scholarly journals Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments

2020 ◽  
Vol 8 (8) ◽  
pp. 1245
Author(s):  
Cyrus Rutere ◽  
Kirsten Knoop ◽  
Malte Posselt ◽  
Adrian Ho ◽  
Marcus A. Horn
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Hyporheic Zone ◽  
Community Dynamics ◽  
Environmental Concern ◽  
Transformation Products ◽  
Pollutant Removal ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Microbial Community Dynamics

Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.

scholarly journals Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e93827 ◽  
Author(s):  
Rachel Poretsky ◽  
Luis M. Rodriguez-R ◽  
Chengwei Luo ◽  
Despina Tsementzi ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Dynamics ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbial Community Dynamics

scholarly journals Microbial community dynamics of surface water in British Columbia, Canada

2019 ◽  
Author(s):  
Miguel I. Uyaguari-Diaz ◽  
Matthew A. Croxen ◽  
Kirby Cronin ◽  
Zhiyao Luo ◽  
Judith Isaac-Renton ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Dynamics ◽  
Fecal Contamination ◽  
Rrna Gene ◽  
Microbial Culture ◽  
Sample Collection ◽  
Fecal Indicator ◽  
E Coli

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

scholarly journals ‘Nitrification kinetics and microbial community dynamics of attached biofilm in wastewater treatment’

2020 ◽  
Vol 81 (5) ◽  
pp. 891-905
Author(s):  
Adam Skoyles ◽  
Subba Rao Chaganti ◽  
Scott O. C. Mundle ◽  
Chris G. Weisener
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
Stable Isotope Analysis ◽  
Community Dynamics ◽  
Isotope Analysis ◽  
Ammonia Removal ◽  
Nitrifying Bacteria ◽  
Rrna Gene ◽  
Bench Scale ◽  
Microbial Community Dynamics

Abstract A comparative bench-scale and field site analysis of BioCord was conducted to investigate seasonal microbial community dynamics and its impact on nitrogen removal in wastewater. This was assessed using metabolite (NO3−) stable isotope analysis, high-throughput sequencing of the 16S rRNA gene, and RT-qPCR of key genes in biological treatment representing nitrification, anammox, and denitrification. Bench-scale experiments showed an increase in nitrifiers with increasing ammonia loading resulting in an ammonia removal efficiency up to 98 ± 0.14%. Stable isotope analysis showed that 15ɛ and δ18ONO3 could be used in monitoring the efficiency of the enhanced biological nitrification. In the lagoon field trials, an increase in total nitrogen promoted three principle nitrifying genera (Nitrosomonas, Nitrospira, Candidatus Nitrotoga) and enhanced the expression of denitrification genes (nirK, norB, and nosZ). Further, anaerobic ammonia oxidizers were active within BioCord biofilm. Even at lower temperatures (2–6°C) the nitrifying bacteria remained active on the BioCord.

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 Rare Taxa Maintain Microbial Diversity and Contribute to Terrestrial Community Dynamics throughout Bark Beetle Infestation

2016 ◽  
Vol 82 (23) ◽  
pp. 6912-6919 ◽  
Author(s):  
Kristin M. Mikkelson ◽  
Chelsea M. Bokman ◽  
Jonathan O. Sharp
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Bark Beetle ◽  
Large Scale ◽  
Tree Mortality ◽  
Community Dynamics ◽  
Alpha Diversity ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Edaphic Parameters

ABSTRACTA global phenomenon of increasing bark beetle-induced tree mortality has heightened concerns regarding ecosystem response and biogeochemical implications. Here, we explore microbial dynamics under lodgepole pines through the analysis of bulk (16S rRNA gene) and potentially active (16S rRNA) communities to understand the terrestrial ecosystem responses that are associated with this form of large-scale tree mortality. We found that the relative abundances of bulk and potentially active taxa were correlated across taxonomic levels, but at lower levels, cladal differences became more apparent. Despite this correlation, there was a strong differentiation of community composition between bulk and potentially active taxa, with further clustering associated with the stages of tree mortality. Surprisingly, community clustering as a function of tree phase had limited correlation to soil water content and total nitrogen concentrations, which were the only two measured edaphic parameters to differ in association with tree phase. Bacterial clustering is more readily explained by the observed decrease in the abundance of active, rare microorganisms after tree death in conjunction with stable alpha diversity measurements. This enables the rare fraction of the terrestrial microbial community to maintain metabolic diversity by transitioning between metabolically active and dormant states during this ecosystem disturbance and contributes disproportionately to community dynamics and archived metabolic capabilities. These results suggest that analyzing bulk and potentially active communities after beetle infestation may be a more sensitive indicator of disruption than measuring local edaphic parameters.IMPORTANCEForests around the world are experiencing unprecedented mortality due to insect infestations that are fueled in part by a changing climate. While aboveground processes have been explored, changes at the terrestrial interface that are relevant to microbial biogeochemical cycling remain largely unknown. In this study, we investigated the changing bulk and potentially active microbial communities beneath healthy and beetle-killed trees. We found that, even though few edaphic parameters were altered from beetle infestation, the rare microbes were more likely to be active and fluctuate between dormancy and metabolic activity. This indicates that rare as opposed to abundant taxa contribute disproportionately to microbial community dynamics and presumably biogeochemical cycling within these types of perturbed ecosystems.

