Marine crude-oil biodegradation: a central role for interspecies interactions

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such " microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons. © 2012 McGenity et al.; licensee BioMed Central Ltd

Extremely Halophilic Archaeal Communities are Resilient to Short‐Term Entombment in Halite

Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite‐entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory‐grown halite over 21 weeks, using high‐throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite‐entombed communities. These results show that halite‐entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of ‘halite specialists’ observed in ancient halite must occur over periods of years, rather than months, hinting at long‐term successional dynamics in this environment

Protein expression in the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8 during alkane degradation and cold tolerance

In cold marine environments, the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8, which utilizes aliphatic alkanes almost exclusively as substrates, dominates microbial communities following oil spills. In this study, LC–MS/MS shotgun proteomics was used to identify changes in the proteome induced during growth on n‐alkanes and in cold temperatures. Specifically, proteins with significantly higher relative abundance during growth on tetradecane (n‐C14) at 16°C and 4°C have been quantified. During growth on n‐C14, O. antarctica expressed a complete pathway for the terminal oxidation of n‐alkanes including two alkane monooxygenases, two alcohol dehydrogenases, two aldehyde dehydrogenases, a fatty‐acid‐CoA ligase, a fatty acid desaturase and associated oxidoreductases. Increased biosynthesis of these proteins ranged from 3‐ to 21‐fold compared with growth on a non‐hydrocarbon control. This study also highlights mechanisms O. antarctica may utilize to provide it with ecological competitiveness at low temperatures. This was evidenced by an increase in spectral counts for proteins involved in flagella structure/output to overcome higher viscosity, flagella rotation to accumulate cells and proline metabolism to counteract oxidative stress, during growth at 4°C compared with 16°C. Such species‐specific understanding of the physiology during hydrocarbon degradation can be important for parameterizing models that predict the fate of marine oil spills

Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments

Abstract Background The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored. Results Eighty nine isolates were obtained from the sediments of four deep-sea, hypersaline anoxic brine lakes in the Eastern Mediterranean Sea: l'Atalante, Bannock, Discovery and Urania basins. This culture collection was dominated by representatives of the genus Bacillus and close relatives (90% of all isolates) that were investigated further. Physiological characterization of representative strains revealed large versatility with respect to enzyme activities or substrate utilization. Two third of the isolates did not grow at in-situ salinities and were presumably present as endospores. This is supported by high numbers of endospores in Bannock, Discovery and Urania basins ranging from 3.8 × 105 to 1.2 × 106 g-1 dw sediment. However, the remaining isolates were highly halotolerant growing at salinities of up to 30% NaCl. Some of the novel isolates affiliating with the genus Pontibacillus grew well under anoxic conditions in sulfidic medium by fermentation or anaerobic respiration using dimethylsulfoxide or trimethylamine N-oxide as electron acceptor. Conclusion Some of the halophilic, facultatively anaerobic relatives of Bacillus appear well adapted to life in this hostile environment and suggest the presence of actively growing microbial communities in the NaCl-rich, deep-sea brine-lake sediments. </jats:sec

Cryptic microbial hydrocarbon cycling.

Cyanobacteria, which produce ~25% of global oxygen, also release around 100 times more hydrocarbons into the ocean than all petroleum sources. A cryptic microbial cycle explains why these hydrocarbons do not accumulate in the sea

<i>amoA</i> Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

ABSTRACT Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase ( amoA ) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw] −1 day −1 in June, increasing to 37.4 μmol N gdw −1 day −1 in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw −1 day −1 in June, increasing to 11.7 μmol N gdw −1 day −1 in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. </jats:p

Mineralization and nitrification: Archaea dominate ammonia-oxidising communities in grassland soils

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were <24 h, whilst several days for nitrate. In clay soils, bacterial, archaeal, AOA, and AOB communities were clearly distinct from those in Chalk and Greensand soils. Spatially and temporally, AOA were more abundant than AOB. Notably, Nitrososphaera were predominant, comprising 37.4% of archaeal communities, with the vast majority of AOA found in Chalk and Greensand soils. AOA abundance positively correlated with nitrate concentration, whereas AOB abundance correlated with ammonium and nitrite concentrations, suggesting that these N compounds may be potential drivers for AOA/AOB niche differentiation in these grassland soils

Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece

In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093–3,773 μg g–1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil

Marine Oil Snow, a Microbial Perspective

Under certain conditions, dispersed crude oil in the sea combines with organisms, organic matter, and minerals to form marine oil snow (MOS), thereby contributing to the sinking of oil to the seafloor. Marine microbes are the main players in MOS formation, particularly via the production of extracellular polymeric substances. Distinct groups of microbes also consume the majority of the hydrocarbons during descent, leading to enrichment of the less bioavailable hydrocarbons and asphaltenes in the residue. Here we discuss the dynamics of microbial communities in MOS together with their impacts on MOS evolution. We explore the effects of dispersant application on MOS formation, and consider ways in which laboratory experiments investigating MOS formation can be more representative of the situation in the marine environment, which in turn will improve our understanding of the contribution of MOS to the fate of spilled oil

Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees

Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4–31% and 15–52% in soils subjected to a lower (7.2 × 105 ppbv) and a higher (7.2 × 106 ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene