Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition

2021 ◽  
Author(s):  
Chuwen Zhang ◽  
Rainer U Meckenstock ◽  
Shengze Weng ◽  
Guangshan Wei ◽  
Casey R J Hubert ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Aromatic Hydrocarbons ◽  
Anthropogenic Activities ◽  
Hydrocarbon Degradation ◽  
Anaerobic Microorganisms ◽  
Anaerobic Hydrocarbon Degradation ◽  
Wide Range ◽  
Functional Profiling ◽  
Fumarate Addition ◽  
Hydrocarbon Degraders

Abstract Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.

scholarly journals Marine Sediments Harbor Diverse Archaea and Bacteria With Potentials for Anaerobic Hydrocarbon Degradation via Fumarate Addition

2020 ◽  
Author(s):  
Chuwen Zhang ◽  
Rainer U. Meckenstock ◽  
Shengze Weng ◽  
Guangshan Wei ◽  
Casey R.J. Hubert ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Aromatic Hydrocarbons ◽  
Anthropogenic Activities ◽  
Hydrocarbon Degradation ◽  
Anaerobic Microorganisms ◽  
Anaerobic Hydrocarbon Degradation ◽  
Wide Range ◽  
Functional Profiling ◽  
Fumarate Addition ◽  
Hydrocarbon Degraders

Abstract Background: Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. Previous gene- and genome-based surveys have detected ubiquitous and novel fumarate-adding enzymes (FAE), but these were neither confirmed as occurring within full degradation pathways nor affiliated with known organisms. The identity and ecological roles of a significant fraction of anaerobic hydrocarbon degraders in marine sediments therefore remains unknown.Results: By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available and newly sequenced metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Deltaproteobacteria that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. The biogeography survey reveals these bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems.Conclusions: Our results expand the knowledge of novel microbial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons, and shed new light on the importance of marine sedimentary archaea in hydrocarbon degradation.

scholarly journals Exposure to Atmospheric Particulate Matter-Bound Polycyclic Aromatic Hydrocarbons and Their Health Effects: A Review

2021 ◽  
Vol 18 (4) ◽  
pp. 2177
Author(s):  
Lu Yang ◽  
Hao Zhang ◽  
Xuan Zhang ◽  
Wanli Xing ◽  
Yan Wang ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Particulate Matter ◽  
Real Time ◽  
Health Effects ◽  
Aromatic Hydrocarbons ◽  
Anthropogenic Activities ◽  
Personal Exposure ◽  
Epidemiological Studies ◽  
Atmospheric Particulate Matter ◽  
Polycyclic Aromatic

Particulate matter (PM) is a major factor contributing to air quality deterioration that enters the atmosphere as a consequence of various natural and anthropogenic activities. In PM, polycyclic aromatic hydrocarbons (PAHs) represent a class of organic chemicals with at least two aromatic rings that are mainly directly emitted via the incomplete combustion of various organic materials. Numerous toxicological and epidemiological studies have proven adverse links between exposure to particulate matter-bound (PM-bound) PAHs and human health due to their carcinogenicity and mutagenicity. Among human exposure routes, inhalation is the main pathway regarding PM-bound PAHs in the atmosphere. Moreover, the concentrations of PM-bound PAHs differ among people, microenvironments and areas. Hence, understanding the behaviour of PM-bound PAHs in the atmosphere is crucial. However, because current techniques hardly monitor PAHs in real-time, timely feedback on PAHs including the characteristics of their concentration and composition, is not obtained via real-time analysis methods. Therefore, in this review, we summarize personal exposure, and indoor and outdoor PM-bound PAH concentrations for different participants, spaces, and cities worldwide in recent years. The main aims are to clarify the characteristics of PM-bound PAHs under different exposure conditions, in addition to the health effects and assessment methods of PAHs.

scholarly journals The Role of Methyl Groups in the Early Stage of Thermal Polymerization of Polycyclic Aromatic Hydrocarbons Revealed by Molecular Imaging

2020 ◽  
Author(s):  
Pengcheng Chen ◽  
Shadi Fatayer ◽  
Bruno Schuler ◽  
Jordan N. Metz ◽  
Leo Gross ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Early Stage ◽  
Complex Mixture ◽  
Thermal Polymerization ◽  
Industrial Applications ◽  
Thermal Reactions ◽  
Force Microscopy ◽  
Wide Range ◽  
Polycyclic Aromatic

The initial thermal reactions of aromatic hydrocarbons are relevant to many industrial applications. However, tracking the growing number of heavy polycyclic aromatic hydrocarbon (PAH) products is extremely challenging because many reactions are unfolding in parallel from a mixture of molecules. Herein, we studied the reactions of 2,7-dimethylpyrene (DMPY) to decipher the roles of methyl substituents during mild thermal treatment. We found that the presence of methyl substituents is key for reducing the thermal severity required to initiate chemical reactions in natural molecular mixtures. A complex mixture of thermal products including monomers, dimers, and trimers were characterized by NMR, mass spectrometry and non-contact atomic force microscopy (nc-AFM). A wide range of structural transformations including methyl transfer and polymerization reactions were identified. A detailed mechanistic understanding was obtained on the roles of H radicals during the polymerization of polycyclic aromatic hydrocarbons.

scholarly journals Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50° in latitude

2013 ◽  
Vol 10 (9) ◽  
pp. 14595-14626 ◽  
Author(s):  
A. Canion ◽  
J. E. Kostka ◽  
T. M. Gihring ◽  
M. Huettel ◽  
J. E. E. van Beusekom ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Marine Sediments ◽  
Metabolic Response ◽  
Anammox Bacteria ◽  
Advective Flow ◽  
Permeable Sediments ◽  
N Removal ◽  
In Situ Conditions ◽  
Wide Range

