Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites

Abstract Background Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities. Results The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome. Conclusions Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs.

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Achieving similar root microbiota composition in neighbouring plants through airborne signalling

The ISME Journal ◽

10.1038/s41396-020-00759-z ◽

2020 ◽

Author(s):

Hyun Gi Kong ◽

Geun Cheol Song ◽

Hee-Jung Sim ◽

Choong-Min Ryu

Keyword(s):

Microbial Community ◽

Environmental Changes ◽

Tomato Seedling ◽

Environmental Signals ◽

Plant Volatile ◽

The Status ◽

Plant Growth Promoting ◽

The Impact ◽

First Time ◽

Rhizosphere Microbial Community

Abstract The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is not well understood. Here, we investigated the effect of VOCs on the rhizosphere microbial community of tomato plants inoculated with a plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain GB03 and that of their neighbouring plants. Interestingly, high similarity (up to 69%) was detected in the rhizosphere microbial communities of the inoculated and neighbouring plants. Leaves of the tomato plant treated with strain GB03-released β-caryophyllene as a signature VOC, which elicited the release of a large amount of salicylic acid (SA) in the root exudates of a neighbouring tomato seedling. The exposure of tomato leaves to β-caryophyllene resulted in the secretion of SA from the root. Our results demonstrate for the first time that the composition of the rhizosphere microbiota in surrounding plants is synchronized through aerial signals from plants.

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Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

10.21203/rs.3.rs-600995/v1 ◽

2021 ◽

Author(s):

Laís Farias Oliveira Lima ◽

Amanda Alker ◽

Bhavya Papudeshi ◽

Megan Morris ◽

Robert Edwards ◽

...

Keyword(s):

Microbial Community ◽

Nutrient Cycling ◽

Ecosystem Functioning ◽

Environmental Changes ◽

Coral Host ◽

Shotgun Metagenomics ◽

Patch Reefs ◽

Coral Microbiome ◽

Gene Functions ◽

Coral Health

Abstract Background The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes and tied to ecosystem functioning, as it constitutes the direct interface between the coral host and the environment. The functional profile of microbial genes in the coral SML is underexplored and the use of shotgun metagenomics is relatively rare among coral microbiome studies. Here we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. Results The analysis was conducted using metagenomes and metagenome assemble genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs . Our results showed that the microbial community structure is simultaneously selected by the host medium (i.e., coral SML versus water) and the local environment (i.e., inner reefs versus outer reefs), both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and that are related to higher levels of microbial activity, competition, and stress response, such as dimethylsulfoniopropionate (DMSP) breakdown. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. Conclusion The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome; potentially increasing holobiont resilience to environmental changes and disease. Our results reveal microbial taxa and functions selected at reef scale in the coral SML microbiome that can leverage disease management, microbiome engineering, and microbial eco-evolutionary theories.

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The role of chronic kidney disease-associated dysbiosis in cardiovascular disease

Experimental Biology and Medicine ◽

10.1177/1535370219826526 ◽

2019 ◽

Vol 244 (6) ◽

pp. 514-525 ◽

Cited By ~ 6

Author(s):

Mark A Bryniarski ◽

Fares Hamarneh ◽

Rabi Yacoub

Keyword(s):

Cardiovascular Disease ◽

Chronic Kidney Disease ◽

Microbial Community ◽

Kidney Disease ◽

Cardiovascular Events ◽

Environmental Changes ◽

Intestinal Microbiome ◽

Intestinal Lumen ◽

Stage Renal Disease ◽

The Impact

Survival outcomes of patients with end stage renal disease are worse than those of many metastatic cancers. Kidney disease patients are often inflicted with higher rates of cardiovascular disease, in which nearly half of the mortalities are attributed to adverse cardiovascular events. Of the multifarious reasons for this detrimental impact, dysbiosis in the intestinal microbiome is surfacing as a potential participant. This is likely due to the numerous metabolic and inflammatory shifts found in chronic kidney disease, as well as environmental changes within the intestinal lumen. Studies are beginning to link microbiota alterations mediated by chronic kidney disease to negative cardiovascular outcomes. Here, recent findings connecting dysbiosis in chronic kidney disease and various cardiovascular insults are reviewed. Impact statement Negative alterations, or dysbiosis, in the intestinal microbial community balance in response to chronic kidney disease is emerging as a substantial and important factor in inducing and exacerbating multiple comorbid conditions. Patients with renal insufficiency experience a substantial increase in cardiovascular risk, and recent evidence is shedding light on the close interaction between microbiome dysbiosis and increased cardiovascular events in this population. Previous association and recent causality studies utilizing experimental animal models have enriched our understanding and confirmed the impact of microbial community imbalance on cardiac health in both the general population and in patients with renal impairment.

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Investigation of petroleum hydrocarbon pollution along the coastline of South Attica, Greece, after the sinking of the Agia Zoni ΙΙ oil tanker

SN Applied Sciences ◽

10.1007/s42452-020-04114-x ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Konstantinos Kapsalis ◽

Maria Kavvalou ◽

Ioanna Damikouka ◽

Olga Cavoura

Keyword(s):

Marine Environment ◽

Oil Spills ◽

Natural Weathering ◽

Total Petroleum Hydrocarbons ◽

Negative Effects ◽

Hydrocarbon Pollution ◽

Weathering Processes ◽

The Status ◽

The Impact ◽

Oil Tanker

AbstractOil spills at sea pose risks to the marine environment and to the economy of many nations. Marine ecosystems are very vulnerable and precious as producers of oxygen and as regulators of climate. Therefore, their protection and preservation are necessary. In the event of an oil spill, anthropogenic clean-up activities and natural weathering processes can minimize the negative effects on marine organisms, and the marine environment in general. The target of this study was to investigate the status of the sea along the coastline of the Saronic Gulf, Greece, a year after the sinking of the Agia Zoni II oil tanker. Seawater samples from 15 sampling locations from Phlisvos coast to Anavissos, an area easily approached by bathers with recreational interest, were collected and analysed for total petroleum hydrocarbons. Concentrations up to a maximum of 56.6 μg/L were detected. Despite the large extent of the initial hydrocarbon pollution, the immediate clean-up operations and natural weathering and/or sorption processes have reduced the impact of the spill on surface waters.

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The Impact of Terrestrial Oil Pollution on Parasitoid Wasps Associated With Vachellia (Fabales: Fabaceae) Trees in a Desert Ecosystem, Israel

Environmental Entomology ◽

10.1093/ee/nvaa123 ◽

2020 ◽

Vol 49 (6) ◽

pp. 1355-1362

Author(s):

Daniella M Möller ◽

Marco Ferrante ◽

Gabriella M Möller ◽

Tamir Rozenberg ◽

Michal Segoli

Keyword(s):

Community Composition ◽

Oil Spill ◽

Oil Spills ◽

Oil Pollution ◽

Sampling Site ◽

Desert Ecosystem ◽

Parasitoid Wasps ◽

Negative Effects ◽

Animal Diversity ◽

The Impact

Abstract Oil is a major pollutant of the environment, and terrestrial oil spills frequently occur in desert areas. Although arthropods account for a large share of animal diversity, the effect of oil pollution on this group is rarely documented. We evaluated the effects of oil pollution on parasitoid wasps associated with Vachellia (formerly Acacia) tortilis (Forssk.) and Vachellia raddiana (Savi) trees in a hyper-arid desert that was affected by two major oil spills (in 1975 and 2014). We sampled the parasitoid populations between 2016 and 2018 in three sampling sites and compared their abundance, diversity, and community composition between oil-polluted and unpolluted trees. Parasitoid abundance in oil-polluted trees was lower in one of the sites affected by the recent oil spill, but not in the site affected by the 1975 oil spill. Oil-polluted trees supported lower parasitoid diversity than unpolluted trees in some sampling site/year combinations; however, such negative effects were inconsistent and pollution explained a small proportion of the variation in parasitoid community composition. Our results indicate that oil pollution may negatively affect parasitoid abundances and diversity, although the magnitude of the effect depends on the tree species, sampling site, and the time since the oil spill.

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Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms

Applied and Environmental Microbiology ◽

10.1128/aem.03462-16 ◽

2017 ◽

Vol 83 (10) ◽

Cited By ~ 46

Author(s):

Stephen M. Techtmann ◽

Mobing Zhuang ◽

Pablo Campo ◽

Edith Holder ◽

Michael Elk ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Microbial Communities ◽

Bacterial Community Structure ◽

Oil Spills ◽

Content Type ◽

Corexit 9500 ◽

Oil Biodegradation ◽

Degrading Bacteria ◽

The Impact

ABSTRACT To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses indicated that several OTUs were inhibited by the addition of Corexit. Conversely, a number of OTUs were stimulated by the addition of the dispersant, many of which were identified as known hydrocarbon-degrading bacteria. The results highlight the value of using RNA-based methods to further understand the impact of dispersant on the overall activity of different hydrocarbon-degrading bacterial groups.

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Negative Effects of Sample Pooling on PCR-Based Estimates of Soil Microbial Richness and Community Structure

Applied and Environmental Microbiology ◽

10.1128/aem.03017-09 ◽

2010 ◽

Vol 76 (7) ◽

pp. 2086-2090 ◽

Cited By ~ 35

Author(s):

Daniel K. Manter ◽

Tiffany L. Weir ◽

Jorge M. Vivanco

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Bacterial Communities ◽

Microbial Community Composition ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Negative Effects ◽

Soil Microbial ◽

Sample Pooling ◽

The Impact

ABSTRACT In this study, we examined the effect of various pooling strategies on the characterization of soil microbial community composition and phylotype richness estimates. Automated ribosomal intergenic spacer analysis (ARISA) profiles were determined from soil samples that were (i) unpooled (extracted and amplified individually), (ii) pooled prior to PCR amplification, or (iii) pooled prior to DNA extraction. Regression analyses suggest that the less even the soil microbial community (i.e., low Shannon equitability, EH ), the greater was the impact of either pooling strategy on microbial detection (R 2 = 0.766). For example, at a tropical rainforest site, which had the most uneven fungal (EH of 0.597) and bacterial communities (EH of 0.822), the unpooled procedure detected an additional 67 fungal and 115 bacterial phylotypes relative to either of the pooled procedures. Phylotype rarity, resulting in missed detection upon pooling, differed between the fungal and bacterial communities. Fungi were typified by locally abundant but spatially rare phylotypes, and the bacteria were typified by locally rare but spatially ubiquitous phylotypes. As a result, pooling differentially influenced plot comparisons, leading to an increase in similarity for the bacterial community and a decrease in the fungal community. In conclusion, although pooling reduces sample numbers and variability, it could mask a significant portion of the detectable microbial community, particularly for fungi due to their higher spatial heterogeneity.

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The interactive effect of pH variation and cadmium stress on wheat (Triticum aestivum L.) growth, physiological and biochemical parameters

PLoS ONE ◽

10.1371/journal.pone.0253798 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253798

Author(s):

Shafeeq Ur Rahman ◽

Qi Xuebin ◽

Luqman Riaz ◽

Ghulam Yasin ◽

Adnan Noor Shah ◽

...

Keyword(s):

Triticum Aestivum ◽

Nutrient Availability ◽

Anthropogenic Activities ◽

Interactive Effect ◽

Membrane Damage ◽

Acidic Ph ◽

Negative Effects ◽

Wheat Growth ◽

Neutral Ph ◽

The Impact

Anthropogenic activities such as mining, manufacturing, and application of fertilizers release substantial quantities of cadmium (Cd) into the environment. In the natural environment, varying pH may play an important role in the absorption and accumulation of Cd in plants, which can cause toxicity and increase the risk to humans. We conducted a hydroponic experiment to examine the impact of pH on cadmium (Cd) solubility and bioavailability in winter wheat (Triticum aestivum L.) under controlled environmental conditions. The results showed that Cd concentration was significantly reduced in wheat with an increase in pH from 5 to 7, while it was dramatically increased at pH ranging from 7 to 9. However, in both cases, a significant reduction in physiological traits was observed. The addition of Cd (20, 50, and 200 μmol L-1) at all pH levels caused a substantial decline in wheat growth, chlorophyll and carotenoids contents, nutrient availability, while elevated cell membrane damage was observed in terms of electrolytic leakage (EL), osmoprotectants, and antioxidants activity. In our findings, the negative effects of acidic pH (5) on wheat growth and development were more pronounced in the presence of Cd toxicities. For instance, Cd concentration with 20, 50, and 200 μmol L-1 at acidic pH (5) reduced shoot dry biomass by 45%, 53%, and 79%, total chlorophyll contents by 26%, 41%, 56% while increased CAT activity in shoot by 109%, 175%, and 221%, SOD activity in shoot by 122%, 135%, and 167%, POD activity in shoot by 137%, 250%, and 265%, MDA contents in shoot by 51%, 83%, and 150%, H2O2 contents in shoot by 175%, 219%, and 292%, EL in shoot by 108%, 165%, and 230%, proline contents in shoot by 235%, 280%, and 393%, respectively as compared to neutral pH without Cd toxicities. On the other hand, neutral pH with Cd toxicities alleviated the negative effects of Cd toxicity on wheat plants by limiting Cd uptake, reduced reactive oxygen species (ROS) formation, and increased nutrient availability. In conclusion, neutral pH minimized the adverse effects of Cd stress by minimizing its uptake and accumulation in wheat plants.

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Impact of NaCl, nitrate and temperature on the microbial community of a methanol-fed, denitrifying marine biofilm

10.1101/607028 ◽

2019 ◽

Cited By ~ 1

Author(s):

Richard Villemur ◽

Geneviève Payette ◽

Valérie Geoffroy ◽

Florian Mauffrey ◽

Christine Martineau

Keyword(s):

Microbial Community ◽

Environmental Changes ◽

Heterotrophic Bacteria ◽

Denitrifying Bacteria ◽

Metagenomic Data ◽

Strong Impact ◽

Anoxic Conditions ◽

Pure Cultures ◽

Denitrification Genes ◽

The Impact

AbstractBackgroundThe biofilm of a continuous, methanol-fed, fluidized denitrification system that treated a marine effluent at the Montreal Biodome is composed of a multi-species microbial community, among whichHyphomicrobium nitrativoransNL23 andMethylophaga nitratireducenticrescensJAM1 are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm taken from the denitrification system was cultured at laboratory scale in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific physico-chemical parameters. We previously showed that the seawater formulation and the NaCl concentrations had a strong impact on theH. nitrativoransNL23 population, with its displacement by a new denitrifier,M. nitratireducenticrescensGP59. Here, we report the impact of these cultures conditions on the dynamics of the overall microbial community of the denitrifying biofilm.MethodsThe original biofilm (OB) taken from the denitrification system was acclimated for five weeks in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate concentrations and temperatures. The OB was also acclimated to the commercial Instant Ocean seawater medium (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA amplicon metagenome sequencing. Culture-dependent approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of some of the biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures ofH. nitrativoransNL23 andM. nitratireducentricrescensGP59 cultivated under denitrifying conditions.ResultsThe 16S metagenomic data revealed very high proportions ofM. nitratireducenticrescensin the biofilm cultures.H. nitrativoransNL23 was found in high proportion in the OB, both was absent in the biofilm cultures with 2.75% NaCl in the ASW medium. It was found however in low proportions in the biofilm cultures with 0 to 1% NaCl in the ASW medium and in the IO biofilm cultures. Emergence ofMarinicellaspp. occurred in these biofilm cultures. Denitrifying bacterial isolates affiliated toMarinobacterspp. andParacoccusspp. were isolated. Up regulation of the denitrification genes in strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to theStappiaspp. were metabolically active in the biofilm cultures.ConclusionsThese results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes in strain GP59 and strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm compared to the planktonic pure cultures. Other denitrifying heterotrophic bacteria are present in low proportions in the biofilm, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments.

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Shoreline Evolution and Environmental Changes at the NW Area of the Gulf of Gela (Sicily, Italy)

Land ◽

10.3390/land10101034 ◽

2021 ◽

Vol 10 (10) ◽

pp. 1034

Author(s):

Laura Borzì ◽

Giorgio Anfuso ◽

Giorgio Manno ◽

Salvatore Distefano ◽

Salvatore Urso ◽

...

Keyword(s):

Environmental Changes ◽

Anthropogenic Activities ◽

Shoreline Change ◽

Coastal Structures ◽

Medium Term ◽

Change Analysis ◽

Dune System ◽

Coastal Evolution ◽

Shoreline Evolution ◽

The Impact

Coastal areas are among the most biologically productive, dynamic and valued ecosystems on Earth. They are subject to changes that greatly vary in scale, time and duration and to additional pressures resulting from anthropogenic activities. The aim of this work was to investigate the shoreline evolution and the main environmental changes of the coastal stretch between the towns of Licata and Gela (in the Gulf of Gela, Sicily, Italy). The methodology used in this work included the analysis of: (i) shoreline changes over the long- and medium-term periods (1955–2019 and 1989–2019, respectively), (ii) dune system fragmentation and (iii) the impact of coastal structures (harbours and breakwaters) on coastal evolution. The shoreline change analysis mainly showed a negative trend both over the long- and medium-term periods, with a maximum retreat of 3.87 m/year detected over the medium-term period down-drift of the Licata harbour. However, a few kilometres eastward from the harbour, significant accretion was registered where a set of breakwaters was emplaced. The Shoreline Change Envelope (SCE) showed that the main depositional phenomena occurred during the decade between 1955 and 1966, whereas progressive and constant erosion was observed between 1966 and 1989 in response to the increasing coastal armouring.

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