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Anaerobic ammonium oxidation (anammox) is a significant process for bioavailable nitrogen removal from marine systems. A bacteriohopanetetrol (BHT) isomer, with unknown stereochemistry, eluting later than BHT using high performance liquid chromatography (HPLC), was detected in ‘Ca. Scalindua profunda’ and proposed as a biomarker for anammox in marine paleo-environments. Four non-marine, non-anammox genera also produce late-eluting BHT stereoisomers. Of these, the stereochemistry in Acetobacter pasteurianus, Komagataeibacter xylinus and Frankia sp. was shown to be 17β, 21β(H), 22R, 32R, 33R, 34R (BHT-34R), while the stereochemistry of the late-eluting BHT in Methylocella palustris was unknown. We studied the BHT distributions and stereochemistry of these known BHT isomer producers and of previously unscreened marine (‘Ca. Scalindua brodeae’) and freshwater (‘Ca. Brocadia sp.’) anammox species and genera using HPLC and gas chromatographic (GC) analysis of acetylated BHTs and ultra high performance liquid chromatography (UHPLC)-High Resolution Mass Spectrometry (HRMS) analysis of non-acetylated BHTs. The 34R stereochemistry was confirmed for the BHT isomers in Ca. Brocadia sp., and Methylocella palustris. However, ‘Ca. Scalindua sp.’ synthesise a stereochemically distinct BHT isomer, with a still unconfirmed stereochemistry (BHT-x). ‘Ca. Kuenenia sp.’ was confirmed not to produce any late-eluting BHT stereoisomers. Only GC analysis of acetylated BHT and UHPLC analysis of non-acetylated BHT distinguished between late-eluting BHT isomers. Acetylated BHT-x and BHT-34R co-elute by HPLC. As BHT-x is so far only known to be produced by ‘Ca. Scalindua spp.’, it may be applied as a biomarker for marine anammox. As ‘Ca. Brocadia sp.’ produces BHT-34R, this BHT isomer is a potential, albeit less specific, biomarker for anammox in non-marine settings.

N and P are the key limiting nutrients considered most important for the stimulation of crude oil degradation but other trace nutrients may also be important. Experimental soil microcosms were setup to investigate crude oil degradation in the context of Ni amendments. Amended Nickel as NiO, NiCl2, or, a porphyrin complex either inhibited, had no effect, or, enhanced aerobic hydrocarbon degradation in an oil-contaminated soil. Biodegradation was significantly (95% confidence) enhanced (70%) with low levels of Ni-Porph (12 mg/kg) relative to an oil-only control; whereas, NiO (200 and 350 mg/kg) significantly inhibited (36 and 87%) biodegradation consistent with oxide particle induced reactive oxygen stress. Microbial community compositions were also significantly affected by Ni. In 16S rRNA sequence libraries, the enriched hydrocarbon degrading genus, Rhodococcus, was partially replaced by a Nocardia sp. in the presence of low levels of NiO (12 and 50 mg/kg). In contrast, the highest relative and absolute Rhodococcus abundances were coincident with the maximal rates of oil degradation observed in the Ni-Porph-amended soils. Growth dependent constitutive requirements for Ni-dependent urease or perhaps Ni-dependent superoxide dismutase enzymes (found in Rhodococcus genomes) provided a mechanistic explanation for stimulation. These results suggest biostimulation technologies, in addition to N and P, should also consider trace nutrients such as Ni tacitly considered adequately supplied and available in a typical soil.