Abstract. Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from −5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m−2 d−1. For the majority of sites studied, N2 removal was 2 to 7 times more rapid under advective flow conditions. Anammox comprised 6 to 14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of −1 to 42 °C. The highest optimum temperature (Topt) for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. To our knowledge, we provide the first rates of denitrification and anammox from permeable sediments of a polar permanently cold ecosystem. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N removal is highly dependent on community structure.

scholarly journals Assessment of the ecological structure of Posidonia oceanica (L.) Delile on the northern coast of Lazio, Italy (central Tyrrhenian, Mediterranean)

2020 ◽  
Vol 9 ◽  
pp. 1-19
Author(s):  
Valentina Gnisci ◽  
Selvaggia Cognetti de Martiis ◽  
Alessandro Belmonte ◽  
Carla Micheli ◽  
Viviana Piermattei ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
Morphological Variability ◽  
Posidonia Oceanica ◽  
Shoot Density ◽  
Northern Coast ◽  
Site Specific ◽  
Fragmented Habitat ◽  
Ecological Structure ◽  
Wide Range

The ecological structure of Posidonia oceanica (L.) Delile meadows was evaluated on the northern coast of Lazio, Italy (central Tyrrhenian, Mediterranean sea). This is an infra-littoral zone with a wide range of anthropogenic activities and high geo-morphological variability, which reflects heterogeneity in shoot density, leaf morphology and biomass in fragmented patches. Genetic variability in populations corresponds to the formation of 3 sub-clusters, in the diverse impacted zones (north, centre and south), being correlated to the geographical distance between sites. AMOVA estimated a high genetic variation showing 43.05% individual differences within populations with a marked differentiation among the populations (56.9%) indicated by Fst value (0.57). These results revealed the role of the genetic structure of seagrasses for determining selectivity of fragmented habitat, in response to natural drivers. They showed that site-specific self-recruitment is related to biodiversity capacity and to the geo-morphological characteristic of the coast.

scholarly journals Source Identification and Ecological Risk of Polycyclic Aromatic Hydrocarbons in Soils and Groundwater

2021 ◽  
Vol 28 (3) ◽  
pp. 355-363
Author(s):  
Predrag Ilić ◽  
Svetlana Ilić ◽  
Dragana Nešković Markić ◽  
Ljiljana Stojanović Bjelić ◽  
Zia Ur Rahman Farooqi ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Ecological Risk ◽  
Aromatic Hydrocarbons ◽  
Soil Depth ◽  
Anthropogenic Activities ◽  
Industrial Complex ◽  
Industrial Emissions ◽  
Mean Values ◽  
Polycyclic Aromatic ◽  
Banja Luka

Abstract Polycyclic aromatic hydrocarbons (PAHs) are formed from anthropogenic activities, i.e. industrial emissions, incomplete combustion of petroleum, coal and other fossil fuels and other industrial and domestic activities. Research areas of this study are four representative locations in the industrial complex, in the city of Banja Luka, Republic of Srpska, Bosnia and Herzegovina. The main objective of the paper is to determine the ecological risk and to assess probable sources of PAHs contamination in soil and groundwater. The results of this study reflect the effects of coal combustion (pyrogenic origin), petrogenic and biomass origin and may provide basic data for the remediation of PAHs in the location. The ecological risk in soil (at depths of 30, 100, 200, 300 and 400 cm) and groundwater is determined. The mean values of ecological risk in soil and groundwater decreased with soil depth. Values of RQ(NCs) for groundwater were found at high ecological risk, for Ant, Chr, DahA, Acy, Pyr, BaA, Phe, Flo, Nap, Ace and Fluo, with values 28.57, 20.59, 300.00, 242.86, 185.71, 1700.0, 76.67, 53.33, 15.83, 100.00 and 57.14, respectively. ∑16PAH indicated high ecological risk for most PAHs, which decreased with soil depth. The value of RQ(NCs) for ΣPAHs in groundwater indicates high ecological risk (ΣPAHs ≥ 800 and RQ(MPCs) ≥ 1). This is the first study on the ecological risk of PAHs in soil and groundwater in industrial soils in Banja Luka and provides baseline information for further studies and additional investigations of this industrial complex.

Ultrasonic micellar extraction of polycyclic aromatic hydrocarbons from marine sediments

Talanta ◽  
2001 ◽  
Vol 54 (1) ◽  
pp. 15-23 ◽  
Author(s):  
Verónica Pino ◽  
Juan H. Ayala ◽  
Ana M. Afonso ◽  
Venerando González
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Marine Sediments ◽  
Aromatic Hydrocarbons ◽  
Micellar Extraction ◽  
Polycyclic Aromatic

ViDiT–CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications

2018 ◽  
Vol 64 (10) ◽  
pp. 761-773 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Marta Canuti ◽  
Hannah J. Munro ◽  
Suzanne C. Dufour ◽  
Andrew S. Lang
Keyword(s):  
Influenza A ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Quality Data ◽  
Library Preparation ◽  
Virus Discovery ◽  
Influenza A Viruses ◽  
Wide Range ◽  
Functional Profiling ◽  
Biology Laboratory

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (less than US$5 per sample), and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing, and microbiome profiling. ViDiT–CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal–cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT–CACTUS demonstrated its validity in a wide range of microbiology applications, and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

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