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The article discusses the ongoing issue of hydrocarbon pollution and the need to harness the hydrocarbon-degrading microbiome to mitigate its impact on the environment. It highlights the various sources of hydrocarbon pollution, including industrial and petroleum activities, wildfires, and natural sources. The article also explores the microbial communities that inhabit hydrocarbon-contaminated sites and their role in hydrocarbon degradation. It discusses the challenges and potential of using synthetic biology approaches to design engineered microbial communities for bioremediation. The article emphasizes the importance of monitoring methods and holistic approaches for evaluating the effectiveness of bioremediation treatments. The research work of the authors was funded by various projects, and they declare no competing interests. [Extracted from the article]

Highlights • Bacterial alkyl glycerol lipid (AGEs) composition unrelated to the growth stage. • AGEs diagenetic fate simulated during long term anoxic and oxic incubation. • Preferential degradation of fatty acids and monoalkyl glycerols (MAGEs). • Selective oxic degradation of sn -1 relative to sn -2 positional isomers of MAGEs. • Excellent diagenetic stability of dialkyl glycerols whatever the redox conditions. Abstract Bacterial mono- and dialkyl glycerol ether lipids (MAGEs and DAGEs) are potential powerful lipid biomarkers whose respective diagenetic fate still needs to be precisely assessed. To do so, the lipid content of cultures of an anaerobic bacterium synthesizing both MAGEs and DAGEs was analyzed at different growth stages and after long-term incubation under aerobic or anaerobic conditions. The proportions of the different lipid classes (fatty acids, MAGEs and DAGEs), as well as their structural distributions, did not significantly vary during anaerobic growth under optimal conditions until the stationary phase. Long-term exposure to oxygen (up to 480 days) induced the preferential degradation of fatty acids and MAGEs relative to DAGEs and of sn -1 relative to sn -2 positional isomers of MAGEs. The degradation of fatty acids and MAGEs appeared slower under anaerobic conditions and no specific structures appeared preferentially degraded. All DAGE structures were very well preserved whatever the redox conditions and the time of incubation considered (480 days and 13 years under oxic and anoxic conditions, respectively). The results highlight the excellent diagenetic stability of DAGEs and the much lower potential of preservation of MAGEs, warranting caution for an eventual use of the latter compounds as tracers of environmental or microbial community changes. [ABSTRACT FROM AUTHOR]

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4–V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans , SEEP-SRB1 , Spirochaeta 2 , among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula , Blastopirellula , Aquibacter , among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment. [Display omitted] • Contaminants exert strong selective pressure on sediment prokaryotic taxa. • Microbial taxa are resistant to high level of chronic metal contamination. • Microbial community differs according to sectors & Quality Ratio risk rank. • Metal pollutants favor anaerobic microbial taxa identified as bioindicators. [ABSTRACT FROM AUTHOR]

Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms. [ABSTRACT FROM AUTHOR]

Microbial communities from Sepetiba Bay (SB, Rio de Janeiro, Brazil), characterized by 16S rRNA gene (V4–V5 region) sequencing analysis, were found to be correlated with the metallic contamination factor and the Quality Ratio (QR) index. Consistently, the predicted function of microbial communities, obtained with Tax4Fun2, showed that the functional patterns in SB internal sector under the highest anthropogenic pressure were different from that observed in the external sector with the lowest contamination level. Signal transduction, cellular community, membrane transport, and energy metabolism were among the KEGG pathways favored by metallic contamination in the SB internal sector, while lipid metabolism, transcription, and translation were among the pathways favored in the SB external sector. Noteworthy, the relative proportions of KEGG pathways and genes associated with metallic homeostasis showed significant differences according to the SB sectors, consistently with the ecological risk classification (QR index) of sediments. The functional prediction approach is an economically viable alternative and presents an overview of the main pathways/genes favored in the SB microbiota exposed to long-term pollution. In contrast, the microgAMBI, ecological status index based on bacterial community composition, was not consistent with the metallic contamination of SB, suggesting that this index requires improvements to be applied in tropical areas. Our study also revealed a strong correlation between metal resistance genes (MRG) and antibiotic resistance genes (ARG), indicating that MRG and ARG are co-selected by the metallic contamination prevailing in SB. [Display omitted] • Quality ratio index is accurate to reveal the ecological risk in tropical areas. • Specific KEGG pathways are favored in high eutrophic/pollution sector. • Metal resistance genes attest that prokaryotic community is adapted to pollution. • Metallic pollutants contribute to the emergence of antibiotic resistant bacteria. [ABSTRACT FROM AUTHOR]

