What makes a habitat a home? Habitat associations of juvenile European sea bass, Dicentrarchus labrax, in estuarine nurseries.

Selection of nursery habitats by marine fish, such as European sea bass (Dicentrarchus labrax), is poorly understood. Identifying and protecting the full range of juvenile nursery habitats is vital to supporting resilient fish populations and economically important fisheries. We examined how the condition, stomach fullness, and diet of juvenile European sea bass, along with their abundance, differ at high or low tide between the following estuarine habitats: saltmarsh, oyster reefs, shingle, sand, and mud edge habitats. Using a combination of fyke and seine netting we found no difference in sea bass abundance or condition across high-tide habitats, suggesting that rather than differentially selecting between them, juvenile sea bass use all available shallow habitats at high tide. Stomach fullness was significantly higher on saltmarsh and sand compared to mud, and thus these habitats may support better foraging. Dietary DNA metabarcoding revealed that sand and saltmarsh diets mostly comprised Hediste polychaetes, whereas zooplanktonic taxa dominated diets over mud. At low tide, sea bass abundance was highest in shingle and oyster reefs, where stomach fullness and condition were lowest. This may indicate a potential trade-off between using habitats for foraging and refuge. Although sea bass abundance alone does not capture productivity, the high abundance across all estuarine habitats at high tide suggests that it is important to consider the protection of a mosaic of interconnected habitats to support nursery functions rather than focus on individual habitat types.

Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers.

Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.

Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession.

This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude-oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon-degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h. A succession of obligate hydrocarbonoclastic bacteria (OHCB), driven by metabolite niche partitioning, is demonstrated. Importantly, this succession has revealed how the OHCB Oleispira, hitherto considered to be a psychrophile, can dominate in the early stages of oil-spill response (1 and 3 days), outcompeting all other OHCB, at the relatively high temperature of 16 °C. Additionally, we demonstrate how some dispersants or biosurfactants can select for specific bacterial genera, especially the biosurfactant rhamnolipid, which appears to provide an advantageous compatibility with Pseudomonas, a genus in which some species synthesize rhamnolipid in the presence of hydrocarbons.

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.

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.

Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2T.

Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n-C14 ) or branched (pristane) alkanes. During growth on n-C14 , A. borkumensis expressed a complete pathway for the terminal oxidation of n-alkanes to their corresponding acyl-CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for ß-oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of ß-oxidation proteins to overcome steric hinderance from branched substrates.

Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1.

The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.