2016 yearly report: the year in numbers

Last year 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.

So here is my first ever yearly report: 2016. I’ll soon create a section in my website were all the yearly report will be collected.


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 Washinton 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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