The organisation of denitrifying microorganisms in oil-polluted bioturbated sediments was investigated in mesocosms under conditions as closer as possible to that observed in the environment. Molecular and culture-dependent approaches revealed that denitrifying Gammaproteobacteria were abundant in oil-polluted and bioturbated sediments suggesting that they may play a key role in hydrocarbon degradation in the environment. T- RFLP and gene libraries analyses targeting nir S gene showed that denitrifying microbial communities structure was slightly affected by either the addition of Hediste diversicolor or crude oil revealing the metabolic versatility of denitrifying microorganisms. From oil-polluted sediments, distinct denitrifying hydrocarbonoclastic bacterial consortia were obtained by enrichment cultures on high molecular weight polyaromatic hydrocarbons ( PAHs) (dibenzothiophene, fluoranthene, pyrene and chrysene) under nitrate-reducing conditions. Interestingly, molecular characterisation of the consortia showed that the denitrifying communities obtained from oiled microcosms with addition of H. diversicolor were different to that observed without H. diversicolor addition, especially with fluoranthene and chrysene revealing the bacterial diversity involved in the degradation of these PAHs. [ABSTRACT FROM AUTHOR]

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g−1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities. [ABSTRACT FROM AUTHOR]

A microbial enrichment culture from brackish sediments was able to grow on octadec-1-ene (an unsaturated aliphatic hydrocarbon) as sole source of carbon and energy, under methanogenic conditions. Octadecene degradation is stopped either when bromoethanesulfonic acid, a selective inhibitor of methanogenesis is introduced, or when hydrogen is introduced. In the presence of bromoethanesulfonic acid, the degradation is restored by the addition of a hydrogenotrophic sulfate-reducing microorganism with sulfate. Results of molecular biodiversity, which revealed the presence of bacteria as well as of acetoclastic and hydrogenotrophic methanogens, are consistent with a syntrophic degradation involving Bacteria and Archaea. This is the first demonstration of syntrophic alkene degradation by microbial communities, showing that syntrophy is more widespread than we could have thought so far. These results highlight the need for a better understanding of microbial interactions and their role in the organic-matter degradation in polluted environments. [ABSTRACT FROM AUTHOR]

Abstract: Two alkene-degrading sulphate-reducing bacteria from the genus Desulfatiferula (Desulfatiferula olefinivorans strain LM2801T and Desulfatiferula sp. strain BE2801) were investigated for their 1-alkene metabolism. Their total cellular fatty acids were predominantly C-even when they were grown on C-even 1-alkene (1-hexadecene), whereas a mixture of fatty acids with C-odd or C-even carbon chains predominated when cells were grown on C-odd 1-alkene (1-pentadecene). This is consistent with the fatty acid composition of other sulphate-reducing strains previously reported to grow on n-alkenes. Linear and 3-OH–fatty acids appear to be the main fatty acids produced by the two Desulfatiferula strains. The analysis of their neutral lipids led to identifying several n-alkanols and n-ketones with the same number of carbon atoms as the alkene growth substrate and with functionality located between C-1 and C-5. Growth of strains LM2801T and BE2801 on (per) deuterated 1-alkenes provided direct evidence of their anaerobic transformation to corresponding 1-alkanols, n-ketones and linear (3-OH–) fatty acids. These results demonstrate that Desulfatiferula strains oxidize a 1-alkene by oxidation of the double bond at C-1, but also at C-2 to C-5 (after eventual isomerization of the double bond) yielding the corresponding C-2 to C-5 n-ketones (via the corresponding n-alkanols). The formation of specific 3-OH–fatty acids by elongation of shorter chain fatty acids was also demonstrated. Based on our observations, pathways for anaerobic 1-alkene metabolism in sulphate-reducing bacteria from the genus Desulfatiferula are proposed. They indicate that n-ketones can constitute new metabolites of the biodegradation of n-alkenes in anaerobic environments. [Copyright &y& Elsevier]

Abstract: Little is known about microbial communities involved in hydrocarbon degradation, whether it be their structural and functional diversity or their response to environmental constraints such as oxygen fluctuation. Here, current knowledge of the impact of diversity and redox oscillations upon ecosystem processes is reviewed. In addition, we present the main conclusions of our studies in this field. Oxic/anoxic oscillations had a strong impact upon bacterial community structures, influencing their ability to degrade hydrocarbons and their capacity to reduce hydrocarbon toxicity. Furthermore, a decrease in functional diversity has a strong impact on pollutant degradation. [Copyright &y& Elsevier]

Abstract: Current knowledge of the pathways for the degradation of n-alkanes and n-alkenes by anaerobic bacteria is summarized and new results questioning the existence of an alternative pathway for anaerobic alkane degradation are introduced. Remaining gaps in our knowledge are also mentioned, together with the possible use of some specific metabolites as biomarkers of anaerobic hydrocarbon degradation. [Copyright &y& Elsevier]

The alkane- and alkene-degrading, marine sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T, known to oxidize n-alkanes anaerobically by fumarate addition at C-2, was investigated for its 1-alkene metabolism. The total cellular fatty acids of this strain were predominantly C-(even number) (C-even) when it was grown on C-even 1-alkenes and predominantly C-(odd number) (C-odd) when it was grown on C-odd 1-alkenes. Detailed analyses of those fatty acids by gas chromatography-mass spectrometry after 6- to 10-week incubations allowed the identification of saturated 2- and 4-ethyl-, 2- and 4-methyl-, and monounsaturated 4-methyl-branched fatty acids with chain lengths that correlated with those of the 1-alkene. The growth of D. aliphaticivorans on (per)deuterated 1-alkenes provided direct evidence of the anaerobic transformation of these alkenes into the corresponding 1-alcohols and into linear as well as 10- and 4-methyl-branched fatty acids. Experiments performed with [13C]bicarbonate indicated that the initial activation of 1-alkene by the addition of inorganic carbon does not occur. These results demonstrate that D. aliphaticivorans metabolizes 1-alkene by the oxidation of the double bond at C-1 and by the subterminal addition of organic carbon at both ends of the molecule [C-2 and C-(ω-1)]. The detection of ethyl-branched fatty acids from unlabeled 1-alkenes further suggests that carbon addition also occurs at C-3. Alkylsuccinates were not observed as potential initial intermediates in alkene metabolism. Based on our observations, the first pathways for anaerobic 1-alkene metabolism in an anaerobic bacterium are proposed. Those pathways indicate that diverse initial reactions of 1-alkene activation can occur simultaneously in the same strain of sulfate-reducing bacterium. [ABSTRACT FROM AUTHOR]

The alkane-degrading, sulfate-reducing bacterium Desulfatibadillum aliphaticivorans strain CV2803T, recently isolated from marine sediments, was investigated for n-alkane metabolism. The total cellular fatty acids of this strain had predominantly odd numbers of carbon atoms (C odd) when the strain was grown on a C-odd alkane (pentadecane) and even numbers of carbon atoms (C even) when it was grown on a C-even alkane (hexadecane). Detailed analyses of those fatty acids by gas chromatography/mass spectrometry allowed us to identify saturated 2-, 4-, 6-, and 8-methyl- and monounsaturated 6-methyl-branched fatty acids, with chain lengths that specifically correlated with those of the alkane. Growth of D. aliphaticivorans on perdeuterated hexadecane demonstrated that those methyl -branched fatty acids were directly derived from the substrate. In addition, cultures on pentadecane and hexadecane produced (1-methyltetradecyl) succinate and (1-methylpentadecyl) succinate, respectively. These results indicate that D. aliphalicivorans strain CV2803T oxidizes n-alkanes into fatty acids anaerobically, via the addition of fumarate at C-2. Based on our observations and on literature data, a pathway for anaerobic n-alkane metabolism by D. aliphaticivorans is proposed. This involves the transformation of the initial alkylsuccinate into a 4-methyl-branched fatty acid which, in addition to catabolic reactions, can alternatively undergo chain elongation and desaturation to form storage fatty acids. [ABSTRACT FROM AUTHOR]

The anaerobic degradation of n-alkenes by a sulphate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803T was investigated. Results suggest that enzymes required for alkene degradation are inducible. Moreover, total cellular fatty acids of strain CV2803T were predominantly C-odd when the strain was grown on C-odd substrates and C-even when grown on C-even substrates. In addition to classical bacterial fatty acids, unusual 4-Me-17:1Δ11 and 4-Me-18:1Δ11 fatty acids and their saturated homologues were detected when strain CV2803T was grown on 1-pentadecene and 1-hexadecene, respectively. These methyl-branched monounsaturated fatty acids could constitute specific metabolites of n-alkene degradation by sulphate-reducing bacteria. To cite this article: C. Cravo-Laureau et al., C. R. Biologies 327 (2004). [Copyright &y& Elsevier]

COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP) were developed for the detection of the dsz B desulfinase gene (2′-hydroxybiphenyl-2-sulfinate desulfinase; EC 3.13.1.3) by polymerase chain reaction (PCR), which allow to reveal larger diversity than traditional primers. The new developed primers were used as molecular monitoring tool to drive a procedure for the isolation of desulfurizing microorganisms. The primers revealed a large dsz B gene diversity in environmental samples, particularly in diesel-contaminated soil that served as inoculum for enrichment cultures. The isolation procedure using the dibenzothiophene sulfone (DBTO 2) as sole sulfur source reduced drastically the dsz B gene diversity. A dsz B gene closely related to that carried by Gordonia species was selected. The desulfurization activity was confirmed by the production of desulfurized 2-hydroxybiphenyl (2-HBP). Metagenomic 16S rRNA gene sequencing showed that the Gordonia genus was represented at low abundance in the initial bacterial community. Such observation highlighted that the culture medium and conditions represent the bottleneck for isolating novel desulfurizing microorganisms. The new developed primers constitute useful tool for the development of appropriate cultural-dependent procedures, including medium and culture conditions, to access novel desulfurizing microorganisms useful for the petroleum industry. [ABSTRACT FROM AUTHOR]

Worldwide, the corrosion of petroleum pipelines is the cause of severe operational failures and damages to the environment, and the majority of them may have been intensified by microbial activities. However, few scientific publications have investigated the influence of seawater with indigenous microorganisms in internal corrosion of welded joints in long-distance pipelines, which has motivated this study. Here, a combination of culture-based and molecular microbiological methods was applied to measure the microbial abundance, diversity and composition of biofilms formed on two corroded weldments (gas tungsten arc - GTAW and shielded metal arc - SMAW) of an API 5L X65 microalloyed steel under laminar and turbulent flow regimes using seawater from Guanabara Bay (Rio de Janeiro, Brazil). Overall, turbulent flow did not reduce the biomass of sessile microorganisms on welded joints compared to laminar flow. Phylogenetic analysis revealed that the Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla in biofilms attached to GTAW and SMAW joints. At the genus level, all samples showed similar microbial composition with dominance of Desulfovibrio. However, analysis at OTU level revealed that there were specific microorganisms in each corrosive sample, even though they were affiliated to sulfate-reducers. Thus, microbial community compositions were influenced by type of weld, flow regime and biofilm age. The results of our study will be of benefit to the further studies of weld biocorrosion and biofilm ecology within pipelines. Image 1 • Characterization of biofilms development on welded joints exposed to laminar and turbulent flows. • Turbulent flow did not reduce the number of sessile microorganisms on welded joints. • Both fluid flow regime and type of weld influenced the microbial composition at OTU level. • Oxygen and sulfide concentrations in the fluid driven the assembly of the microbial communities. • Corrosion rate was more severe in welded joints exposed to laminar flow regime. [ABSTRACT FROM AUTHOR]

Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of Desulfatibacillum alkenivorans strain PF2803T, a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen-and sulfur-containing polar head groups, moving beyond a reliance on conventional nonphospholipid types. [ABSTRACT FROM AUTHOR]

[Display omitted] • Higher bacterial diversity and richness found in abandoned salterns. • Higher eukaryotic diversity and richness found in exploited salterns. • Abandoned and exploited salterns own specific microorganisms. • Salinity drives bacterial community structures. • Salterns exploitation affects eukaryotic predator composition. In order to understand the effect of human practices on microbial mats organisation, the study aimed to investigate the biodiversity within microbial mats from exploited and abandoned salterns. Despite several attempts, archaeal 16S rRNA gene fragment sequences were not obtained, indicating that microbial mats were probably dominated by Bacteria with very low abundance of Archaea (< 1%). Thus, the study compared the bacterial and meiofaunal diversity of microbial mats from abandoned and exploited salterns. The higher salinity (101 ± 3.7 psu vs. 51.1 ± 0.7 psu; Welch t -test p < 0.05) of the exploited site maintained lower bacterial diversity in comparison to the abandoned site where the salinity gradient was no longer maintained. However, the microbial mats exhibited similar bacterial class composition while the eukaryotic diversity was significantly higher in the exploited saltern. The abandoned saltern was dominated by sulfate-reducing bacteria and Nematoda, while the exploited saltern was characterized by the presence of halophilic bacteria belonging to Marinobacter , Salinivibrio and Rhodohalobacter genera, and the larger abundance of Hypotrichia (ciliates). Such bacterial and eukaryotic diversity difference might be explained by human actions for salt recovery in exploited salterns such as scraping the surface of microbial mat and increasing salinity renewing the microbial mat each year. Such action decreases the bacterial diversity changing the food web structure that favour the presence of a larger diversity of eukaryotic organisms. Our study provides new insights on microbial mat communities inhabiting salterns, especially the consequences of abandoning saltern exploitation. [ABSTRACT FROM AUTHOR]

Pitting corrosion in microalloyed steel and its welded joints occur in fabricated structures, such as pipelines for oil and gas transport, which are exposed to corrosive environments. Although the formation of the pits consumes only a relatively small mass of material, the role of the pits as defect sites for crack initiation and continuing corrosion can be substantial. Furthermore, in natural and industrial environments where microorganisms are widely distributed, pitting corrosion is aggravated by the release of many reactive microbial metabolites. This is a report of a 28-day study aimed at the microbiologically influenced corrosion of joint welds by gas tungsten arc welding (GTAW) and shielded metal arc welding (SMAW) exposed to laminar and turbulent flows. The characterization of the planktonic microbial community indicated that laminar flow created an anoxic environment promoting the dominance of anaerobic microorganisms, in particular sulfate reducing bacteria (SRB). Both types of welded joints showed similar pit densities in the base metal (BM), heat-affected zone (HAZ) and weld metal (WM), nevertheless the pit depth was higher in the HAZ than the BM and WM. On the other hand, turbulent flow retained dissolved oxygen content, ensuring the presence of aerobic microorganisms, but there was no inhibition of SRB growth. Although the pit depth was low in both types of welded joints, the pit density was exacerbated in only one HAZ of each welded joint due to WM reinforcement height, while the other HAZ showed low pit density. This study demonstrates that turbulent flow can reduce the biocorrosion of non-welded areas but can aggravate welded joints biocorrosion. Image 1 • Biocorrosion of joints welded by gas tungsten arc welding and shielded metal arc welding were investigated. • The type of fluid flow regiment influenced the planktonic microbial community. • Planktonic sulfate reducing bacteria number was not affected by turbulent flow. • Pitting corrosion was more severe in the heat-affected zone, regardless of the welding process and flow regime. • Turbulent flow promoted a differentiated distribution of pits in the welded joints. [ABSTRACT FROM AUTHOR]

Air samples from four contrasting outdoor environments including a park, an arable farm, a waste water treatment plant and a composting facility were analysed during the summer and winter months. The aim of the research was to study the feasibility of differentiating microbial communities from urban, rural and industrial areas between seasons with chemical and molecular markers such as microbial volatile organic compounds (MVOCs) and phospholipid fatty acids (PLFAs). Air samples (3 l) were collected every 2 h for a total of 6 h in order to assess the temporal variations of MVOCs and PLFAs along the day. MVOCs and VOCs concentrations varied over the day, especially in the composting facility which was the site where more human activities were carried out. At this site, total VOC concentration varied between 80 and 170 μg m −3 in summer and 20–250 μg m −3 in winter. The composition of MVOCs varied between sites due to the different biological substrates including crops, waste water, green waste or grass. MVOCs composition also differed between seasons as in summer they are more likely to get modified by oxidation processes in the atmosphere and in winter by reduction processes. The composition of microbial communities identified by the analysis of PLFAs also varied among the different locations and between seasons. The location with higher concentrations of PLFAs in summer was the farm (7297 ng m −3 ) and in winter the park (11,724 ng m −3 ). A specific set of MVOCs and PLFAs that most represent each one of the locations was identified by principal component analyses (PCA) and canonical analyses. Further to this, concentrations of both total VOCs and PLFAs were at least three times higher in winter than in summer. The difference in concentrations between summer and winter suggest that seasonal variations should be considered when assessing the risk of exposure to these compounds. [ABSTRACT FROM AUTHOR]

Performic acid (PFA), a new generation of disinfectant, has shown outstanding performance for wastewater treatment. However, the effect of PFA on wastewater microbial community changes as well as the differences in comparison to the commonly disinfectants used are poorly documented. We provide an overview of the PFA effect and that of chlorine and UV, two commonly used disinfectants, on microbial community diversity and structure. The study was performed using wastewaters from three municipal wastewater treatment plants (WWTPs) processed by activated sludge, lagoon and reed beds, and biofilter. We focused on disinfection of pathogen microorganisms, identifying sensitive and resistant bacteria to disinfectants that can serve as biomarkers for evaluating the disinfectant performances. As well, we investigated the modifications of microbial functions after treatment by functional predictive analysis. The more efficient E. coli inactivation was obtained with initial concentration of 4 mg/L of PFA with 15 min disinfectant contact time that achieved 95.71–99.99% inactivation efficiency. Although the origin of wastewater was the main factor determining the microbial community diversity and composition, the microbial communities were specific to the disinfectant used. Linear discriminant analysis Effect Size (LEfSe) identified 18 and 10 biomarkers, including pathogenic microorganisms affiliated to Chromobacterium , Flavobacterium , Aeromonas , Enterobacteriaceae, Escherichia_Shigella and Fusobacteriaceae, which were sensitive to PFA, while being resistant to chlorine and/or UV. Consistently, the predicted bacterial functional patterns diverged according to the wastewater origin and the disinfectant used. Pathogen microorganisms were more sensitive to PFA than the other treatments, demonstrating its potential for implementing a safe reuse of wastewater. • PFA was an efficient disinfectant comparing to chlorine and UV. • Microbial communities from treated water were specific to the disinfectant used. • Biomarkers sensitive to PFA and resistant to chlorine and/or UV were identified. • Bacterial predicted functions diverge according to WWTP and disinfectants. [ABSTRACT FROM AUTHOR]

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment. [ABSTRACT FROM AUTHOR]

Bacterial non-isoprenoid alkyl glycerol ether lipids (AGEs) are widespread in the environment but little is known about their biological precursors and mode of formation as a function of varying growth conditions. Here, we searched for the presence of AGEs in five pure strains of mesophilic (growth temperature between 20 and 40 °C) and heterotrophic sulfate reducing bacteria from the family Desulfobacteraceae grown on a wide range of hydrocarbons and organic acids as sole carbon and energy source. Gas chromatography–mass spectrometry (GC–MS) analysis of hydrolyzed cells revealed the presence of monoalkyl glycerols (MAGEs) in one Desulfatiferula species and of MAGEs and dialkyl glycerols (DAGEs) in two Desulfatibacillum species. Species from the genus Desulfococcus did not produce AGEs. The ether lipid composition appeared strongly dependent on the nature and the chain length of the carbon substrate, with few to > 50 homologues of AGEs formed from a single substrate. Growth on long chain n -alkyl compounds (C 14 to C 18 alk-1-enes and fatty acids) generated a much lower diversity of MAGEs and DAGEs than short chain substrates (nonanoate, octanoate and pyruvate) or isoprenoid alkenes (phytadienes). Such variation in alkyl glycerol production could be linked to the distinct pathways involved in the metabolism of the different substrates. Despite this substrate-dependent AGE composition, the average chain length and level of branching of each class of ether lipid remained remarkably stable whatever the growth substrate and the number of MAGE and DAGE homologues formed, indicating a compositional control of ether lipids by heterotrophic bacteria to maintain optimal membrane properties. [ABSTRACT FROM AUTHOR]

Bacterial glycerol ether lipids (alkylglycerols) have received increasing attention during the last decades, notably due to their potential role in cell resistance or adaptation to adverse environmental conditions. Major uncertainties remain, however, regarding the origin, biosynthesis, and modes of formation of these uncommon bacterial lipids. We report here the preponderance of monoalkyl- and dialkylglycerols (1-O-alkyl-, 2-O-alkyl-, and 1,2-O-dialkylglycerols) among the hydrolyzed lipids of the marine mesophilic sulfate-reducing proteobacterium Desulfatibacillum alkenivorans PF2803T grown on n-alkenes (pentadec-1-ene or hexadec-1-ene) as the sole carbon and energy source. Alkylglycerols account for one-third to two-thirds of the total cellular lipids (alkylglycerols plus acylglycerols), depending on the growth substrate, with dialkylglycerols contributing to one-fifth to two-fifths of the total ether lipids. The carbon chain distribution of the lipids of D. alkenivorans also depends on that of the substrate, but the chain length and methyl-branching patterns of fatty acids and monoalkyl- and dialkylglycerols are systematically congruent, supporting the idea of a biosynthetic link between the three classes of compounds. Vinyl ethers (1-alken-1'-yl-glycerols, known as plasmalogens) are not detected among the lipids of strain PF2803T. Cultures grown on different (per)deuterated n-alkene, n-alkanol, and n-fatty acid substrates further demonstrate that saturated alkylglycerols are not formed via the reduction of hypothetic alken-1'-yl intermediates. Our results support an unprecedented biosynthetic pathway to monoalkyl/monoacyl- and dialkylglycerols in anaerobic bacteria and suggest that n-alkyl compounds present in the environment can serve as the substrates for supplying the building blocks of ether phospholipids of heterotrophic bacteria. [ABSTRACT FROM AUTHOR]

