Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals.

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.

In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change.

Abyssal plains cover more than half of Earth's surface, and the main food source in these ecosystems is phytodetritus, mainly originating from primary producers in the euphotic zone of the ocean. Global climate change is influencing phytoplankton abundance, productivity, and distribution. Increasing importance of picoplankton over diatom as primary producers in surface oceans (especially projected for higher latitudes) is projected and hence altering the quantity of organic carbon supplied to the abyssal seafloor as phytodetritus, consequences of which remain largely unknown. Here, we investigated the in situ responses of abyssal biota from viruses to megafauna to different types of phytoplankton input (diatoms or cyanobacteria which were labeled with stable isotopes) at equatorial (oligotrophic) and temperate (eutrophic) benthic sites in the Pacific Ocean (1°N at 4277 m water depth and 39°N at 5260 m water depth, respectively). Our results show that meiofauna and macrofauna generally preferred diatoms as a food source and played a relatively larger role in the consumption of phytodetritus at higher latitudes (39°N). Contrarily, prokaryotes and viruses showed similar or even stronger responses to cyanobacterial than to diatom supply. Moreover, the response of prokaryotes and viruses was very rapid (within 1-2 days) at both 1°N and 39°N, with quickest responses reported in the case of cyanobacterial supply at higher latitudes. Overall, our results suggest that benthic deep-sea eukaryotes will be negatively affected by the predicted decrease in diatoms in surface oceans, especially at higher latitudes, where benthic prokaryotes and viruses will otherwise likely increase their quantitative role and organic carbon cycling rates. In turn, such changes can contribute to decrease carbon transfer from phytodetritus to higher trophic levels, with strong potential to affect oceanic food webs, their biodiversity and consequently carbon sequestration capacity at the global scale.

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest.

Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs' prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.

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

Viruses are key biological agents of prokaryotic mortality in the world oceans, particularly in deep-sea ecosystems where nearly all of the prokaryotic C production is transformed into organic detritus. However, the extent to which the decomposition of viral particles (i.e., organic material of viral origin) influences the functioning of benthic deep-sea ecosystems remains completely unknown. Here, using various independent approaches, we show that in deep-sea sediments an important fraction of viruses, once they are released by cell lysis, undergo fast decomposition. Virus decomposition rates in deep-sea sediments are high even at abyssal depths and are controlled primarily by the extracellular enzymatic activities that hydrolyze the proteins of the viral capsids. We estimate that on a global scale the decomposition of benthic viruses releases ∼37-50 megatons of C per year and thus represents an important source of labile organic compounds in deep-sea ecosystems. Organic material released from decomposed viruses is equivalent to 3 ± 1%, 6 ± 2%, and 12 ± 3% of the input of photosynthetically produced C, N, and P supplied through particles sinking to bathyal/abyssal sediments. Our data indicate that the decomposition of viruses provides an important, previously ignored contribution to deep-sea ecosystem functioning and has an important role in nutrient cycling within the largest ecosystem of the biosphere.

High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents.

Viruses are the most abundant life forms in the world's oceans and they are key drivers of biogeochemical cycles, but their impact on the microbial assemblages inhabiting hydrothermal vent ecosystems is still largely unknown. Here, we analysed the viral life strategies and virus-host interactions in the sediments of a newly discovered shallow-water hydrothermal field of the Mediterranean Sea. Our study reveals that temperate viruses, once experimentally induced to replicate, can cause large mortality of vent microbes, significantly reducing the chemoautotrophic carbon production, while enhancing the metabolism of microbial heterotrophs and the re-cycling of the organic matter. These results provide new insights on the factors controlling primary and secondary production processes in hydrothermal vents, suggesting that the inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.

Marine Microbial-Derived Molecules and Their Potential Use in Cosmeceutical and Cosmetic Products.

The oceans encompass a wide range of habitats and environmental conditions, which host a huge microbial biodiversity. The unique characteristics of several marine systems have driven a variety of biological adaptations, leading to the production of a large spectrum of bioactive molecules. Fungi, fungi-like protists (such as thraustochytrids) and bacteria are among the marine organisms with the highest potential of producing bioactive compounds, which can be exploited for several commercial purposes, including cosmetic and cosmeceutical ones. Mycosporines and mycosporine-like amino acids, carotenoids, exopolysaccharides, fatty acids, chitosan and other compounds from these microorganisms might represent a sustainable, low-cost and fast-production alternative to other natural molecules used in photo-protective, anti-aging and skin-whitening products for face, body and hair care. Here, we review the existing knowledge of these compounds produced by marine microorganisms, highlighting the marine habitats where such compounds are preferentially produced and their potential application in cosmetic and cosmeceutical fields.

The challenge of proving the existence of metazoan life in permanently anoxic deep-sea sediments.

The demonstration of the existence of metazoan life in absence of free oxygen is one of the most fascinating and difficult challenges in biology. Danovaro et al. (2010) discovered three new species of the Phylum Loricifera, living in the anoxic sediments of the L'Atalante, a deep-hypersaline anoxic basin of the Mediterranean Sea. Multiple and independent analyses based on staining, incorporation of radiolabeled substrates, CellTracker Green incorporation experiments and ultra-structure analyses, allowed Danovaro et al. (2010) to conclude that these animals were able to spend their entire life cycle under anoxic conditions. Bernhard et al. (2015) investigated the same basin. Due to technical difficulties in sampling operations, they could not collect samples from the permanently anoxic sediment, and sampled only the redoxcline portion of the L'Atalante basin. They found ten individuals of Loricifera and provided alternative interpretations of the results of Danovaro et al. (2010). Here we analyze these interpretations, and present additional evidence indicating that the Loricifera encountered in the anoxic basin L'Atalante were actually alive at the time of sampling. We also discuss the reliability of different methodologies and approaches in providing evidence of metazoans living in anoxic conditions, paving the way for future investigations.This paper is a response to Bernhard JM, Morrison CR, Pape E, Beaudoin DJ, Todaro MA, Pachiadaki MG, Kormas KAr, Edgcomb VG. 2015. Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins. BMC Biology 2015 13:105.See research article at http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-015-0213-6.

Enhanced viral activity and dark CO2 fixation rates under oxygen depletion: the case study of the marine Lake Rogoznica.

Global change is determining the expansion of marine oxygen-depleted zones, which are hot spots of microbial-driven biogeochemical processes. However, information on the functioning of the microbial assemblages and the role of viruses in such low-oxygen systems remains largely unknown. Here, we used the marine Rogoznica Lake as a natural model to investigate the possible consequences of oxygen depletion on virus-prokaryote interactions and prokaryotic metabolism in pelagic and benthic ecosystems. We found higher bacterial and archaeal abundances in oxygen-depleted than in oxic conditions, associated with higher heterotrophic carbon production, enzymatic activities and dark inorganic carbon fixation (DCF) rates. The oxygen-depleted systems were also characterized by higher viral abundance, production and virus-induced prokaryotic mortality. The highest DCF relative contribution to the whole total C production (> 30%) was found in oxygen-depleted systems, at the highest virus-induced prokaryotic mortality values (> 90%). Our results suggest that the higher rates of viral lysis in oxygen-depleted conditions can significantly enhance DCF by accelerating heterotrophic processes, organic matter cycling, and hence the supply of inorganic reduced compounds fuelling chemosynthesis. These findings suggest that the expansion of low-oxygen zones can trigger higher viral impacts on prokaryotic heterotrophic and chemoautotrophic metabolism, with cascading effects, neglected so far, on biogeochemical processes.

Microbial assemblages for environmental quality assessment: Knowledge, gaps and usefulness in the European Marine Strategy Framework Directive.

The EU Marine Strategy Framework Directive 2008/56/EC (MSFD) defines a framework for Community actions in the field of marine environmental policy in order to achieve and/or maintain the Good Environmental Status (GES) of the European seas by 2020. Microbial assemblages (from viruses to microbial-sized metazoa) provide a major contribution to global biodiversity and play a crucial role in the functioning of marine ecosystems, but are largely ignored by the MSFD. Prokaryotes are only seen as "microbial pathogens," without defining their role in GES indicators. However, structural or functional prokaryotic variables (abundance, biodiversity and metabolism) can be easily incorporated into several MSFD descriptors (i.e. D1. biodiversity, D4. food webs, D5. eutrophication, D8. contaminants and D9. contaminants in seafood) with beneficial effects. This review provides a critical analysis of the current MSFD descriptors and illustrates the reliability and advantages of the potential incorporation of some prokaryotic variables within the set of indicators of marine environmental quality. Following a cost/benefit analysis against scientific and economic criteria, we conclude that marine microbial components, and particularly prokaryotes, are highly effective for detecting the effects of anthropogenic pressures on marine environments and for assessing changes in the environmental health status. Thus, we recommend the inclusion of these components in future implementations of the MSFD.

Major viral impact on the functioning of benthic deep-sea ecosystems.

Viruses are the most abundant biological organisms of the world's oceans. Viral infections are a substantial source of mortality in a range of organisms-including autotrophic and heterotrophic plankton-but their impact on the deep ocean and benthic biosphere is completely unknown. Here we report that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality increases with increasing water depth, and beneath a depth of 1,000 m nearly all of the prokaryotic heterotrophic production is transformed into organic detritus. The viral shunt, releasing on a global scale approximately 0.37-0.63 gigatonnes of carbon per year, is an essential source of labile organic detritus in the deep-sea ecosystems. This process sustains a high prokaryotic biomass and provides an important contribution to prokaryotic metabolism, allowing the system to cope with the severe organic resource limitation of deep-sea ecosystems. Our results indicate that viruses have an important role in global biogeochemical cycles, in deep-sea metabolism and the overall functioning of the largest ecosystem of our biosphere.

Effects of seagrass (Cymodocea nodosa) restoration on nematode biodiversity.

Seagrass meadows are hot spots of biodiversity and play a key role in the provisioning of ecosystem goods and services but are often subjected to a regression due to a combination of multiple anthropogenic and climate-induced impacts. The ecological restoration of these habitat-forming species is a priority to reverse biodiversity loss and for the recovery of key ecosystem functions. Here we investigated the effects of seagrass (Cymodocea nodosa) restoration action on benthic biodiversity recovery assessed by a time-series analysis carried out for one year. We used nematode assemblages, the most widespread metazoan on global sediments, as a proxy of benthic biodiversity and compared the species richness, expected species number (ES51) and composition in donor and in restored seagrasses and in the adjacent unvegetated sediments. One year after the intervention, nematode biodiversity in restored seagrasses was more similar to that of the donor site than in unvegetated sediments, suggesting a progressive recovery. Overall, the nematode biodiversity of the restored seagrasses resulted in an intermediate level between unvegetated and pristine seagrass meadows, providing evidence that restoration intervention contributed to biodiversity recovery. Pristine and restored seagrass meadows hosted a high number of exclusive species, which resulted in an increase in the overall biodiversity in the investigated location. Our results indicate that the restoration of seagrass meadows has positive effects on benthic biodiversity and contributes to enhance the local biodiversity.

Microbes as marine habitat formers and ecosystem engineers.

Despite their small individual size, marine prokaryotic and eukaryotic microbes can form large 3D structures and complex habitats. These habitats contribute to seafloor heterogeneity, facilitating colonization by animals and protists. They also provide food and refuge for a variety of species and promote novel ecological interactions. Here we illustrate the role of microbes as ecosystem engineers and propose a classification based on five types of habitat: microbial mats, microbial forests, microbial-mineralized habitats, microbial outcrops and microbial nodules. We also describe the metabolic processes of microbial habitat formers and their ecological roles, highlighting current gaps in knowledge. Their biogeography indicates that these habitats are widespread in all oceans and are continuously being discovered across latitudes and depths. These habitats are also expected to expand under future global change owing to their ability to exploit extreme environmental conditions. Given their high ecological relevance and their role in supporting endemic species and high biodiversity levels, microbial habitats should be included in future spatial planning, conservation and management measures.

Fungal Abundance and Diversity in the Mariana Trench, the Deepest Ecosystem on Earth.

