Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60–100%) and HMs removal (21–100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs

Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome

The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications

Trophic status and meiofauna biodiversity in the Northern Adriatic Sea: insights for the assessment of good environmental status

The Descriptor 5 (Eutrophication) of the EU Marine Strategy Framework Directive aims at preventing the negative effects of eutrophication. However, in coastal systems all indicators based on water column parameters fail in identifying the trophic status and its effects on biodiversity and ecosystem functioning. We investigated benthic trophic status, in terms of sedimentary organic matter quantity, composition and quality, along with meiofaunal abundance, richness of taxa and community composition in three coastal sites (N Adriatic Sea) affected by different levels of anthropogenic stressors. We show that, on the basis of organic matter quantity and composition, the investigated areas can be classified from oligo-to mesotrophic, whereas using meiofauna as a descriptor, their environmental quality ranged from sufficient to moderately impacted. Our results show that the benthic trophic status based on organic matter variables, is not sufficient to provide a sound assessment of the environmental quality in marine coastal ecosystems. However, data reported here indicate that the integration of the meiofaunal variable allows providing robust assessments of the marine environmental statu

Methodologies for inter-dependency assessment

We report on an recent European Project aimed at assessment of suited Methodologies to measure interdependencies between the Electric and the ICT System. Based on best practices and available data, several different metrics have been defined. Depending on the methodology involved, three main types of metrics can be identified; namely "topological"; "system theory based" and "simulation based" metrics. The selected methodologies have been applied to the Roma Area electric and communication system. Results from all the different approaches are discussed. All metrics provide quantitative measures of the inter-dependence between both the two systems and their components. In addition to the established metrics, a novel "spectral" metric has been introduced specific for cascade effects. Such an innovative methodology has also been applied to the US Power Grid and results compared with those from the Roma Area

Ocean acidification alters meiobenthic assemblage composition and organic matter degradation rates in seagrass sediments

Seagrass meadows are an important organic matter (OM) reservoir but, are currently being lost due to global and regional stressors. Yet, there is limited research investigating the cumulative impacts of anthropogenic stressors on the structure and functioning of seagrass benthic assemblages, key drivers of OM mineralization and burial. Here, using a 16-month field experiment, we assessed how meiobenthic assemblages and extracellular enzymatic activities (as a proxy of OM degradation) in Posidonia oceanica sediments responded to ocean acidification (OA) and nutrient loadings, at CO2 vents. P. oceanica meadows were exposed to three nutrient levels (control, moderate, and high) at both ambient and low pH sites. OA altered meiobenthic assemblage structure, resulting in increased abundance of annelids and crustaceans, along with a decline in foraminifera. In addition, low pH enhanced OM degradation rates in seagrass sediments by enhancing extracellular enzymatic activities, potentially decreasing the sediment carbon storage capacity of seagrasses. Nutrient enrichment had no effect on the response variables analyzed, suggesting that, under nutrient concentration unlikely to cause N or P imitation, a moderate increase of dissolved nutrients in the water column had limited influence on meiobenthic assemblages. These findings show that OA can significantly alter meiobenthic assemblage structure and enhance OM degradation rates in seagrass sediments. As meiofauna are ubiquitous key actors in the functioning of benthic ecosystems, we postulated that OA, altering the structure of meiobenthic assemblages and OM degradation, could affect organic carbon sequestration over large spatial scales

Data from: Below-ground processes control the success of an invasive seaweed

1. Whilst the successful establishment and spread of invasive species can be determined by above ground processes, results are often equivocal. Emergent research, mostly from terrestrial ecosystems, demonstrates that below-ground processes (nutrient cycling, chemical properties) under microbial control can mediate interactions between native and invasive plants. Because microbes can control similar sediment properties in marine ecosystem that influence plant fitness, we argue that below-ground properties should also exert strong control interactions between native and invasive marine macrophytes. 2. We coupled surveys of microbial communities and chemistry of sediments collected from an invasive alga (Caulerpa cylindracea), a native competitor (the seagrass Posidonia oceanica) and unvegetated sediments with a large field experiment, in which we manipulated the presence/absence of the canopies of both species to determine the effects of above- and below-ground processes on the success of C. cylindracea. 3. P. oceanica and C. cylindracea sediments have microbial communities and predicted metabolic process that reflect aerobic and anaerobic conditions, respectively. Moreover, the nutritional quantity of organic matter was higher, but quality was lower in C. cylindracea sediments compared to the two native habitats. The growth of C. cylindracea fragments was equally low in the presence or absence of a P. oceanica canopy, whereas the growth of C. cylindracea was higher in the canopy removed vs. present treatment, possibly because, in the absence of a C. cylindracea canopy, fragments are released from intra-specific competition for resources. 4. Synthesis: Sediment/soil processes are increasingly recognised as important drivers of the success and hence impacts of invasive plants. We extended this theory to marine ecosystems and suggest biotic resistance to invasion may not always be attributable to intact canopies, but may also result from indirect effects of native macrophytes on sediment quality and microbial processes. This information may, in part, resolve why above-ground interactions don’t always explain invasive plant success and thus can be used to develop better informed management strategies

Below-ground processes control the success of an invasive seaweed

Whilst the successful establishment and spread of invasive species can be determined by above-ground processes, results are often equivocal. Emergent research, mostly from terrestrial ecosystems, demonstrates that below-ground processes (nutrient cycling, chemical properties) under microbial control can mediate interactions between native and invasive plants. Because microbes can control similar sediment properties in marine ecosystem that influence plant fitness, we argue that below-ground properties should also exert strong control interactions between native and invasive marine macrophytes. We coupled surveys of microbial communities and chemistry of sediments collected from an invasive alga (Caulerpa cylindracea), a native competitor (the seagrass Posidonia oceanica) and unvegetated sediments with a large field experiment, in which we manipulated the presence/absence of the canopies of both species to determine the effects of above- and below-ground processes on the success of C. cylindracea. Posidonia oceanica and C. cylindracea sediments have microbial communities and predicted metabolic process that reflect aerobic and anaerobic conditions, respectively. Moreover, the nutritional quantity of organic matter was higher, but quality lower in C. cylindracea sediments compared to the two native habitats. The growth of C. cylindracea fragments was equally low in the presence or absence of a P. oceanica canopy, whereas the growth of C. cylindracea was higher in the canopy removed vs. present treatment, possibly because, in the absence of a C. cylindracea canopy, fragments are released from intraspecific competition for resources. Synthesis. Sediment/soil processes are increasingly recognized as important drivers of the success and hence impacts of invasive plants. We extended this theory to marine ecosystems and suggest biotic resistance to invasion may not always be attributable to intact canopies, but may also result from indirect effects of native macrophytes on sediment quality and microbial processes. This information may, in part, resolve why above-ground interactions do not always explain invasive plant success and thus can be used to develop better informed management strategies