Dispersants, used for combating oil spills, increase hydrocarbon bioavailability promoting their biodegradation. Oil weathering process introduces harmful soluble hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), into the water column, resulting in water-accommodated fraction (WAF). The presence of dispersants can influence the weathering process by increasing PAHs solubility, toxicity and biodegradability. However, little is known on how dispersants affect microbial communities and their degradation capacities, especially in cold environment where low temperature decreases microbial activity and thus hydrocarbon degradation. Here, we investigated the microbial community dynamics in cold water contaminated by WAF prepared from crude oil with or without a commercial dispersant (Finasol OSR52). The WAFs, prepared with Naphthenic North Atlantic crude oil, were used to contaminate seawater from Norwegian cold sites, one oil-contaminated and the other pristine. The WAF-contaminated seawaters were maintained in microcosms at 4 °C for 21 days. The content of PAHs and microbial compositions (16S rRNA gene sequencing) were determined at days 0, 7, 14 and 21. In addition, the 96 h toxicity assay with adult Acartia tonsa revealed WAFs toxicity at days 0 and 21. The toxicity of WAF mixtures, with and without dispersant, against Acartia tonsa was reduced during the experiment, but PAHs removal was not increased. The water from the oil-contaminated site showed the highest PAHs removal revealing legacy effect (presence of microorganisms adapted to PAHs). Additionally, our results reveal: i) microbial community plasticity allowing the adaptation to the presence of PAHs and dispersant, ii) specific bacteria taxa probably involved in PAHs degradation, and iii) dispersants shape the microbial communities dynamics by stimulating potential dispersant-degrading taxa, such as Fusibacter. Thus, our results provide valuable insights on the role of microbial community in determining the fate of water-solubilized hydrocarbon in cold environment while questioning the role of dispersant used for fighting oil spill. • Evidence of PAH biodegradation in water accommodated fraction at low temperature. • Toxicity toward Acartia tonsa reduced during PAH biodegradation. • Microbial community dynamics followed an ecological succession. • The legacy effect shapes microbial community rather than the addition of dispersant. • Dispersant impact microbial community dynamics favoring dispersant degrading taxa. [ABSTRACT FROM AUTHOR]

Dispersants, used for combating oil spills, increase hydrocarbon bioavailability promoting their biodegradation. Oil weathering process introduces harmful soluble hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), into the water column, resulting in water-accommodated fraction (WAF). The presence of dispersants can influence the weathering process by increasing PAHs solubility, toxicity and biodegradability. However, little is known on how dispersants affect microbial communities and their degradation capacities, especially in cold environment where low temperature decreases microbial activity and thus hydrocarbon degradation. Here, we investigated the microbial community dynamics in cold water contaminated by WAF prepared from crude oil with or without a commercial dispersant (Finasol OSR52). The WAFs, prepared with Naphthenic North Atlantic crude oil, were used to contaminate seawater from Norwegian cold sites, one oil-contaminated and the other pristine. The WAF-contaminated seawaters were maintained in microcosms at 4 °C for 21 days. The content of PAHs and microbial compositions (16S rRNA gene sequencing) were determined at days 0, 7, 14 and 21. In addition, the 96 h toxicity assay with adult Acartia tonsa revealed WAFs toxicity at days 0 and 21. The toxicity of WAF mixtures, with and without dispersant, against Acartia tonsa was reduced during the experiment, but PAHs removal was not increased. The water from the oil-contaminated site showed the highest PAHs removal revealing legacy effect (presence of microorganisms adapted to PAHs). Additionally, our results reveal: i) microbial community plasticity allowing the adaptation to the presence of PAHs and dispersant, ii) specific bacteria taxa probably involved in PAHs degradation, and iii) dispersants shape the microbial communities dynamics by stimulating potential dispersant-degrading taxa, such as Fusibacter. Thus, our results provide valuable insights on the role of microbial community in determining the fate of water-solubilized hydrocarbon in cold environment while questioning the role of dispersant used for fighting oil spill. • Evidence of PAH biodegradation in water accommodated fraction at low temperature. • Toxicity toward Acartia tonsa reduced during PAH biodegradation. • Microbial community dynamics followed an ecological succession. • The legacy effect shapes microbial community rather than the addition of dispersant. • Dispersant impact microbial community dynamics favoring dispersant degrading taxa. [ABSTRACT FROM AUTHOR]

The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed. [ABSTRACT FROM AUTHOR]

Highlights: [•] Pollutants can severely impact structure and function of microbial communities. [•] Biological interactions play a major role in structuring benthic food webs. [•] We studied the impact of meiofauna on bacteria facing contamination by a mixture of 3 PAHs. [•] Top down control by meiofauna was more effective than PAH in shaping bacterial diversity. [•] The structural role of meiofauna disappeared when nutrients were added to enhance PAH biodegradation. [ABSTRACT FROM AUTHOR]

Microbial diversity is generally considered as having no effect on the major processes of the ecosystem such as respiration or nutrient assimilation. However, information about the impact of diversity on minor functions such as xenobiotic degradation is scant. We studied the role of diversity on the capacity of an activated-sludge microbial community to eliminate phenanthrene, a polycyclic aromatic hydrocarbon. We also assessed the impact of diversity erosion on the ability of activated sludge to oxidize a wide range of organic compounds. The diversity of activated sludge was artificially modified by dilution to extinction followed by regrowth stage which led to communities with similar biomass but displaying a diversity gradient. The capacity of activated-sludge community to degrade phenanthrene was greatly modified: at high levels of diversity, the community was able to mineralize phenanthrene whereas at medium levels it first of all partially lost its ability to mineralize this pollutant and at the lowest diversity, the activated sludge completely lost its capacity to transform phenanthrene. Diversity depletion also reduced the metabolic diversity and biomass productivity of sewage-activated sludge. This study demonstrates that diversity erosion can greatly affect major ecosystem services such as pollutant removal. [ABSTRACT FROM AUTHOR]

This study evaluates the in vitro impact of three bioremediation techniques: biostimulation, bioaugmentation, and a combination of biostimulation and bioaugmentation on microflora and nematofauna after an artificial contamination of lagoon sediments by anthracene. This sediment contamination tends to reduce the average load in aerobic heterotrophic bacteria in the water column, at the sediment interface and at the same time induces a highly significant decrease in the average densities of nematodes in all microcosms contaminated by this pollutant. After inoculation with the Staphylococcus sp. bacterial strain, the increase in bacterial load was significant ( p < 0.05) in the three compartments of anthracene-contaminated microcosms with relation to the controls. The addition of nitrates and phosphates to the contaminated microcosms generated a highly significant increase in the average concentration of free-living nematodes with relation to the controls. [ABSTRACT FROM AUTHOR]

Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems. [Display omitted] • Evidence of microbial community coalescence within a soil-river-lake continuum. • Specialist species identified are specifically associated to pollutant type. • Prediction of degradation functions of the microbial specialists. • New insights gained to develop biomonitoring tools for environmental pollution. [ABSTRACT FROM AUTHOR]

This work aimed to evaluate the effect of acid mist on microbial communities developed on mortar with same composition from the wall of the National Museum in Rio de Janeiro. Five autochthonous microbial groups were inoculated on coated with acrylic paint and uncoated mortar surfaces and submitted to acid mist or water mist for 100 days. A heterogeneous biofilm was well developed in uncoated coupons under acid mist. Molecular analysis revealed that the bacterial communities were structured according to the incubation condition. The impact of coating on bacterial community structure was more important than the acid mist effect. The eukaryotic community structure was not affected by the acid mist, whereas the impact of coating by paint has been observed. The alpha diversity indexes also varied according to the treatment. H' and D were higher for uncoated conditions, particularly when submitted to acid mist. Actinobacteria, Chloroflexi, Cyanobacteria, Firmicutes and Proteobacteria were dominant. Additionally, eukaryotic community was not affected by the acid mist and paint and Tremellomycetes dominated. Image 1 • Evaluation of coating and acid mist in the mortar biodeterioration. • Experimental ecology, culture and molecular biology, and imagery provided good tools. • Acid mist promotes the development of microorganisms. • Bacterial and fungal communities were impacted by coating. [ABSTRACT FROM AUTHOR]