Year by the numbers

In 2016 I decided to post publicly each year a summary of my scientific activities. I was inspired by Piet Hut, my host at the Institute for Advanced Studies in Princeton, who’s posting every year detailed yearly report of his activities. I think this benefits both myself, as it bring into focus what I’ve been spending my time on during the year, and the public at large, since my science is largely funded with taxpayers money it is good to be transparent about the activities carried out.

 


 

2017 yearly report: the year in numbers

Meetings, Conferences and Presentations. Invited keynote speaker at the StartUp Business plan competition CNA “Cambiamenti” award ceremony. Invited speaker at the Caveats event “What is life” in New York City, organized by New York Time Science Writer Carl Zimmer. Participated to weekly meeting at ELSI during the first four months of 2017 on different aspect of origins research. Attended the Goldschmidt 2017 conference in Paris and co-chaired Session 15b “Hydrothermal Biogeochemistry and Geobiology”. Invited speaker at the Deep Carbon Observatory International Science meeting in St. Andrews, UK. Invited speaker at the Microbiology 2017 meeting of the Italian Society of General Microbiology and Biotechnology in Palermo, Italy. Invited participant at the ICDP workshop to drill the Ivrea-Verbano Zone in Baveno, Italy (read the workshop report on Scientific Drilling). Panel member at the 43rd G7 summit, All4TheGreen round table on Entrepreneurship and Environmental Sustainability in Bologna, Italy. Invited participant at the CNR workshop on Polar Biology and Research, Venezia, Italy. Co-authored three posters at the Goldschmidt conference, 1 poster at the International Society for the Study of the Origin of Life Meeting, 1 poster at the Southeastern Biogeochemical Society meeting, 1 presentation at the Annual Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) Conference. Attended the AGU fall meeting in New Orleans and the DCO Biology Meets Subduction integration session. Contributed to 2 abstract to the XIIth SCAR Biology Symposium, Belgium. Invited talk at the Institute for Marine Science, National Research Council of Italy, Ancona. Member of the Scientific Organizing Committee of the 6th ELSI International Symposium (2018), Tokyo. Member of the International Scientific Committee of the next Extremophiles conference, Ischia (2018). Member of the Organizing Committee of the international workshop 4D Deep-time Data Driven Discovery, Washington DC (2018). Member of the Organizing Committee of the DCO international workshop Earth in Five Reactions, Washington DC (2018). Invited speaker at the next Gordon Research Conference in Marine Microbiology (2018).

Laboratory, Data Analysis and Field Work. Contributed in organizing and participated in a field sampling expedition to the Costa Rica arc volcanoes as part of the funded DCO project Biology Meets Subduction. Organized and led a sampling expedition to the Aeolian Islands shallow-vents. Participated in two distinct expeditions in Iceland, one to sample the alkaline shallow-water hydrothermal vents in the north fjords (ELSI), the other to sample the microbial communities of different icelanding hot springs (Oxford, University of Iceland). Conducted SEM analysis on Costa Rica hot spring samples in collaboration with Francesco Smedile. Extracted and sequenced the DNA from the Costa Rica project. Started enrichment of new isolates from Costa Rica hot springs. Collaborated with colleagues to complete a study on Azores shallow-water hydrothermal vents. Performed comparative genomic analyses on the evolution of metabolism and the role of adaptation vs innovation in colonizing new environments. Assisted in the data analysis of several ongoing project, both at Rutgers, CNR-ISMAR and ELSI. Assisted in the data analysis of new MinION sequencing data.

Research Grants and Proposals. Submitted 1 proposal to the Italian Ministry of Education “Montalcini grant” for the re-entry of Italian researchers working abroad (PI); 1 Japanese KAKHENI grants on the Tokyo Microbiome during the Olympics as part of the Meta-Sub consortia (Co-PI); contributed to 1 pre-proposal to the NASA Exobiology call to develop a genetic system in chemolithoautotrophic extremophiles (Collaborator); submitted 1 large community sequencing initiative to the Joint Genome Institute (Co-PI); submitted 1 proposal to the Alfred P. Sloan Foundation for the development of integrated visualizing tool with the EarthByte consortia (awarded, Co-PI); submitted 1 proposal to the Alfred P. Sloan Foundation to fund the 4D workshop on big-data approaches to the study of the co-evolution of life and planet (awarded, science organizing committee member); submitted 1 pre-proposal to the John Templeton Foundation for the study of a shadow biosphere (collaborator).

Papers, Manuscripts and Technical Reports. Published a paper in Marine Environmental Research on the abundance of heavy metals in deep-sea hydrothermal vents tubeworms (co-authors). Published a paper in Frontiers in Marine Science on the relationship between biodiversity and ecosystem functioning in the deep-sea (co-author). Published an Editorial to the DCO Research Topic in Frontiers in Earth Science (first and corresponding author). Contributed to a CNR technical report on the status of taxonomy work at the Italian national research lab (contributor). Published a paper in eLife on the evolution of carbon fixation in the *Aquificae* (first and co-corresponding author). Published a Nature Geoscience paper on the relationship between geologic preserved isotopic signatures and major microbial lineages evolution (co-author). Published a review on the geochemistry and microbiology of shallow-water hydrothermal vents in Elsevier module in Earth System and Environmental Science (co-author). Submitted a paper on the genome of Sulfurovum riftiae (first and corresponding author). Contributed to a paper on the philosophy and epistemology of the Origin of Life field (co-author). Wrote a paper on the metagenomic of Milos shallow-water hydrothermal vent biofilms (first author). Wrote a paper on the influence of glacier melt on the diversity of microbial assemblages in Antarctica (first author). Contributed to a paper on the mechanism of elemental sulfur reduction in T. ammonificans. Deposited a patent for the dispersion of carbon nanotubes in epoxy resins (co-inventor).

Editorial Roles and Servicing. Concluded the coordination the Frontiers in Research Topic featuring contribution from DCO Early Career Scientist, which collected 16 articles and 82 authors across the four different science communities of the Deep Carbon Observatory. Reviewed eight manuscript for international peer-reviewed journals and several proposal for Sloan and NASA. Participated in a grant review panel. Nominated review editor for Frontiers in Microbiology, section in extreme microbiology. Signed a publishing agreement with Springer Nature to co-edit a book expected in Spring 2019.

Teaching and Outreach. Member of the PhD committee of a PhD candidate at Rutgers University. Member of the master committee of a MSc student at the University of Naples Federico II. Wrote an invited contribution for the international Biochemistry Society Journal The Biochemist. See the award winning documentary on the “Biology Meets Subduction” expedition.

Prizes and awards. Awarded a Frontiers Community Support Fund Grant. The documentary from the Costa Rica “Biology meets subduction” expedition won the first prize at the Orbit Science Documentary context during the Goldschmidt conference in Paris. Awarded the Best Seminar of the Year Award from the Ancona Institute for Marine Science, CNR-ISMAR.

*Other Activities.* Obtained the Italian Ministry of Education and Research habilitation to serve as Associate Professor in Microbiology (ASN II Fascia). Contributed to the vision and strategy of Nano-Tech SpA as member of the Board of Directors. Founded the business accelerator Foundry (www.thefoundry.it).


2016 yearly report: the year in numbers

Meetings, Conferences and Presentations. Participated to weekly meeting at Columbia University and the Institute for Advanced Studies on the foundation of a new interdisciplinary Institute in Manhattan in the spring. Gave a guest seminar at Stony Brook University SoMAS. Held a public lecture in the “Family Science Talk” series at the Institute for Advanced Studies (here is the link to the youtube video). Attended the ELSI 4th Symposium in Tokyo and the first annual EON meeting. Participated to the DCO ExCom meeting in Washington DC in March 2016. Attended the Goldschmidt 2016 conference in Yokohama and presented a talk on the microbiology of shallow-water hydrothermal vents. Attended as instructor the Second DCO Summer School in Yellowstone and presented a talk on open source and open access. Attended the Italian Federation of Life Sciences conference in Rome. Attended the NanoInnovation 2016 European conference on nanotechnology in Rome and presented a talk on the static properties of nanotube reiforced thermosetting resins. Guest seminar at the University of Naples Federico II. Guest seminar at the Consiglio Nazionale delle Ricerche (CNR) in Naples. Invited speaker at the YHouse Caffé series in Manhattan, NYC, USA. Served as member in the committee for the direction of research of the new no-profit research institute YHouse on the study of awareness. Presented two posters as co-author at the 2016 American Geophysical Union fall meeting in San Francisco.

Research Grants and Proposals. Submitted several research proposal for funding: 1 NSF pre-proposal on the evolution of pathogens (Co-PI); 1 NSF BIO-OCE on the study of the relationship between microbial biofilm and macrofauna larvae at deep-sea vents (Co-PI); 1 pre-proposal (PI) to the Alfred P. Sloan foundation for a DCO Field Focus Site Initiative; transformed in 1 full proposal to the Alfred P. Sloan foundation under the DCO umbrella for a multidisciplinary study of carbon cycling in a subduction zone (Co-PI); 1 pre-proposal to the NASA Earth Observatory call (Co-PI); 1 large community sequencing initiative to the Joint Genome Institute (Co-PI); 1 small sequencing proposal to the Joint Genome Institute (Co-PI); 1 DCO Census of Deep Life proposal (Co-PI); 1 proposal to the Italian Antarctic Program for the study of climate induced change in the benthic microbial community in proximity of a melting glacier in the Ross Bay (PI); 1 proposal to the Italian Ministry of Education PRIN call to study the community at shallow-water hydrothermal vents in Panarea (Project Collaborator); 1 ELSI Origin Network Seed Grant proposal for the study of metabolic evolution and adaptation in Epsilonproteobacteria (PI); 2 different Japanese KAKHENI grants on different aspect of the reconstruction of the ancestral metabolism and reconstruction of the metabolic network in Aquificae (Co-PI); 1 Japanese KAKHENI grants on the Tokyo Urban Microbiome during the Olympics as part of the Meta-Sub consortia (Co-PI); drafted 3 different short grant ideas with colleagues of ELSI (Co-PI).

Papers, Manuscripts and Technical Reports. Submitted the description of a new species for publication to the International Journal of Systematic and Evolutionary Microbiology, Sulfurovum riftiae (first author) and the description of its genome was submitted for publication and it is currently under review (first author). Published a paper in Frontiers in Microbiology on the microbiology of shallow-water Adriatic pockmarks (first and co-corresponding author). Published a review paper on the co-evolution of geosphere and biosphere in Annual Review of Microbiology (co-author). Published a paper on the genome of Sedimenticola selenatireducens (co-author). Submitted a paper on the abundance of heavy metals in deep-sea hydrothermal vents tubeworms (co-author). Submitted a paper on the relationship between biodiversity and ecosystem functioning in the deep-sea (co-author). Published a meeting report on the DCO Early Career Scientist workshop in EOS (first author). Published an invited contribution in the Institute for Advanced Studies Institute Letter. Wrote and submitted a review on shallow-water hydrothermal vents in collaboration with Roy Price (co-author). Wrote and submitted a paper on the relationship between geologic preserved isotopic signatures and major microbial lineages evolution (co-author).

Editorial Roles and Servicing. Continued organizing the Second DCO Summer School 2016 held in Yellowstone National Park. Continued coordinating the Frontiers in Research Topic featuring contribution from DCO Early Career Scientist. The Research Topic is cross listed by 4 different Frontiers Journals. Reviewed seven manuscripts for international peer-reviewed journals and several proposal for Sloan, NSF and NASA. Participated in a grant review panel.

Teaching and Outreach. Taught a master level class in Marine Microbial Diversity at the University of Naples Federico II.

Laboratory, Data Analysis and Field Work. Conducted SEM analysis on elemental sulfur particles pre and post microbial growth of T. ammonificans and on the white mats of the shallow-water hydrothermal vents of Milos Islands. Completed the analysis of the Milos metagenome and dataset and wrote the paper. Collaborated with Lucia Bongiorni to complete data analysis on viral production in the tissue and mucus of hermatypic corals. Continued coordinating the compilation of data from the collective sampling carried out during the DCOECS15 workshop. Carried out phylogenetic analysis of the bacterial DNA-directed RNA-polymerase for the analysis of promiscuity and permissivity of extant polymerase on RNA isoforms in collaboration with Chris Butch. Coordinated and collaborated to the analysis of the transcriptome and proteome of T. ammonificans with Benjamin Jelen. Contributed to the analysis of several prokaryotic genomes, and metagenomes. Supervised the study of the possible induction of a thermophilic prophage. Contributed to the planning of the field campaign in Costa Rica (2017) as part of the funded Sloan project “Biology meets subduction“.

Other Activities. Moved to Tokyo to start the ELSI Origins Network Fellowship during the spring. Continued visiting weekly the PIDS program at the Institute for Advanced Studies in Princeton during the first 4 months of 2016 and re-appointed visiting scholar at the Institute for 2017. Appointed visiting professor at the University of Naples Federico II. Applied to the national calls for a full-time permanent researcher position at the Italian National Research Council of Italy and the Zoological Station “Anthon Dorn” of Naples. Contributed to found and structure the YHouse Research Institute for the study of awareness.


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