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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The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Annual dynamics of meiobenthic communities in the Ligurian Sea (northwestern Mediterranean): preliminary results

The dynamics of meiobenthic community were investigated on sandy sediments of the pilot station of Zoagli (Ligurian Sea) between January 1991 and January 1992. Meiofaunal densities ranged between 447 (April) and 3421 (July) ind./10 cm2. Nematodes were the dominant group comprising on the average 75 % of the total fauna. Harpacticoid copepods were the second most abundant group (from 1.7 to 55.3 %) followed by Turbellaria (on the average 5.5 % of total fauna) and Polychaeta (on average 1.2 % of total fauna). The importance of several environmental parameters (such as total organic matter, grain size and RPD depth) in structuring the meiobenthic community is discussed

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

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

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

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

Seafloor heterogeneity influences the biodiversity-ecosystem functioning relationships in the deep sea

Theoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale, and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystem

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