cultured in the presence of 1.6% acid glyphosate. Overall, 58 strains were isolated. Soils S1 and S2 presented several multidrug resistant (MDR) strains, the majority resistant to ampicilin. Although there was a small percentage of strains resistant to ertapenem (33%, soil S1), the fact they were found is concerning, as Carbapenem antibiotics are used to treat clinical cases of MDR bacteria, which are not common outside hospital settings. Stenotrophomonas maltophilia (soil S2), resistant to six of the eight ABs tested, was identified by MALDI-TOF mass spectrometry, and was found as one of the most common opportunistic bacteria in ICUs of Ceará hospitals.

scholarly journals Keratinolytic protease from Pseudomonas aeruginosa for leather skin processing

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yeasmin Akter Moonnee ◽  
Md Javed Foysal ◽  
Abu Hashem ◽  
Md Faruque Miah
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Enzyme Production ◽  
Biochemical Characterization ◽  
Animal Feed ◽  
Inorganic Nitrogen ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Leather Industry ◽  
Gram Negative ◽  
Maximum Production

Abstract Background The leather industry generates huge volume of waste each year. Keratin is the principal constituents of this waste that is resistant to degradation. Some bacteria have the ability to degrade keratin through synthesis of a protease called keratinase that can be used as sources of animal feed and industrial production of biodiesel, biofertilizer, and bioplastic. Majority of the studies focused on keratin degradation using gram-positive bacteria. Not much of studies are currently available on production of keratinase from gram-negative bacteria and selection of best parameters for the maximum production of enzyme. The aim of this study was to isolate and characterize both groups of bacteria from soil for keratinase and optimize the production parameters. Results A total of 50 isolates were used for initial screening of enzyme production in skim milk, casein, and feather meal agar. Out of 50, five isolates showed significantly higher enzyme production in preliminary screening assays. Morphological and biochemical characterization revealed 60% of the isolates as gram-negative bacteria including two highest enzyme-producing isolates. The isolates were identified as Pseudomonas aeruginosa through sequencing of 16S rRNA gene. Maximum production of enzyme from P. aeruginosa YK17 was achieved with 2% chicken feather, beef extract, and ammonium nitrate as organic and inorganic nitrogen sources and glucose as a carbon source. Further analysis revealed that 3% inoculum, 40 °C growth temperature and 72-h incubation, resulted in maximum production of keratinase. Conclusion The overall results showed significant higher production of enzyme by the P. aeruginosa YK17 that can be used for the degradation of recalcitrant keratin waste and chemical dehairing in leather industries, thereby preventing environmental pollution.

scholarly journals Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7152
Author(s):  
Fabiola Gómez-Basurto ◽  
Miguel Vital-Jácome ◽  
Elizabeth Selene Gómez-Acata ◽  
Frederic Thalasso ◽  
Marco Luna-Guido ◽  
...  
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Community Dynamics ◽  
Batch Reactor ◽  
Rrna Gene ◽  
Batch Reactors ◽  
Aerobic Granules ◽  
Reactor Operation ◽  
Granule Formation ◽  
Microbial Community Dynamics

Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.

scholarly journals Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

2008 ◽  
Vol 12 (1) ◽  
pp. 277-291 ◽  
Author(s):  
W. K. Balasooriya ◽  
K. Denef ◽  
J. Peters ◽  
N. E. C. Verhoest ◽  
P. Boeckx
Keyword(s):  
Microbial Community ◽  
Ground Water ◽  
Relative Abundance ◽  
Water Depth ◽  
Structural Changes ◽  
Gram Negative Bacteria ◽  
Vegetation Composition ◽  
Gram Positive ◽  
Gram Negative ◽  
Lower Site

Abstract. Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

scholarly journals 919. Understanding Intermittent Detection of Multidrug-Resistant Organisms (MDROs) in Rectally Colonized Patients

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S494-S494
Author(s):  
Sarah Sansom ◽  
Michael Y Lin ◽  
Michael Schoeny ◽  
Christine Fukuda ◽  
Christine Bassis ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Community Dynamics ◽  
Limit Of Detection ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Rrna Gene ◽  
Multilevel Regression ◽  
Microbial Community Dynamics ◽  
Culture Positivity ◽  
Phenotypic Methods

Abstract Background MDRO detection in colonized patients may be intermittent for reasons that are incompletely understood. We examined temporal patterns of gut MDRO colonization after initial MDRO detection by rectal swab screening, and determined the relationship of culture positivity to the relative abundance of corresponding MDRO operational taxonomic units (OTUs) identified by 16S rRNA gene sequence analysis. Methods Rectal or fecal swabs were collected daily from MICU patients 1/11/2017-1/11/2018. First MICU admissions with ≥2 swabs and MICU stays ≥3 days were studied. Samples were cultured for vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE) and P. aeruginosa (CRPA), and extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae by selective media. Resistance mechanisms were confirmed by phenotypic methods and/or PCR. Limit of detection was similar for different MDROs (24-52 CFU/sample). OTU categories corresponding to MDRO species were identified by taxonomy and BLAST. Multilevel regression models estimated the association between MDRO detection and relative abundance of the corresponding OTU. Results 796 unique patients with 3519 swabs were studied. Median (IQR) age was 64 (51-74) years, MICU length of stay was 5 (3-8) days, and number of samples-per-patient was 3 (2-5). Following initial MDRO detection, the probability of subsequent detection varied by MDRO type, and was highest for VRE and lowest for CRPA [Figure 1]. Within each sample, we found a significant association between MDRO detection and relative abundance of the corresponding OTU [Table 1]. In contrast, relative OTU abundance in the first sample with MDRO detection was not predictive of odds of future MDRO detection (p &gt;0.05 for all comparisons). Carriage of &gt;1 MDRO did not affect the odds of MDRO detection in later samples. Figure 1. Probability of Subsequent MDRO Detection after First Positive Varies by MDRO Type Table 1. Higher Mean Corresponding OTU Relative Abundance Within Each Sample is Associated with MDRO Detection Conclusion MDRO culture positivity in rectally colonized patients was correlated with relative abundance of the corresponding OTU in the same sample. Serial detection of different MDRO types was variable, possibly due to distinct microbial community dynamics of different MDRO types. Intermittent failure to detect MDROs could result in misattribution of MDRO acquisition, resulting in inappropriate investigation or intervention. Disclosures All Authors: No reported disclosures

scholarly journals Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

2007 ◽  
Vol 4 (5) ◽  
pp. 3869-3907 ◽  
Author(s):  
W. K. Balasooriya ◽  
K. Denef ◽  
J. Peters ◽  
N. E. C. Verhoest ◽  
P. Boeckx
Keyword(s):  
Microbial Community ◽  
Ground Water ◽  
Relative Abundance ◽  
Water Depth ◽  
Structural Changes ◽  
Gram Negative Bacteria ◽  
Vegetation Composition ◽  
Gram Positive ◽  
Gram Negative ◽  
Lower Site

Abstract. Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; \\textit{Caricetum gracilis} at the wet depression and \\textit{Arrhenatherum elatioris} at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria was significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

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