Impact of Coal-Coking Effluent on Sediment Microbial Communities: a Multivariate Approach

The functional response to and recovery from coal-coking waste effluent was evaluated for sediment microbial communities. Twenty estimates of microbial population density, biomass, and activity were measured five times during a 15-month period. Significant effects on microbial communities were observed in response to both wastewater contamination and diversion of the wastewater. Multivariate analysis of variance and discriminant analysis indicated that accurate differentiation between uncontaminated and contaminated sediments required a minimum of nine estimates of community response. Total viable population density, ATP, alkaline phosphatase, naphthalene, and phenanthrene mineralization rates were found to be highly weighted variables in site discrimination. Lipid and glucose mineralization, nitrogen fixation, and sediment protein also contributed significantly to explaining variation among sites. Estimates of anaerobic population densities and rates of methane production contributed little to discrimination among sites in the environment examined. In general, total viable population density, ATP, and alkaline phosphatase activity were significantly depressed in contaminated sediments. However, after removal of this contamination, the previously affected sites demonstrated greater temporal variability but a closer approximation of the mean response at the control site. Naphthalene and phenanthrene mineralization did not follow the general trend and were elevated at the contaminated sites throughout the investigation. Results of the investigation supported the hypothesis that multiple functional measures of microbial community response are required to evaluate the effect of and recovery from environmental contamination. In addition, when long-term effects are evaluated, select physiological traits, i.e., polyaromatic hydrocarbon mineralization, may not reflect population and biomass estimates of community response.     

Effects of naphthalene on microbial community composition in the Delaware estuary

The effects of naphthalene on microbial communities in the bottom boundary layer of the Delaware Bay estuary were investigated in microcosms using denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) with oligonucleotide probes. Three days after the addition of naphthalene, rates of bacterial production and naphthalene mineralization were higher than in no-addition controls and than in cases where glucose was added. Analyses using both DGGE and FISH indicated that the bacterial community changed in response to the addition of naphthalene. FISH data indicated that a few major phylogenetic groups increased in response to the glucose addition and especially to the naphthalene addition. DGGE also demonstrated differences in community composition among treatments, with four phylotypes being unique to naphthalene-amended treatments and three of these having 16S rRNA genes similar to known hydrocarbon degraders. The bacterial community in the naphthalene-amended treatment was distinct from the communities in the glucose-amended treatment and in the no-addition control. These data suggest that polycyclic aromatic hydrocarbons may have large effects on microbial community structure in estuaries and probably on microbially mediated biogeochemical processes.     

Naphthalene biodegradation in environmental microcosms: estimates of degradation rates and characterization of metabolites

Naphthalene biodegradation was investigated in microcosms containing sediment and water collected from three ecosystems which varied in past exposure to anthropogenic and petrogenic chemicals. Mineralization half-lives for naphthalene in microcosms ranged from 2.4 weeks in sediment chronically exposed to petroleum hydrocarbons to 4.4 weeks in sediment from a pristine environment. Microbiological analysis of sediments indicated that hydrocarbon-utilizing microbial populations also varied among ecosystems and were 5 to 12 times greater in sediment after chronic petrogenic chemical exposure than in sediment from an uncontaminated ecosystem. Sediment from an ecosystem exposed to agricultural chemicals had a mineralization half-life of 3.2 weeks for naphthalene and showed about a 30-fold increase in heterotrophic bacterial populations in comparison to uncontaminated sediments, but only a 2- to 3-fold increase in hydrocarbon-degrading bacteria. Analysis of organic solvent-extractable residues from the microcosms by high-pressure liquid chromatography detected polar metabolites which accounted for 1 to 3% of the total radioactivity. Purification of these residues by thin-layer chromatography and further analysis by gas chromatography-mass spectrometry indicated that cis-1,2-dihydroxy-1,2-dihydronaphthalene, 1-naphthol, salicylic acid, and catechol were metabolites of naphthalene. These results provide useful estimates for the rates of naphthalene mineralization in different natural ecosystems and on the degradative pathway for microbial metabolism of naphthalene in freshwater and estuarine environments.     

Naphthalene biodegradation in environmental microcosms: estimates of degradation rates and characterization of metabolites.

