scholarly journals Prokaryotic community shifts during soil formation on sands in the tundra zone

2018 ◽  
Author(s):  
Alena Zhelezova ◽  
Timofey Chernov ◽  
Azida Tkhakakhova ◽  
Natalya Xenofontova ◽  
Mikhail Semenov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Quantitative Polymerase Chain Reaction ◽  
Plant Cover ◽  
Soil Formation ◽  
Rrna Gene ◽  
Tundra Zone ◽  
Microbial Community Dynamics ◽  
Β Diversity ◽  
Prokaryotic Diversity

AbstractA chronosequence approach,i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but they have not been considered for the tundra zone, where the environmental conditions are unfavourable for the establishment of complicated biocoenoses. In this research, we characterized the prokaryotic diversity and abundance of microbial genes found in a typical tundra and wooded tundra along a gradient of increasing vegetation – unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. Microbial communities from typical tundra and wooded tundra plots at three stages of sand fixation were compared using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing of 16S rRNA gene libraries. The abundances of ribosomal genes increased gradually in both chronosequences, and a similar trend was observed for the functional genes related to the nitrogen cycle (nifH, bacterialamoA, nirKandnirS). The relative abundance ofPlanctomycetesincreased, while those ofThaumarchaeota, CyanobacteriaandChloroflexidecreased from unfixed sands to mature soils. According to β-diversity analysis, prokaryotic communities of unfixed sands were more heterogeneous compared to those of mature soils. Despite the differences in the plant cover of the two mature soils, the structural compositions of the prokaryotic communities were shaped in the same way.

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 Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

2018 ◽  
Vol 9 ◽  
Author(s):  
Christina J. Fiedler ◽  
Christoph Schönher ◽  
Philipp Proksch ◽  
David Johannes Kerschbaumer ◽  
Ernest Mayr ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
River Bank ◽  
Microbial Community Dynamics

The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters

2020 ◽  
Author(s):  
Tatiana A Belevich ◽  
Irina A Milyutina ◽  
Galina A Abyzova ◽  
Aleksey V Troitsky
Keyword(s):  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Global Climate ◽  
Atmospheric Oxygen ◽  
18S Rrna Gene ◽  
Anthropogenic Activity ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Russian Arctic ◽  
Arctic Seas

Abstract Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To get more knowledge about Mamiellophyceae distribution and diversity special study were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July-September 2017 in the Barents, Kara, and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A—uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with M. polaris dominating north of 72°N. The presence of Ostreococcus tauri, O. lucimarinus and O. mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.

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 DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

2013 ◽  
Vol 10 (6) ◽  
pp. 3817-3838 ◽  
Author(s):  
I. Domaizon ◽  
O. Savichtcheva ◽  
D. Debroas ◽  
F. Arnaud ◽  
C. Villar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Environmental Conditions ◽  
Trophic Status ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Additive Models ◽  
Phosphorus Concentration ◽  
Rrna Gene

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). In particular, we investigated the long-term (100 yr) diversity and dynamics of Synechococcus,, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided the ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR; quantitative Polymerase Chain Reaction) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus, (fraction of Synechococcus, in total cyanobacteria). The diversity of Synechococcus, in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and the following internally transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, the study of ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (in temperature and phosphorus concentration) affected Synechococcus, community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus, clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

scholarly journals Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 407 ◽  
Author(s):  
Sonia Rodríguez-Ruano ◽  
Manuel Martín-Vivaldi ◽  
Juan Peralta-Sánchez ◽  
Ana García-Martín ◽  
Ángela Martínez-García ◽  
...  
Keyword(s):  
Breeding Season ◽  
Community Dynamics ◽  
Quantitative Polymerase Chain Reaction ◽  
Infection Risk ◽  
Uropygial Gland ◽  
Molecular Fingerprinting ◽  
Microbial Community Dynamics ◽  
High Infection ◽  
Uropygial Secretion

The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the high infection risk experienced during the stay in the hole-nests. However, the knowledge on hoopoes uropygial gland microbial community dynamics is quite limited and based so far on culture-dependent and molecular fingerprinting studies. In this work, we sampled wild and captive hoopoes of different sex, age, and reproductive status, and studied their microbiota using quantitative polymerase chain reaction (qPCR), fluorescence in situ hybridization (FISH) and pyrosequencing. Surprisingly, we found a complex bacterial community in all individuals (including non-nesting ones) during the breeding season. Nevertheless, dark secretions from nesting hoopoes harbored significantly higher bacterial density than white secretions from breeding males and both sexes in winter. We hypothesize that bacterial proliferation may be host-regulated in phases of high infection risk (i.e., nesting). We also highlight the importance of specific antimicrobial-producing bacteria present only in dark secretions that may be key in this defensive symbiosis. Finally, we discuss the possible role of environmental conditions in shaping the uropygial microbiota, based on differences found between wild and captive hoopoes.

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 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 Effect of inoculated azotobacteria and Phanerochaete chrysosporium on the composting of olive pomace: Microbial community dynamics and phenols evolution

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vesna Milanović ◽  
Andrea Osimani ◽  
Federica Cardinali ◽  
Manuela Taccari ◽  
Cristiana Garofalo ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Denaturing Gradient Gel Electrophoresis ◽  
White Rot Fungi ◽  
Water Soluble ◽  
White Rot ◽  
Rrna Gene ◽  
Phenol Content ◽  
Microbial Community Dynamics ◽  
Gradient Gel Electrophoresis ◽  
Uninoculated Control

AbstractThe effect of inoculated azotobacteria and basidiomycetes white-rot fungi on the population dynamics of bacteria and eumycetes during the co-composting of olive mill pomace and wheat straw was evaluated by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis combined with sequencing of rRNA gene amplicons from selected DGGE bands. The evolution of pH, temperature, phytotoxicity and water-soluble phenol content during co-composting was also monitored. In general, a similar evolution of microbial biodiversity was seen in both the inoculated and uninoculated (control) piles, which was in keeping with a similar evolution of phytotoxicity and water-soluble phenol content. Overall, under the conditions applied, data suggest a marginal influence of the inoculated starters on the physical, chemical and microbiological properties of compost piles, with the resident microbiota playing a major role.

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