scholarly journals Effect of Nutrient Periodicity on Microbial Community Dynamics

2006 ◽  
Vol 72 (5) ◽  
pp. 3175-3183 ◽  
Author(s):  
Militza Carrero-Col�n ◽  
Cindy H. Nakatsu ◽  
Allan Konopka
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Growth Rates ◽  
Community Dynamics ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pulse Interval ◽  
Substrate Affinity ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Microbial Community Dynamics

ABSTRACT When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h−1 to 0.15 h−1 as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions, Bacteroidetes, Proteobacteria, and Actinobacteria. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.

scholarly journals Methanotrophic activity and microbial community dynamics in a UASB sludge

2020 ◽  
Vol 12 (1) ◽  
pp. 312-321
Author(s):  
Luciene Alves Batista Siniscalchi ◽  
Juliano Curi de Siqueira ◽  
Paula Peixoto Assemany ◽  
Ana Maria Moreira Batista ◽  
Giuliano Siniscalchi Martins ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Community Dynamics ◽  
Pilot Scale ◽  
Uasb Reactor ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Microbial Community Dynamics ◽  
Treated Effluent ◽  
Production And Consumption

This study determined the methanotrophic activity in anaerobic sludge from a pilot-scale UASB reactor. Four batch experiments, with three replicates, were performed in 110 mL antibiotic flasks. The results showed that the maximum rate was 115 µmolCH4.d-1 and the methanotrophic activity was 2.3 mmolCH4.gTVS-1.d-1, indicating that the methanotrophic microorganisms play a key role within the UASB reactor since they are part of the sludge microbiota and may consume some of the methane produced inside the reactor. Therefore, these microorganisms may reduce possible methane losses, either atmospheric and/or dissolved in the treated effluent. The microbial community was investigated by molecular tools (PCR-DGGE) and two DNA sequences related to methanotrophic bacteria, Methylocystis sp. (similarity of 93%) and Methylocaldum sp. (similarity of 98%) to 16S rRNA gene sequences, were detected. The methanotrophic activity and the identification of the community of main microorganisms involved allow the reduction of methane into the atmosphere and contribute to the system’s mass balance between production and consumption.

scholarly journals Influence of the Depth and Season on Microbial Community Dynamics of the Black Sea

2021 ◽  
Author(s):  
Rafet Cagri Ozturk ◽  
Ilhan Altinok ◽  
Ali Muzaffer Feyzioglu ◽  
Erol Capkin ◽  
Ilknur Yildiz
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Black Sea ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
The Black Sea ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Similar Species ◽  
Microbial Community Dynamics

Abstract The Black Sea is a unique environment having a thin layer of oxic-zone above and anoxic-zone below. Seasonal, vertical, and horizontal microbial assemblages were studied in terms of diversity, abundance, community structure using NGS of the 16S rRNA gene. Total of 750 bacteria species from 23 different phyla were identified. The number of species richness increased from the surface to deeper zones. Although microbial community compositions between sampling stations were similar, microbial community compositions were significantly different vertically between zones. Community compositions of the seawater and sediment were also significantly different. Community composition at 5 meters in summer was significantly different from other seasons, while remaining depths appeared similar. Species of nitrite-oxidizing, sulfate-reducing, thiosulfate reducing, Iron-reducing, Fe-Mn reducing and electricity-producing bacteria were reported for the first time in the Black Sea. Proteobacteria dominated all the sampling depths. Proteobacteria, Cyanobacteria, Bacteroidetes, and Verrucomicrobia were present in the whole water column, while Nitrospinae, Chloroflexi, and Kiritimatiellaeota were restricted, appearing abundant at 75 meters and deeper layers. Vertical microbial community composition variation is attributable to environmental factors and their adaptations to the various ecological niches.

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