Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

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 The Growth of Leaf Lettuce and Bacterial Communities in a Closed Aquaponics System with Catfish

Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 222
Author(s):  
Kenji Yamane ◽  
Yuuki Kimura ◽  
Keita Takahashi ◽  
Isamu Maeda ◽  
Masayuki Iigo ◽  
...  
Keyword(s):  
Plant Growth ◽  
Early Stage ◽  
Amplicon Sequencing ◽  
Small Scale ◽  
Rrna Gene ◽  
Culture Solution ◽  
Beneficial Effects ◽  
Sustainable Cultivation ◽  
Microbial Groups ◽  
Production Period

Aquaponics is a circulating and sustainable system that combines aquaculture and hydroponics and forms a symbiotic relationship between fish, plants, and microorganisms. We hypothesized that feed alone could support plant growth, but the symbiosis with fish adds some beneficial effects on plant growth in aquaponics. In this study, we created three closed culture systems, namely, aquaponics, hydroponics without nitrogen (N) and phosphorus (P), and aquaculture, and added the same amount of feed containing N and P to all the treatments in order to test the hypothesis. Accumulation of NO3− and PO43− was alleviated in aquaponics and hydroponics as a result of plant uptake. Lettuce plants grown in aquaponics grew vigorously until 2 weeks and contained a constant level of N in plants throughout the production period, whereas those in hydroponics grew slowly in the early stage and then vigorously after 2 weeks with a late increment of N concentration. These results suggest that catfish help with the faster decomposition of the feed, but, in hydroponics, feed can be slowly dissolved and decomposed owing to the absence of the fish. The bacterial community structures of the culture solution were investigated using 16S rRNA gene amplicon sequencing. At the class level, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the major microbial groups in the solutions. Aquaponics prevented the pollution of tank solution and maintained a higher water quality compared with hydroponics and aquaculture, suggesting that aquaponics is a more sustainable cultivation system even in a small-scale system.

scholarly journals Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Janneke Schreuder ◽  
Francisca C. Velkers ◽  
Alex Bossers ◽  
Ruth J. Bouwstra ◽  
Willem F. de Boer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Intestinal Microbiota ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Sudden Change ◽  
Rrna Gene ◽  
Poultry House ◽  
Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

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 Environmental Surveillance Can Dynamically Track Ecological Changes in Enteroviruses

2019 ◽  
Vol 85 (24) ◽  
Author(s):  
Hiroki Ozawa ◽  
Hiromu Yoshida ◽  
Shuzo Usuku
Keyword(s):  
Multidimensional Scaling ◽  
Large Scale ◽  
Local Community ◽  
Amino Acid Sequences ◽  
Time Dependent ◽  
Small Scale ◽  
Dependent Manner ◽  
Environmental Surveillance ◽  
Ecological Changes ◽  
Over Time

ABSTRACT Environmental surveillance can be used to trace enteroviruses shed from human stool using a sewer network that is independent of symptomatic or asymptomatic infection. In this study, the local transmission of enteroviruses was analyzed using two wastewater treatment plants, which were relatively close to each other (15 km), designated as sentinels. Influent was collected at both sentinels once a month from 2013 to 2016, and viruses were isolated. Using neutralizing tests with type-specific polyclonal antisera and molecular typing, 933 isolates were identified as enteroviruses. Our results showed that the frequency of virus isolation varied for each serotype at the two sentinels in a time-dependent manner. Because echovirus 11 (Echo11) and coxsackievirus B5 isolates showed a high frequency and were difficult to distinguish, they were further grouped into various lineages based on the VP1 amino acid sequences. The prevalence of each lineage was visualized using multidimensional scaling. The results showed that Echo11 isolates of the same lineage were isolated continuously, similar to coxsackievirus B5 isolates of three lineages. Conversely, Echo1, Echo13, Echo18, Echo19, Echo20, Echo29, and Echo33 were isolated only once each. Our findings suggested that if an enterovirus is imported into the population, it may result in small-scale transmission, whereas if there are initially many infected individuals, it may be possible for the virus to spread to a wide area, beyond the local community, over time. In addition, our findings could provide insights into risk assessment of transmission for importation of poliovirus in polio-free countries and regions. IMPORTANCE In this study, we showed that environmental enterovirus surveillance can be used to monitor the propagation of nonpolio enteroviruses in addition to poliovirus detection. Since epidemiological studies of virus transmission based on the past were performed using specimens from humans, there were limitations to research design, such as specimen collection for implementation on a large-scale target population. However, environmental monitoring can dynamically track the ecological changes in enteroviruses in the region by monitoring viruses in chronological order and targeting the population within the area by monitoring viruses over time. We observed differences in the transmission of echovirus 11 and coxsackievirus B5 in the region according to lineage in a time-dependent manner and with a multidimensional scaling pattern.

