scholarly journals Simulation ofDeepwater Horizonoil plume reveals substrate specialization within a complex community of hydrocarbon degraders

2017 ◽  
Vol 114 (28) ◽  
pp. 7432-7437 ◽  
Author(s):  
Ping Hu ◽  
Eric A. Dubinsky ◽  
Alexander J. Probst ◽  
Jian Wang ◽  
Christian M. K. Sieber ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Species Abundance ◽  
Compositional Analysis ◽  
Deep Ocean ◽  
Microbial Succession ◽  
Metabolic Pathway Analysis ◽  
Oil Droplets ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
Substrate Specialization

TheDeepwater Horizon(DWH) accident released an estimated 4.1 million barrels of oil and 1010mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as aBermanellaspecies), multiple species ofColwellia,Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.

Biological granulated activated carbon fluidized bed reactor for atrazine remediation

2004 ◽  
Vol 49 (11-12) ◽  
pp. 215-222 ◽  
Author(s):  
M. Herzberg ◽  
C.G. Dosoretz ◽  
S. Tarre ◽  
M. Beliavski ◽  
M. Green
Keyword(s):  
Fluidized Bed ◽  
Fluidized Bed Reactor ◽  
Batch Adsorption ◽  
Pseudomonas Sp ◽  
Partial Penetration ◽  
Biofilm Carrier ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
Atrazine Degradation ◽  
Granulated Activated Carbon

To show that an adsorbing biofilm carrier (GAC) can be advantageous for atrazine bioremediation over a non-adsorbing carrier, fluidized bed (FB) reactors were operated under atrazine limiting concentrations using Pseudomonas sp. strain ADP as the atrazine degrading bacteria. The following interrelated subjects were investigated: 1) atrazine adsorption to GAC under conditions of atrazine partial penetration in the biofilm, 2) differences in atrazine degradation rates and 3) stability of atrazine biodegradation under non-sterile anoxic conditions in the GAC reactor versus a reactor with a non-adsorbing biofilm carrier. Results from batch adsorption tests together with modeling best described the biofilm as patchy in nature with covered and non-biofilm covered areas. Under conditions of atrazine partial penetration in the biofilm, atrazine adsorption occurs in the non-covered areas and is consequently desorbed at the base of the biofilm substantially increasing the active biofilm surface area. The double flux of atrazine to the biofilm in the GAC reactor results in lower effluent atrazine concentrations as compared to a FB reactor with a non-adsorbing carrier. Moreover, under non-sterile denitrification conditions, atrazine degradation stability was found to be much higher (several months) using GAC as a biofilm carrier while non-adsorbing carrier reactors showed sharp deterioration within 30 days due to contamination of non-atrazine degrading bacteria.

Using acoustic tomography to monitor deep ocean currents in the eastern Gulf of Mexico

OCEANS 2009 ◽  
2009 ◽  
Author(s):  
D. A. Rosenfield ◽  
J. W. Caruthers ◽  
D. A. Nechaev ◽  
G. E. Ioup ◽  
J. W. Ioup ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Deep Ocean ◽  
Ocean Currents ◽  
Acoustic Tomography ◽  
Eastern Gulf Of Mexico ◽  
Deep Ocean Currents

scholarly journals Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter Pittii SW-1

2021 ◽  
Vol 18 (12) ◽  
pp. 6365
Author(s):  
Weina Kong ◽  
Cheng Zhao ◽  
Xingwang Gao ◽  
Liping Wang ◽  
Qianqian Tian ◽  
...  
Keyword(s):  
Unsaturated Fatty Acids ◽  
Sulfur Metabolism ◽  
Quantitative Polymerase Chain Reaction ◽  
Deep Ocean ◽  
Rrna Gene ◽  
Alkane Hydroxylase ◽  
Degradation Rates ◽  
Acinetobacter Pittii ◽  
Ocean Environment ◽  
Long Chain

Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.