Naphthalene biodegradation was investigated in microcosms containing sediment and water collected from three ecosystems which varied in past exposure to anthropogenic and petrogenic chemicals. Mineralization half-lives for naphthalene in microcosms ranged from 2.4 weeks in sediment chronically exposed to petroleum hydrocarbons to 4.4 weeks in sediment from a pristine environment. Microbiological analysis of sediments indicated that hydrocarbon-utilizing microbial populations also varied among ecosystems and were 5 to 12 times greater in sediment after chronic petrogenic chemical exposure than in sediment from an uncontaminated ecosystem. Sediment from an ecosystem exposed to agricultural chemicals had a mineralization half-life of 3.2 weeks for naphthalene and showed about a 30-fold increase in heterotrophic bacterial populations in comparison to uncontaminated sediments, but only a 2- to 3-fold increase in hydrocarbon-degrading bacteria. Analysis of organic solvent-extractable residues from the microcosms by high-pressure liquid chromatography detected polar metabolites which accounted for 1 to 3% of the total radioactivity. Purification of these residues by thin-layer chromatography and further analysis by gas chromatography-mass spectrometry indicated that cis-1,2-dihydroxy-1,2-dihydronaphthalene, 1-naphthol, salicylic acid, and catechol were metabolites of naphthalene. These results provide useful estimates for the rates of naphthalene mineralization in different natural ecosystems and on the degradative pathway for microbial metabolism of naphthalene in freshwater and estuarine environments.     

Both Cycloclasticus spp. and Pseudomonas spp. as PAH-degrading bacteria in the Seine estuary (France)

Like other highly urbanized and industrialized estuaries, the Seine estuary (France) has, for decades, received high inputs of polycyclic aromatic hydrocarbons (PAHs). In order to estimate the bioremediation potentials and to identify the bacterial species involved in hydrocarbon degradation, we used microcosms containing seawater from the Seine estuary supplemented with either naphthalene, phenanthrene, fluorene or pyrene. In the microcosms enriched with naphthalene or phenanthrene, hydrocarbon biodegradation was significant within 9 weeks (43% or 46%, respectively), as shown by analyses in GC-MS. In similar microcosms incubated also with naphthalene or phenanthrene, analysis of the 16S rRNA gene sequences (DNA and cDNA) with denaturing gradient gel electrophoresis and clone libraries indicated that the PAH-degrading communities were dominated by Cycloclasticus spp., confirming their universal key role in degradation of low-molecular-weight PAHs in marine environments. However, in contrast to previous studies, we found that Pseudomonas spp. also degraded naphthalene and phenanthrene in seawater; this occurred only after 21 days, as was confirmed by real-time PCR. Although this genus has been abundantly described in the literature as a good PAH-degrading bacterial group in soil or in sediment, to our knowledge, this is the first evidence of a significant fitness in PAH degradation in seawater.     

Effects of co-occurring aromatic hydrocarbons on degradation of individual polycyclic aromatic hydrocarbons in marine sediment slurries

Rates of polycyclic aromatic hydrocarbon (PAH) degradation and mineralization were influenced by preexposure to alternate PAHs and a monoaromatic hydrocarbon at relatively high (100 ppm) concentrations in organic-rich aerobic marine sediments. Prior exposure to three PAHs and benzene resulted in enhanced [14C]naphthalene mineralization, while [14C]anthracene mineralization was stimulated only by benzene and anthracene preexposure. Preexposure of sediment slurries to phenanthrene stimulated the initial degradation of anthracene. Prior exposure to naphthalene stimulated the initial degradation of phenanthrene but had no effect on either the initial degradation or mineralization of anthracene. For those compounds which stimulated [14C]anthracene or [14C]naphthalene mineralization, longer preexposures (2 weeks) to alternative aromatic hydrocarbons resulted in an even greater stimulation response. Enrichment with individual PAHs followed by subsequent incubation with one or two PAHs showed no alteration in degradation patterns due to the simultaneous presence of PAHs. The evidence suggests that exposure of marine sediments to a particular PAH or benzene results in the enhanced ability of these sediments to subsequently degrade that PAH as well as certain other PAHs. The enhanced degradation of a particular PAH after sediments have been exposed to it may result from the selection and proliferation of specific microbial populations capable of degrading it. The enhanced degradation of other PAHs after exposure to a single PAH suggests that the populations selected have either broad specificity for PAHs, common pathways of PAH degradation, or both.     

Effects of co-occurring aromatic hydrocarbons on degradation of individual polycyclic aromatic hydrocarbons in marine sediment slurries.

Rates of polycyclic aromatic hydrocarbon (PAH) degradation and mineralization were influenced by preexposure to alternate PAHs and a monoaromatic hydrocarbon at relatively high (100 ppm) concentrations in organic-rich aerobic marine sediments. Prior exposure to three PAHs and benzene resulted in enhanced [14C]naphthalene mineralization, while [14C]anthracene mineralization was stimulated only by benzene and anthracene preexposure. Preexposure of sediment slurries to phenanthrene stimulated the initial degradation of anthracene. Prior exposure to naphthalene stimulated the initial degradation of phenanthrene but had no effect on either the initial degradation or mineralization of anthracene. For those compounds which stimulated [14C]anthracene or [14C]naphthalene mineralization, longer preexposures (2 weeks) to alternative aromatic hydrocarbons resulted in an even greater stimulation response. Enrichment with individual PAHs followed by subsequent incubation with one or two PAHs showed no alteration in degradation patterns due to the simultaneous presence of PAHs. The evidence suggests that exposure of marine sediments to a particular PAH or benzene results in the enhanced ability of these sediments to subsequently degrade that PAH as well as certain other PAHs. The enhanced degradation of a particular PAH after sediments have been exposed to it may result from the selection and proliferation of specific microbial populations capable of degrading it. The enhanced degradation of other PAHs after exposure to a single PAH suggests that the populations selected have either broad specificity for PAHs, common pathways of PAH degradation, or both.     

Naphthalene and Anthracene Mineralization Linked to Oxygen, Nitrate, Fe(III) and Sulphate Reduction in a Mixed Microbial Population

A microbial consortium from a mixture of garden soil and an enrichment of a coal-tar contaminated sediment mineralized naphthalene and anthracene when oxygen, nitrate, Fe(III) (soluble and insoluble) or sulphate were provided as terminal electron acceptors (TEAs). Rates of polyaromatic hydrocarbon disappearance and mineralization were similar in the presence of oxygen and nitrate, and slower with the other TEAs. A maximum mineralization of 37.5% naphthalene and 8.% anthracene occurred in 30 and 160 days respectively when oxygen was provided as the TEA. On the other hand, only 9.5% naphthalene and 3.2% anthracene were mineralized in 42 and 160 days respectively with FeOOH. Mineralization occurred only when a TEA was provided and ceased when the naphthalene concentration decreased to non-detectable levels (less than 0.008 moles/L), as measured by fluorescence spectroscopy. CH₄ was not detected in the headspace of any microcosm. These results showed that mineralization of polyaromatic hydrocarbons such as naphthalene and anthracene can be linked to wide range of TEAs demonstrating that intrinsic polyaromatic hydrocarbon bioremediation is possible if any of these TEAs were available.     

Molecular characterization of polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities

Previous research demonstrated that methanogenic cultures enriched from Baltimore Harbor (Baltimore, MD) sediments were able to degrade naphthalene and phenanthrene. In this report, the degradation activity was maintained through a sequential transfer without adding additional sediments and the established polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities were characterized via comparative sequence analysis of clone libraries of 16S rRNA genes amplified using bacteria-specific and Archaea-specific primers. The phylogenetic analysis indicated that the addition of PAHs clearly shifted the structure of the methanogenic community and resulted in an increase in populations of species previously found in other hydrocarbon-degrading communities. Of particular interest is the fact that the dominant microbial population of the naphthalene cultures was different from that of the phenanthrene cultures, suggesting that different species are involved in the degradation. Finally, this information may lead to the identification and isolation of methanogenic populations that can degrade PAHs.     

Populations of heavy fuel oil-degrading marine microbial community in presence of oil sorbent materials

Aims:  To investigate the feasibility of applying sorbent material X-Oil^® in marine oil spill mitigation and to survey the interactions of oil, bacteria and sorbent.
Methods and Results:  In a series of microcosms, 25 different treatments including nutrient amendment, bioaugmentation with Alcanivorax borkumensis and application of sorbent were tested. Microbial community dynamics were analysed by DNA fingerprinting methods, RISA and DGGE. Results of this study showed that the microbial communities in microcosms with highly active biodegradation were strongly selected in favour of A. borkumensis . Oxygen consumption measurements in microcosms and gas chromatography of oil samples indicated the fast and intense depletion of linear alkanes as well as high oxygen consumption within 1 week followed by consequent slower degradation of branched and polyaromatic hydrocarbons.
Conclusion:  Under given conditions, A. borkumensis was an essential organism for biodegradation, dominating the biofilm microbial community formation and was the reason of emulsification.
Significance and Impact of the Study:  This study strongly emphasizes the pivotal importance of A. borkumensis as an essential organism in the initial steps of marine hydrocarbon degradation. Interaction with the sorbent material X-Oil^® proved to be neutral to beneficial for biodegradation and also promoted the growth of yet unknown micro-organisms.     

Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial

The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.     

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using ¹⁴C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of ¹⁴C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)''s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.     

Indigenous Sediment Microbial Activity in Response to Nutrient Enrichment and Plant Growth Following a Controlled Oil Spill on a Freshwater Wetland

The population density and activity of a microbial community associated with the sediment and rhizosphere of an intertidal freshwater wetland dominated by Scirpus pungens was monitored before and following the application of weathered Mesa light crude oil and fertilizers. The influence of nutrient enrichment (fertilizers) and plant growth on oil degradation rates was determined from the resulting data. The study plots (four blocks of replicates) were subjected to five treatments: oil only (natural attenuation); oil plus ammonium nitrate and phosphate, with regular cropping of the plants; oil plus ammonium nitrate and phosphate; oil plus sodium nitrate and phosphate; no oil, ammonium nitrate and phosphate. The plots were regularly monitored in the field for gas production (carbon dioxide and nitrous oxide), and samples were collected for laboratory analysis of denitrification activity, aliphatic and aromatic hydrocarbon degradation activity, and total heteroptrophic bacteria.

The viable bacterial population density increased during the first 4 weeks in oiled and unoiled experimental plots that were fertilized. In contrast, population densities in untreated areas remained relatively unchanged throughout the monitoring period. The microbial population demonstrated a rapid and sustained increase in naphthalene mineralization activity in plots that were both fertilized and oiled. Hexadecane mineralization activity increased in response to fertilizer application, with ammonium nitrate causing a larger increase than sodium nitrate. A very significant difference observed in the mineralization of hexadecane was that the surface sediments were much more active than the subsurface sediments. This difference became even more pronounced in the second year of monitoring, even though the treatment regime had been discontinued. This compartmentalization of mineralization activity was not observed for naphthalene. Following fertilizer application, field and laboratory evaluation of nitrogen metabolism in the sediments indicated significant denitrification activity that was not adversely affected by oiling. The results demonstrated that the application of fertilizers stimulated the activities of indigenous hydrocarbon-degrading and denitrifying bacteria, and the presence of oil either enhanced or had no detrimental effect on these activities. As a remediation strategy, the application of fertilizers to a wetland shoreline following an oil spill would promote the growth of indigenous plants and their associated microbial flora, resulting in increased metabolic activity and the potential for increased oil degradation activity.     

Hydrocarbon Mineralization in Sediments and Plasmid Incidence in Sediment Bacteria from the Campeche Bank

Rates of degradation of radiolabeled hydrocarbons and incidence of bacterial plasmid DNA were investigated in sediment samples collected from the Campeche Bank, Gulf of Mexico, site of an offshore oil field containing several petroleum platforms. Overall rates of mineralization of [¹⁴C]hexadecane and [¹⁴C]phenanthrene measured for sediments were negligible; <1% of the substrate was converted to CO₂ in all cases. Low mineralization rates are ascribed to nutrient limitations and to lack of adaptation by microbial communities to hydrocarbon contaminants. Plasmid frequency data for sediment bacteria similarly showed no correlation with proximity to the oil field, but, instead, showed correlation with water column depth at each sampling site. Significant differences between sites were observed for proportion of isolates carrying single or multiple plasmids and mean number of plasmids per isolate, each of which increased as a function of depth.     

Indigenous Sediment Microbial Activity in Response to Nutrient Enrichment and Plant Growth Following a Controlled Oil Spill on a Freshwater Wetland

The population density and activity of a microbial community associated with the sediment and rhizosphere of an intertidal freshwater wetland dominated by Scirpus pungens was monitored before and following the application of weathered Mesa light crude oil and fertilizers. The influence of nutrient enrichment (fertilizers) and plant growth on oil degradation rates was determined from the resulting data. The study plots (four blocks of replicates) were subjected to five treatments: oil only (natural attenuation); oil plus ammonium nitrate and phosphate, with regular cropping of the plants; oil plus ammonium nitrate and phosphate; oil plus sodium nitrate and phosphate; no oil, ammonium nitrate and phosphate. The plots were regularly monitored in the field for gas production (carbon dioxide and nitrous oxide), and samples were collected for laboratory analysis of denitrification activity, aliphatic and aromatic hydrocarbon degradation activity, and total heteroptrophic bacteria. The viable bacterial population density increased during the first 4 weeks in oiled and unoiled experimental plots that were fertilized. In contrast, population densities in untreated areas remained relatively unchanged throughout the monitoring period. The microbial population demonstrated a rapid and sustained increase in naphthalene mineralization activity in plots that were both fertilized and oiled. Hexadecane mineralization activity increased in response to fertilizer application, with ammonium nitrate causing a larger increase than sodium nitrate. A very significant difference observed in the mineralization of hexadecane was that the surface sediments were much more active than the subsurface sediments. This difference became even more pronounced in the second year of monitoring, even though the treatment regime had been discontinued. This compartmentalization of mineralization activity was not observed for naphthalene. Following fertilizer application, field and laboratory evaluation of nitrogen metabolism in the sediments indicated significant denitrification activity that was not adversely affected by oiling. The results demonstrated that the application of fertilizers stimulated the activities of indigenous hydrocarbon-degrading and denitrifying bacteria, and the presence of oil either enhanced or had no detrimental effect on these activities. As a remediation strategy, the application of fertilizers to a wetland shoreline following an oil spill would promote the growth of indigenous plants and their associated microbial flora, resulting in increased metabolic activity and the potential for increased oil degradation activity.     

Influence of TNT transformation on microbial community structure in four different lake microcosms

After World War II, large amounts of obsolete ammunition were dumped in various lakes in Sweden. Trinitrotoluene, TNT, was one of the main components of the dumped explosives. In this study, four different lake microcosms originating from lakes where relatively large amounts of ammunition were dumped were used to mimic the effect of TNT release on the natural microbial community. Increased microbial growth was found in lake microcosms amended with TNT. However, negligible mineralization of TNT was detected, suggesting that TNT was not utilized as a carbon source, but as a nitrogen source. Random amplified polymorphic DNA (RAPD) analysis indicated that the TNT induced no significant differences in microbial community composition and therefore, no major changes in natural selection, despite the increased microbial growth in the presence of the compound. More than 95% of the added TNT bound irreversibly to the sediments, possibly as a result of microbial transformation to reactive metabolites that subsequently bound covalently to components of the sediment. The results, taken together, suggest that no permanent change in the microbial ecology occurred as a result of the TNT amendment. This was probably due partly to the transient exposure of the microbial communities to the TNT before it became irreversibly bound to the sediment, and partly to the fact that TNT was not a primary growth substrate that strongly affects natural selection.     

Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.     

Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry

The effect of microbial inoculation on the mineralization of naphthalene in a bioslurry treatment was evaluated in soil slurry microcosms. Inoculation by Pseudomonas putida G7 carrying the naphthalene dioxygenase (nahA) gene resulted in rapid mineralization of naphthalene, whereas indigenous microorganisms in the PAH-contaminated soil required a 28 h adaptation period before significant mineralization occurred. The number of nahA-like gene copies increased in both the inoculated and non-inoculated soil as mineralization proceeded, indicating selection towards naphthalene dioxygenase producing bacteria in the microbial community. In addition, 16S rRNA analysis by denaturing gradient gel electrophoresis (DGGE) analysis showed that significant selection occurred in the microbial community as a result of biodegradation. However, the indigenous soil bacteria were not able to compete with the P. putida G7 inoculum adapted to naphthalene biodegradation, even though the soil microbial community slightly suppressed naphthalene mineralization by P. putida G7.     

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n‐octadecane, phenanthrene + n‐octadecane and phenanthrene + n‐octadecane + CdCl₂). Subculturing was performed at 10‐day intervals, followed by high‐throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co‐occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re‐equilibration of microbial communities.     

Formation of Siderite in Microbial Microcosms Derived from a Marine Sediment

Abstract

Exceptionally well-preserved fossils are frequently encased by carbonate concretions. The initial steps of their formation in marine and freshwater sediments are induced by microbial activity. The role of the involved microbial communities, however, is not well understood. In this study, siderite (FeCO₃) formation in microbial microcosms is observed, with various fatty acyl compounds (lipids, surfactants) as substrates and Wadden Sea sediment samples as inocula. In actively growing microcosms, sulfate-reducing bacteria (the genus Desulfofrigus in particular) dominate the microbial community and submicroscopic siderite precipitates on bacterial cell surfaces were identified. We suggest that these biologically induced mineralization processes may, in the natural environment, initiate the formation of large concretions under suboxic conditions in coastal sediments.