Archaeal diversity in deep-sea sediments estimated by means of different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) protocols

Despite the increasing recognition of the quantitative importance of Archaea in all marine systems, the protocols for a rapid estimate of Archaeal diversity patterns in deep-sea sediments have been only poorly tested yet. We collected sediment samples from 11 deep-sea sites covering a wide latitudinal range (from 79°N to 36°N, at depths comprised from 469 to 5500 m) and compared the performance of two different primer sets (ARCH21f/ARCH958r and ARCH109f/ARCH 915r) and three restriction enzymes (AluI, Rsa I and HaeIII) for the fingerprinting analysis (T-RFLP) of Archaeal diversity. In silico and experimental analyses consistently indicated that different combinations of primer sets and restriction enzymes can result in different values of benthic Archaeal ribotype richness and different Archaeal assemblage compositions. The use of the ARCH109f/ARCH 915r primer set in combination with AluI provided the best results (a number ribotypes up to 4-folds higher than other combinations), suggesting that this primer set should be used in future studies dealing with the analysis of the patterns of Archaeal diversity in deep-sea sediments. Multivariate, multiple regression analysis revealed that, whatever the T-RFLP protocol utilized, latitude and temperature explained most of the variance in benthic Archaeal ribotype richness, while water depth had a negligible role

Obituary: Norberto Della Croce (1926–2011)

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Changes and Crises in the Mediterranean Sea: Current problems

As a contribution to the World Environment Day 2017, the Accademia Nazionale dei Lincei promoted the meeting “Changes and Crises in the Mediterranean Sea” devoted to the effects of climate change and human impact on the Mediterranean ecosystems and biodiversity. Here is presented a selection of papers given at the meeting held in Rome, on October 17, 2017. Studies deal with structural changes in the marine communities, the impact of thermal stress, acidification, pollution and fishing activities on benthic communities, and on deep-sea biodiversity and ecosystems. Understanding human impact on the Mediterranean Sea is the first step to manage and protect marine environments in a sustainable way

Restaurare il pianeta blu

Restaurare gli ecosistemi distrutti dall'azione dell'Uomo è una delle più grandi sfide del futuro. L'Uomo ha alterato o distrutto oltre il 75% degli habitat naturali terrestri, alterato 2/3 degli oceani. Sono stati danneggiati in maniera significativa tutti gli ambienti marini più vulnerabili e ricchi di biodiversità, a partire da mangrovie, scogliere coralline, praterie di fanerogame. Nel decennio dedicato dalle Nazioni Unite al "Restauro degli Ecosistemi" e alla "Scienza degli Oceani per lo Sviluppo Sostenibile" si indica la necessità di affrontare con urgenza anche il restauro degli habitat marini. Tuttavia, il rischio è che non si abbiano ancora informazioni sufficienti per operare il restauro degli ambienti marini. Identificare le storie di successo nel ripristino degli ecosistemi marini e incentivare gli investimenti nel restauro ecologico, sono le chiavi per promuovere il recupero della biodiversità e dei servizi ecosistemici. In moltissime parti del mondo gli interventi di restauro di habitat marini stanno registrando un grande successo (circa il 70%), anche grazie allo sviluppo di nuovi approcci e tecnologie che renderanno sempre più economicamente vantaggiosi questi interventi, permettendo di operare su scale spaziali più ampie, anche in ambienti marini profondi. Tuttavia, resta ancora molto lavoro da fare per comunicare la necessità di intervenire e spiegare gli enormi benefici alla Natura, all'Economia e alla Salute che possono essere realizzati attraverso il restauro ecosistemico

Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

Virus decomposition provides an important contribution to benthic deep-sea ecosystem functionin

Restaurare il pianeta blu

Restaurare gli ecosistemi distrutti dall'azione dell'Uomo è una delle più grandi sfide del futuro. L'Uomo ha alterato o distrutto oltre il 75% degli habitat naturali terrestri, alterato 2/3 degli oceani. Sono stati danneggiati in maniera significativa tutti gli ambienti marini più vulnerabili e ricchi di biodiversità, a partire da mangrovie, scogliere coralline, praterie di fanerogame. Nel decennio dedicato dalle Nazioni Unite al "Restauro degli Ecosistemi" e alla "Scienza degli Oceani per lo Sviluppo Sostenibile" si indica la necessità di affrontare con urgenza anche il restauro degli habitat marini. Tuttavia, il rischio è che non si abbiano ancora informazioni sufficienti per operare il restauro degli ambienti marini. Identificare le storie di successo nel ripristino degli ecosistemi marini e incentivare gli investimenti nel restauro ecologico, sono le chiavi per promuovere il recupero della biodiversità e dei servizi ecosistemici. In moltissime parti del mondo gli interventi di restauro di habitat marini stanno registrando un grande successo (circa il 70%), anche grazie allo sviluppo di nuovi approcci e tecnologie che renderanno sempre più economicamente vantaggiosi questi interventi, permettendo di operare su scale spaziali più ampie, anche in ambienti marini profondi. Tuttavia, resta ancora molto lavoro da fare per comunicare la necessità di intervenire e spiegare gli enormi benefici alla Natura, all'Economia e alla Salute che possono essere realizzati attraverso il restauro ecosistemico