Bacterial microencapsulation with three algal polysaccharides

1997 ◽  
Vol 43 (11) ◽  
pp. 1091-1095 ◽  
Author(s):  
Terry B. Hammill ◽  
Ronald L. Crawford
Keyword(s):  
Aqueous Medium ◽  
Guar Gum ◽  
Cell Suspensions ◽  
Type I ◽  
Type Ii ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
Free Cells ◽  
Algal Polysaccharides ◽  
Pressure Nozzle

Methods for encapsulating pollutant-degrading bacteria into microbeads of carrageenan type I, carrageenan type II, and guar gum are described. Cell suspensions in solutions of encapsulating agents were passed through a low-pressure nozzle into an aqueous medium. The resultant aerosols polymerized to form microbeads that ranged in diameter from 2–70 μm. Pentachlorophenol degradation experiments with an encapsulated Sphingomonas sp. showed degradation rates similar to those seen using free cells. These results describe three additional matrices for the microencapsulation of bacteria that have potential for use in bioremediation processes.Key words: Sphingomonas, pentachlorophenol, immobilization, encapsulation, bioremediation.

scholarly journals Extracellular polymeric substances (EPS) producing and oil degrading bacteria isolated from the northern Gulf of Mexico

PLoS ONE ◽  
2018 ◽  
Vol 13 (12) ◽  
pp. e0208406 ◽  
Author(s):  
Hernando P. Bacosa ◽  
Manoj Kamalanathan ◽  
Meng-Hsuen Chiu ◽  
Shih-Ming Tsai ◽  
Luni Sun ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Extracellular Polymeric Substances ◽  
Northern Gulf Of Mexico ◽  
Degrading Bacteria

scholarly journals Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

2019 ◽  
Vol 20 (12) ◽  
pp. 3053 ◽  
Author(s):  
Cheng Zhang ◽  
Qingkai Hao ◽  
Zhengyi Zhang ◽  
Xianghui Zhang ◽  
Hongyu Pan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gene Knockout ◽  
Scientific Evidence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
High Throughput Dna Sequencing ◽  
Chlorimuron Ethyl ◽  
Reading Frames

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8–10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Jean-François Carrias ◽  
Mélanie Gerphagnon ◽  
Héctor Rodríguez-Pérez ◽  
Guillaume Borrel ◽  
Camille Loiseau ◽  
...  
Keyword(s):  
Leaf Litter ◽  
Primary Succession ◽  
Alpha Diversity ◽  
Resource Limitation ◽  
Amplicon Sequencing ◽  
Natural Environments ◽  
Biological Interactions ◽  
Microbial Succession ◽  
Degrading Bacteria ◽  
Bacterial Succession

ABSTRACT Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.

scholarly journals Tidal Datums with Spatially Varying Uncertainty in North-East Gulf of Mexico for VDatum Application

2018 ◽  
Vol 6 (4) ◽  
pp. 114 ◽  
Author(s):  
Liujuan Tang ◽  
Edward Myers ◽  
Lei Shi ◽  
Kurt Hess ◽  
Alison Carisio ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Measurement Errors ◽  
Deep Ocean ◽  
Geodetic Survey ◽  
National Geodetic Survey ◽  
Model Errors ◽  
Large Uncertainty ◽  
North East ◽  
The North ◽  
Spatially Varying

We conducted a VDatum-spatially varying uncertainty study for the North-East Gulf of Mexico. The newly developed tide model incorporated the latest available National Ocean Service (NOS) bathymetry survey data and National Geodetic Survey (NGS) shoreline data, and the datum products reflected the updated tidal datum data from the Center for Operational Oceanographic Products and Services (CO-OPS). A gridding technique based on the wavelength of long waves in the deep ocean was applied to improve model efficiency. In this study, we highlight the creation of the tidal datum products and associated spatially varying uncertainty, which was developed by blending the model results, observations, and measurement errors together using a spatially varying uncertainty method based on a variational approach. The study found that model errors, measurement errors, and lack of observations can contribute to large uncertainty in the tidal datum products. The need for high quality bathymetry data in coastal areas is essential for reducing model error. As for the large uncertainty due to lack of observations or large measurement error, this can be improved by placement of new observations with high precision. Compared to a single uncertainty value, the spatially varying uncertainty provides more accurate representation of the uncertainty for the tidal datum products in VDatum. The uncertainty results will be used to help with decision-making on placement of new tide gauges to further reduce the uncertainty in the VDatum products.

Comparative Study on Rate of Biodegradation of Diluted Bitumen and Conventional Oil in Fresh Water

2017 ◽  
Vol 2017 (1) ◽  
pp. 2256-2267
Author(s):  
Ruta Suresh Deshpande ◽  
Devi Sundaravadivelu ◽  
Pablo Campo ◽  
Jorge W. SantoDomingo ◽  
Robyn N. Conmy
Keyword(s):  
Mixed Culture ◽  
16S Rrna Gene Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Dispersed Oil ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
Rrna Gene Sequencing ◽  
Set Up

Abstract 2017-271 In recent years, diluted bitumen (or dilbit) has become an important source of hydrocarbon-based fuel. While information on the degradation of crude oils has been well researched, dilbit degradation has been studied at a much lesser extent. The objective of this study was to compare biodegradation of dilbit with a conventional crude oil (CCO) under various conditions. Two different microcosm experiments were set up, one containing a mixed culture acclimated to dilbit (Kalamazoo River Enrichment, KRC) and the other having a mixed culture enriched on soil contaminated with hydrocarbons (Anderson Ferry Enrichment, AFC). The microcosms were run for 60 d at 25 °C and for 72 days at 5 °C in flasks containing sterile Bushnell Hass broth and naturally dispersed oil. Each flask was inoculated with the KRC and AFC mixed cultures, and rotated on an orbital shaker (200 rpm) at the above stated temperatures. On each sampling day, triplicates were sacrificed to determine the residual hydrocarbon concentration. Additionally, some samples were used to determine the bacterial composition using 16S rRNA gene sequencing analysis. Hydrocarbon analysis (alkanes and PAHs) was performed by gas chromatography/mass spectrometry (GC/MS/MS). Higher degradation rates were achieved at 25 °C as compared to 5 °C. All the enrichments metabolized CCO as well dilbit, but the nature and extent of the degradation was distinct. KRC meso culture was the most effective among all, as it completely removed alkanes and most of the PAHs. AFC enrichment performed differently at the two temperatures; an acclimation period (8 d) was observed at 5 °C while there was no lag at 25 °C. KRC cryo culture as well as AFC culture at both temperatures degraded alkanes completely while they were not able to metabolize heavier fractions of the oil (C2–4 homologues of 3- and 4-ring compounds). All cultures showed the presence of diverse oil degrading bacteria and the differences in their compositions affected the biodegradation. Although dilbit was biodegraded, for all the treatments except AFC at 5 °C, the rate of degradation and the extent of degradation was greater for CCO owing to the higher concentrations of lighter hydrocarbons.

scholarly journals Common species link global ecosystems to climate change

2016 ◽  
Author(s):  
Bjarte Hannisdal ◽  
Kristian A. Haaga ◽  
Trond Reitan ◽  
David Diego ◽  
Lee Hsiang Liow
Keyword(s):  
Large Scale ◽  
Environmental Changes ◽  
Planktonic Foraminifera ◽  
Species Abundance ◽  
Direct Interaction ◽  
Deep Ocean ◽  
Common Species ◽  
Global Changes ◽  
Ecosystem Structure ◽  
Widespread Species

Common species shape the world around us, and changes in their commonness signify large-scale shifts in ecosystem structure and function. Dominant taxa drive productivity and biogeochemical cycling, in direct interaction with abiotic components of the Earth system. However, our understanding of the dynamic response of ecosystems to global environmental changes in the past is limited by our ability to robustly estimate fossil taxonomic richness, and by our neglect of the importance of common species. To rectify this, we use observations of the most common and widespread species to track global changes in their distribution in the deep geological past. Our simple approach is robust to factors that bias richness estimators, including widely used sampling-standardization methods, which we show are highly sensitive to variability in the species-abundance distribution. Causal analyses of common species frequency in the deep-sea sedimentary record detect a lagged response in the ecological prominence of planktonic foraminifera to oceanographic changes captured by deep-ocean temperature records over the last 65 million years, encompassing one of Earth's major climate transitions. Our results demonstrate that common species can act as tracers of a past global ecosystem and its response to physical changes in Earth's dynamic history.

Sign in / Sign up

Export Citation Format

Share Document