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

Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean

Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment

Diversity of microbiomes associated with benthic invertebrates inhabiting Antarctic ecosystems

Il numero sempre più alto di studi condotti sui microbiomi ha evidenziato l’importanza che queste associazioni rivestono nello sviluppo, nella salute e nella fitness degli organismi con cui i microbiomi vivono associati. In ambienti estremi come l’Antartide, i microbiomi sembrano avere un’importanza cruciale nel creare interazioni fondamentali per l’adattamento dei loro ospiti. Gli obiettivi di questa tesi sono: i) studiare la biodiversità dei microbiomi associati a diversi invertebrati marini antartici, ii) esplorarne l’origine, confrontando i microbiomi associati agli organismi con le comunità batteriche che abitano nei sedimenti circostanti, e iii) verificare se i fattori ambientali svolgano un ruolo attivo nel modellare la loro composizione tassonomica. I risultati hanno mostrato che, nonostante i microbiomi associati ai policheti antartici (Leitoscoloplos geminus, Aphelocaeta palmeri, Aglaophamus trissophyllus) possano variare in modo significativo tra gli individui, è possibile individuare dei core, sia a livello intraspecifico sia interspecifico, che contribuiscono significativamente all'intera comunità batterica associata. I taxa batterici associati ai policheti sono completamente diversi da quelli presenti nei sedimenti circostanti, suggerendo una potenziale trasmissione verticale o diverse capacità adattative dei microbiomi ai due diversi “habitat”. Molteplici fattori (i.e., non solo fattori ambientali ma anche quelli biologici come lo stato fisiologico e le abitudini di alimentazione) influenzano, a diversi gradi, la composizione tassonomica dei microbiomi associati ai policheti antartici. Nella stella marina antartica Odontaster validus la posizione geografica è il principale fattore che spiega le differenze trovate nella composizione tassonomica dei microbiomi, sebbene siano state riscontrate alcune somiglianze tra individui raccolti in luoghi diversi, suggerendo la presenza di altri fattori in grado di selezionare comunità batteriche simili. La presenza esclusiva di batteri specifici associati a stelle marine che vivono in determinate aree suggerisce una potenziale trasmissione orizzontale dei microbiomi, probabilmente acquisiti attraverso diverse abitudini alimentari che le stelle marine hanno sviluppato nelle suddette aree. Questa tesi di dottorato fornisce nuove informazioni sui microbiomi antartici, evidenziando una forte variabilità della loro composizione e complessità delle relazioni con gli ospiti esaminati, potenzialmente dovute, oltre ai fattori ambientali, anche alle caratteristiche biologiche degli ospiti.Growing studies on host-associated microbiomes are highlighting the important role of microbes in the development, health and fitness of their hosts. This might be particularly true in remote and extreme environments, such as the Antarctic ecosystem, where the host and its microbiome could evolve together establishing peculiar and close interactions. This study aims: i) to investigate the biodiversity of microbiomes of different Antarctic invertebrates, ii) to explore the potential sources of the host-associated microorganisms by comparing them with microbial communities inhabiting the surrounding sediments, and iii) to verify the role of environmental setting in shaping their taxonomic composition. Results revealed that microbiomes of Antarctic polychaetes (Leitoscoloplos geminus, Aphelocaeta palmeri, Aglaophamus trissophyllus) showing significant variability among individuals, but that both intra-specific and inter-specific core microbiomes contribute for a significant fraction to the whole microbial assemblage. Bacteria associated with polychaetes were completely different from those in the surrounding sediments, suggesting a potential vertical transmission or the presence of different adaptative/selective conditions of the two “habitats”. Multiple factors (i.e., not only environmental factors but also biological ones such as physiological state and feeding habits) can influence to different extent the taxonomic composition of microbiomes associated with Antarctic polychaetes. In the Antarctic sea star Odontaster validus, the geographic location was identified as the main factor influencing the taxonomic composition of microbiomes, but this was not a general rule. In fact, high similarities were found among microbiomes of individuals collected in different locations, suggesting the presence of other drivers able to select similar microbial communities. The presence of exclusive bacterial families in sea-star microbiomes suggests a potential horizontal transmission of bacterial taxa, probably acquired through different feeding habits that the sea star might have developed in the different basins. This PhD thesis provided new information on Antarctic microbiomes, highlighting a strong variability of their composition and complexity of the relationships with the investigated hosts, potentially due to, besides environmental settings, also to hosts’ biological features

Fungi Can Be More Effective than Bacteria for the Bioremediation of Marine Sediments Highly Contaminated with Heavy Metals

The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. However, information on the efficiency of marine-derived fungi for HM decontamination of marine sediments is still largely lacking, despite evidence of the performance of terrestrial fungal strains on other contaminated matrixes (e.g., soils, freshwater sediments, industrial wastes). Here, we carried out for the first time an array of parallel laboratory experiments by using different combinations of chemical and microbial amendments (including acidophilic autotrophic and heterotrophic bacteria, as well as filamentous marine fungi) for the bioremediation of highly HM-contaminated sediments of the Portman Bay (NW Mediterranean Sea), an area largely affected by long-term historical discharges of mine tailings. Our results indicate that the bioleaching performance of metals from the sediment is based on the addition of fungi (Aspergillus niger and Trichoderma sp.), either alone or in combination with autotrophic bacteria, was higher when compared to other treatments. In particular, fungal addition allowed obtaining bioleaching yields for As eight times higher than those by chemical treatments and double compared with the addition of bacteria alone. Moreover, in our study, the fungal addition was the only treatment allowing effective bioleaching of otherwise not mobile fractions of Zn and Cd, thus overtaking bacterial treatments. We found that the lower the sediment pH reached by the experimental conditions, as in the case of fungal addition, the higher the solubilization yield of metals, suggesting that the specific metabolic features of A. niger and Trichoderma sp. enable lowering sediment pH and enhance HM bioleaching. Overall, our findings indicate that fungi can be more effective than acidophilic autotrophic and heterotrophic bacteria in HM bioleaching, and as such, their use can represent a promising and efficient strategy for the bioremediation of marine sediments highly contaminated with heavy metals

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 howmeiobenthic 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 OMdegradation 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 onmeiobenthic assemblages. These findings showthatOAcan significantly alter meiobenthic assemblage structure and enhance OMdegradation 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 andOMdegradation, could affect organic carbon sequestration over large spatial scales

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