Clay minerals are abundant in soils and sediments and often contain Fe. Some varieties, such as nontronites, contain as much as 40 wt.% Fe2O3 within their molecular structure. Several studies have shown that various Fe-reducing micro-organisms can use ferric iron in Fe-bearing clay minerals as their terminal electron acceptor, thereby reducing it to ferrous iron. Laboratory experiments have also demonstrated that chemically or bacterially reduced clays can promote the reductive degradation of various organics, including chlorinated pesticides and nitroaromatics. Therefore, Fe-bearing clays may play a crucial role in the natural attenuation of various redox-sensitive contaminants in soils and sediments. Although the organochlorinated pesticide p,p−-DDT is one of the most abundant and recalcitrant sources of contamination in many parts of the world, the impact of reduced Fe-bearing clays on its degradation has never been documented. The purpose of the present study was to evaluate the extent of degradation of p,p−-DDT during the bacterial reduction of Fe(III) in an Fe-rich clay. Microcosm experiments were conducted under anaerobic conditions using nontronite (sample NAu-2) spiked withpp−-DDT and the metal-reducing bacteria Shewanella oneidensis MR-1. Similar experiments were conducted using a sand sample to better ascertain the true impact of the clay vs. the bacteria on the degradation of DDT. Samples were analyzed for DDT and degradation products after 0, 3, and 6 weeks of incubation at 30°C. Results revealed a progressive decrease in p,p−-DDT and increase in p,p−-DDD concentrations in the clay experiments compared to sand and abiotic controls, indicating that Fe-bearing clays may substantially contribute toward the reductive degradation of DDT in soils and sediments. These new findings further demonstrate the impact that clay materials can have on the natural attenuation of pollutants in natural and artificial systems and open new avenues for the passive treatment of contaminated land.

In addition to previously reported 25-norhopanoic acids with the 17α(H), 21β(H) and 17β(H), 21α(H) configurations, for the first time we report the identification of 25-norhopanoic acids bearing the 17β(H), 21β(H) configuration in a suite of heavily biodegraded oils from China. The 17β(H), 21β(H) stereochemistry is a thermally unstable biologically-derived structure, suggesting that the 17β(H), 21β(H) 25-norhopanoic acids may derive from petroleum-degrading microbes. Rather than representing a direct input, we propose that demethylation of 17β(H), 21β(H) hopanoic acids derived from bacteria in the reservoir may give rise to 17β(H), 21β(H) 25-norhopanoic acids, implying that microbial reworking of biomass is occurring alongside petroleum degradation.

A field-scale experiment with a complete randomized block design was performed to study the degradation of buried oil on a shoreline over a period of almost 1 year. The following four treatments were examined in three replicate blocks: two levels of fertilizer treatment of oil-treated plots, one receiving a weekly application of liquid fertilizer and the other treated with a slow-release fertilizer; and two controls, one not treated with oil and the other treated with oil but not with fertilizer. Oil degradation was monitored by measuring carbon dioxide evolution and by chemical analysis of the oil. Buried oil was degraded to a significantly greater extent in fertilized plots, but no differences in oil chemistry were observed between the two different fertilizer treatments, although carbon dioxide production was significantly higher in the oil-treated plots that were treated with slow-release fertilizer during the first 14 days of the experiment. Bacterial communities present in the beach sediments were profiled by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments and 16S rRNA amplified by reverse transcriptase PCR. Similarities between the DGGE profiles were calculated, and similarity matrices were subjected to statistical analysis. These analyses showed that although significant hydrocarbon degradation occurred both in plots treated with oil alone and in the plots treated with oil and liquid fertilizer, the bacterial community structure in these plots was, in general, not significantly different from that in the control plots that were not treated with oil and did not change over time. In contrast, the bacterial community structure in the plots treated with oil and slow-release fertilizer changed rapidly, and there were significant differences over time, as well as between blocks and even within plots. The differences were probably related to the higher concentrations of nutrients measured in interstitial water from the plots treated with slow-release fertilizer. Bacteria with 16S rRNA sequences closely related (>99.7% identity) to Alcanivorax borkumensis and Pseudomonas stutzeri sequences dominated during the initial phase of oil degradation in the plots treated with slow-release fertilizer. Field data were compared to the results of previous laboratory microcosm experiments, which revealed significant differences.

Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.