scholarly journals Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater

2019 ◽  
Vol 9 (18) ◽  
pp. 3647 ◽  
Author(s):  
Sotiris I. Patsios ◽  
Sofia Michailidou ◽  
Konstantinos Pasentsis ◽  
Antonios M. Makris ◽  
Anagnostis Argiriou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Biological Treatment ◽  
Large Scale ◽  
Membrane Bioreactor ◽  
Community Dynamics ◽  
Metabolic Adaptation ◽  
Process Step ◽  
Microbial Community Dynamics ◽  
Table Olive ◽  
Acclimatization Period

Biological treatment of table olive processing wastewater (TOPW) may be problematic due to its high organic and polyphenolic compound content. Biomass acclimatization is a necessary, yet sensitive, stage for efficient TOPW biological treatment. Next-generation sequencing technologies can provide valuable insights into this critical process step. An aerobic membrane bioreactor (MBR) system, initially inoculated with municipal activated sludge, was acclimatized to treat TOPW. Operational stability and bioremediation efficiency were monitored for approx. three months, whereas microbial community dynamics and metabolic adaptation were assessed through metagenomic and metatranscriptomic analysis. A swift change was identified in both the prokaryotic and eukaryotic bio-community after introduction of TOPW in the MBR, and a new diverse bio-community was established. Thauera and Paracoccus spp. are dominant contributors to the metabolic activity of the stable bio-community, which resulted in over 90% and 85% removal efficiency of total organic carbon and total polyphenols, respectively. This is the first study assessing the microbial community dynamics in a well-defined MBR process treating TOPW, offering guidance in the start-up of large-scale applications.

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 Analyses of Land Cover Change Trajectories Leading to Tropical Forest Loss: Illustrated for the West Kutai and Mahakam Ulu Districts, East Kalimantan, Indonesia

Land ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 108 ◽  
Author(s):  
Carina van der Laan ◽  
Arif Budiman ◽  
Judith Verstegen ◽  
Stefan Dekker ◽  
Wiwin Effendy ◽  
...  
Keyword(s):  
Land Cover ◽  
Land Cover Change ◽  
Large Scale ◽  
Expert Knowledge ◽  
Small Scale ◽  
Forest Loss ◽  
The West ◽  
East Kalimantan ◽  
Open Forest ◽  
Over Time

In Indonesia, land cover change for agriculture and mining is threatening tropical forests, biodiversity and ecosystem services. However, land cover change is highly dynamic and complex and varies over time and space. In this study, we combined Landsat-based land cover (change) mapping, pixel-to-pixel cross tabulations and expert knowledge to analyze land cover change and forest loss in the West Kutai and Mahakam Ulu districts in East Kalimantan from 1990–2009. We found that about one-third of the study area changed in 1990–2009 and that the different types of land cover changes in the study area increased and involved more diverse and characteristic trajectories in 2000–2009, compared to 1990–2000. Degradation to more open forest types was dominant, and forest was mostly lost due to trajectories that involved deforestation to grasslands and shrubs (~17%), and to a lesser extent due to trajectories from forest to mining and agriculture (11%). Trajectories from forest to small-scale mixed cropland and smallholder rubber occurred more frequently than trajectories to large-scale oil palm or pulpwood plantations; however, the latter increased over time. About 11% of total land cover change involved multiple-step trajectories and thus “intermediate” land cover types. The combined trajectory analysis in this paper thus contributes to a more comprehensive analysis of land cover change and the drivers of forest loss, which is essential to improve future land cover projections and to support spatial planning.

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