Global Deep-Sea Biodiversity Research Trends Highlighted by Science Mapping Approach

17 pages, 7 figures, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2020.00384/full#supplementary-material.-- All datasets generated for this study are included in the article/Supplementary Materia

Biodiversity loss and turnover in alternative states in the Mediterranean Sea: a case study on meiofauna

In the Mediterranean Sea hard-bottom macroalgal meadows may switch to alternative and less-productive barrens grounds, as a result of sea urchins overgrazing. Meiofauna (and especially nematodes) represent key components of benthic ecosystems, are highly-diversified, sensitive to environmental change and anthropogenic impacts, but, so-far, have been neglected in studies on regime shifts. We report here that sedimentary organic matter contents, meiofaunal taxa richness and community composition, nematode α- and β-biodiversity vary significantly between alternative macroalgal and barren states. The observed differences are consistent in six areas spread across the Mediterranean Sea, irrespective of barren extent. Our results suggest also that the low biodiversity levels in barren states are the result of habitat loss/fragmentation, which is associated also with a lower availability of trophic resources. Furthermore, differences in meiofaunal and nematode abundance, biomass and diversity between macroalgal meadow and barren states persist when the latter is not fully formed, or consists of patches interspersed in macroalgal meadows. Since barren grounds are expanding rapidly along the Mediterranean Sea and meiofauna are a key trophic component in marine ecosystems, we suggest that the extension and persistence of barrens at the expenses of macroalgal meadows could also affect resilience of higher trophic level

Nematode biodiversity and benthic trophic state are simple tools for the assessment of the environmental quality in coastal marine ecosystems

A high biodiversity is essential to guarantee the stability and functioning of coastal marine ecosystems. In this perspective, the Marine Strategy Framework Directive provides prescriptions to maintain (or restore) marine biodiversity in order to achieve a Good Environmental Status (GES). Eutrophic conditions - as determined by the accumulation of sedimentary organic matter (OM) – are often associated with biodiversity loss, so that eutrophic conditions are often considered a pre-requisite or a proxy for degraded ecological conditions. The aim of this study was to investigate the feasibility of the combined use of benthic trophic status and nematode biodiversity as integrated indicators of the environmental status of marine coastal ecosystems. To achieve this objective, we investigated nematode species diversity and assemblage composition in three areas of the Adriatic Sea, characterised by different OM quantity and biochemical composition (as proxy of sedimentary trophic status) and affected by different levels of anthropogenic impact. We show that, on the basis of OM quantity and biochemical composition, the investigated sites can be classified from oligo- to meso-trophic, whereas the analysis of nematode biodiversity indicates that the ecological quality status (EQS) ranged from bad to moderately impacted. This result provides evidence that trophic status and environmental quality assessments are not interchangeable tools for the assessment of marine ecosystems EQS. Rather they should be considered as complementary proxies for the overall assessment of the (good) ecological status. Data reported here also indicate that the loss of benthic biodiversity, whatever the source of disturbance, may be associated to a decrease of the functional diversity (either as feeding and life strategies traits), which might have important consequences on ecosystems functioning. Our results suggest that the GES cannot be defined uniquely in terms of sedimentary trophic status, especially when many other multiples stressors can contribute to determine the overall environmental quality of the investigated ecosystems. Nematode biodiversity is highly sensitive to differences in ecological conditions at different spatial and temporal scales and it can provide reliable and complementary information for the assessment of the environmental status in marine coastal sediments

Metabolic Adaptations to Marine Environments: Molecular Diversity and Evolution of Ovothiol Biosynthesis in Bacteria

Ovothiols are sulfur-containing amino acids synthesized by marine invertebrates, protozoans, and bacteria. They act as pleiotropic molecules in signaling and protection against oxidative stress. The discovery of ovothiol biosynthetic enzymes, sulfoxide synthase OvoA and β-lyase OvoB, paves the way for a systematic investigation of ovothiol distribution and molecular diversification in nature. In this work, we conducted genomic and metagenomics data mining to investigate the distribution and diversification of ovothiol biosynthetic enzymes in Bacteria. We identified the bacteria endowed with this secondary metabolic pathway, described their taxonomy, habitat and biotic interactions in order to provide insight into their adaptation to specific environments. We report that OvoA and OvoB are mostly encountered in marine aerobic Proteobacteria, some of them establishing symbiotic or parasitic relationships with other organisms. We identified a horizontal gene transfer event of OvoB from Bacteroidetes living in symbiosis with Hydrozoa. Our search within the Ocean Gene Atlas revealed the occurrence of ovothiol biosynthetic genes in Proteobacteria living in a wide range of pelagic and highly oxygenated environments. Finally, we tracked the evolutionary history of ovothiol biosynthesis from marine bacteria to unicellular eukaryotes and metazoans. Our analysis provides new conceptual elements to unravel the evolutionary and ecological significance of ovothiol biosynthesis