Hadal trenches host abundant and diversified benthic prokaryotic assemblages, but information on benthic fungi is still extremely limited. We investigated the fungal abundance and diversity in the Challenger Deep (at ca. 11,000 m depth) and the slope of the Mariana Trench in comparison with three sites of the adjacent abyssal plain. Our results indicate that trench sediments are a hotspot of fungal abundance in terms of the 18S rRNA gene copy number. The fungal diversity (as the number of amplicon sequence variants, ASVs) was relatively low at all sites (10-31 ASVs) but showed a high turnover diversity among stations due to the presence of exclusive fungal taxa belonging to Aspergillaceae, Trichosphaeriaceae, and Nectriaceae. Fungal abundance and diversity were closely linked to sediment organic matter content and composition (i.e., phytopigments and carbohydrates), suggesting a specialization of different fungal taxa for the exploitation of available resources. Overall, these findings provide new insights into the diversity of deep-sea fungi and the potential ecological role in trench sediments and pave the way for a better understanding of their relevance in one of the most extreme ecosystems on Earth.

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.

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.

Bioaccumulation and biomagnification of heavy metals in marine micro-predators.

Nematodes represent >3/5 of the abundance of the world's metazoans and usually account for nearly 90% of the total benthic fauna, playing a key ecological role in the benthic ecosystem functioning on a global scale. These small metazoans include a relevant number of microscopic predators and, in turn, are the most abundant preys of macro-megafauna and fish juveniles thus playing a key role in marine food webs. Here, using two independent approaches, we test the bioaccumulation in marine nematodes of several heavy metals present in contaminated sediments. We report here that nematodes, despite their short life cycle and small size, bioaccumulate significantly heavy metals. Bioaccumulation increases from deposit feeders and microalgal grazers to predators of microbes and other tiny metazoans. These results suggest that nematodes also contribute to their biomagnification along the food webs and can contribute to increase the transfer of contaminants from the sediments to larger organisms.

Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations.

Viruses are the most abundant 'biological entities' in the world's oceans. However, technical and methodological constraints limit our understanding of their diversity, particularly in benthic abyssal ecosystems (>4000 m depth). To verify advantages and limitations of analyzing virome DNA subjected either to random amplification or unamplified, we applied shotgun sequencing-by-synthesis to two sample pairs obtained from benthic abyssal sites located in the North-eastern Atlantic Ocean at ca. 4700 m depth. One amplified DNA sample was also subjected to single-molecule long-read sequencing for comparative purposes. Overall, we identified 24,828 viral Operational Taxonomic Units (vOTUs), belonging to 22 viral families. Viral reads were more abundant in the amplified DNA samples (38.5-49.9%) compared to the unamplified ones (4.4-5.8%), with the latter showing a greater viral diversity and 11-16% of dsDNA viruses almost undetectable in the amplified samples. From a procedural point of view, the viromes obtained by direct sequencing (without amplification step) provided a broader overview of both ss and dsDNA viral diversity. Nevertheless, our results suggest that the contextual use of random amplification of the same sample and long-read technology can improve the assessment of viral assemblages by reducing off-target reads.

Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.

The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.

Assessing the eco-compatibility of new generation sunscreen products through a combined microscopic-molecular approach.

There is now unequivocal evidence that sunscreen can severely affect marine ecosystems. However, so far, most studies have focused on the impact of single sunscreen ingredients rather than on the whole sunscreen products, which are released into the marine environment. In the present work, we investigated the ecological impact of six formulations, which represent the "new generation" organic UV filters such as diethylamino hydroxybenzoyl hexyl benzoate (DHHB), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), ethylhexyl triazone (EHT), and bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), which are progressively replacing the "old generation" organic UV filters (e.g., oxybenzone, octinoxate) banned in several countries of the world. The six formulations tested were characterized by a different combination of ingredients, on a model species particularly sensitive to environmental alterations: the sea urchin, Paracentrotus lividus. We investigated the sea urchin responses both in terms of gene expression and anomalies in embryonic development. We found that all sunscreen products containing only MBBT, DHHB, BEMT, and EHT as UV filters, are more eco-compatible than those also containing also ES, or other ingredients such as emollients and texturizing compounds, which may act synergistically causing molecular stress, morphological anomalies, and ultimately possible death. Overall, the results presented here provide new insights on the effects of sunscreen products based on "new generation" UV filters, and highlights the urgency of testing complete formulations, rather than just specific UV filters to ascertain the eco-compatibility of sunscreen products, to effectively minimize their impact on marine ecosystems.

Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica).

Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g-1) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants-ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes.