Publications
2023
Santoferrara L., Qureshi A., Sher A., Blanco-Bercial L. The photic-aphotic divide is a strong ecological and evolutionary force determining the distribution of ciliates (Alveolata, Ciliophora) in the ocean. Journal of Eukaryotic Microbiology, 70: jeu12976
Mitra A., Caron D., Faure E., Flynn K., Leles S., Hansen P., McManus G., Not F., Gomes H., Santoferrara L., Stoecker D., Tillmann U. The Mixoplankton Database – diversity of photo-phago-trophic plankton in form, function and distribution across the oceans. Journal of Eukaryotic Microbiology, 70: jeu12972
McManus G., Mitra A., Reguera B., Santoferrara L. The Mixoplankton Paradigm in Plankton Ecology. Harmful Algal News (UNESCO-IOC), 73: 15-18.
Smith S., Ropati D., Santoferrara L., Romano T., McManus G., 2023. The respiratory microbiota of three cohabiting beluga whales (Delphinapterus leucas) under human care. Frontiers in Marine Sciences:10:1168623
2022
Santoferrara L., McManus G., Greenfield D., Smith S. Microbial communities (bacteria, archaea and eukaryotes) in a temperate estuary during seasonal hypoxia. Aquatic Microbial Ecology, 88: 61-79 pdf
Ganser M., Santoferrara L., Agatha S. Molecular signature characters complement taxonomic diagnoses: a bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea). Molecular Phylogenetics and Evolution, 170: 107433
Smith S., Santoferrara L., Katz L., McManus G. Genome architecture used to supplement species delineation in two cryptic marine ciliates. Molecular Ecology Resources, 22: 2880-2896
2021
Agatha S., Ganser M., Santoferrara L. The Importance of type species and their correct identification – a key example from tintinnid ciliates (Alveolata, Ciliophora, Spirotricha). Journal of Eukaryotic Microbiology, 68: e12865
Snyder R., Moss J., Santoferrara L., Head M., Jeffrey W. Ciliate microzooplankton from the Northeastern Gulf of Mexico. ICES Journal of Marine Science, 78: 3356–3371
2020
Santoferrara L., Burki F., Filker S., Logares R., Dunthorn M., McManus G. Perspectives from ten years of protist studies by high-throughput metabarcoding. Journal of Eukaryotic Microbiology, 67: 612-622 pdf
Santoferrara L., McManus G. Diversity and biogeography as revealed by morphologies and DNA sequences: Tintinnid ciliates as an example. In: Zooplankton Ecology. Barbosa A. and Teodósio M.A. (eds.). CRC Press (Taylor & Francis Group), Boca Raton, U.S.A., pp. 85-118 pdf
Smith S., Maurer-Alcalá X., Yan Y., Katz L., Santoferrara L., McManus G. Combined genome and transcriptome analyses of the ciliate Schmidingerella arcuata (Spirotrichea) reveal patterns of DNA elimination, scrambling, and inversion. Genome Biology and Evolution, 12: 1616–1622
Bai Y., Wang R., Song W., Li L., Santoferrara L., Hu X. Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes. BMC Microbiology, 20: 374
2019
Santoferrara L. Current practice in plankton metabarcoding: optimization and error management. Invited Horizons Review at Journal of Plankton Research, 41: 571-582
2018
Smith S., Song W., Gavrilova N., Kurilov A., Liu W., McManus G., Santoferrara L. Dartintinnus alderae n. g., n. sp., a minute brackish tintinnid (Ciliophora, Spirotrichea) with dual-ended lorica collapsibility. Journal of Eukaryotic Microbiology, 65: 400-411 pdf
Santoferrara L., Rubin E., McManus G. Global and local DNA (meta)barcoding reveal new biogeography patterns in tintinnid ciliates. Journal of Plankton Research, 40: 209-221 pdf
Boscaro V., Santoferrara L., Zhang Q., Gentekaki E., Syberg-Olsen M., del Campo J., Keeling P. EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates. Environmental Microbiology, 20: 2218-2230 pdf
del Campo J., Kolisko M., Boscaro V., Santoferrara L., Massana R., Guillou L., Simpson A., Berney C., de Vargas C., Brown M., Keeling P., Wegener Parfrey L. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. Plos Biology, 16: e2005849
2017
Santoferrara L., Alder V., McManus G. Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). Molecular Phylogenetics and Evolution, 112: 12-22 pdf
Santoferrara L., McManus G. Integrating the dimensions of biodiversity in choreotrichs and oligotrichs of marine plankton. European Journal of Protistology, 61: 323-330 pdf
Warren A., et al. Beyond the “Code”: A guide to the description and documentation of biodiversity in ciliated protists (Alveolata, Ciliophora). Journal of Eukaryotic Microbiology, 64: 539-554
2016
Santoferrara L., Grattepanche J.D., Katz L., McManus G. Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? ISME Journal, 10: 1779-1790 pdf
Santoferrara L., Bachy C., Alder V., Gong J., Kim Y-O., Saccà A., da Silva Neto I., Strüder-Kypke M., Warren A., Xu D., Yi Z., Agatha S. Updating biodiversity studies in loricate protists: the case of the tintinnids (Alveolata, Ciliophora, Spirotrichea). Journal of Eukaryotic Microbiology, 63: 651-656 pdf
Grattepanche J.D., Santoferrara L., McManus G., Katz L. Unexpected biodiversity of ciliates in marine samples from below the photic zone. Molecular Ecology, 25: 3987-4000
Ceríaco L., et al. Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa, 4196: 435-445
2015
Santoferrara L., Tian M., Alder V., McManus G. Discrimination of closely related species in tintinnid ciliates: new insights on crypticity and polymorphism in the genus Helicostomella. Protist, 166: 78-92 pdf
Grattepanche J.D., Santoferrara L., McManus G., Katz L. Distinct assemblage of planktonic ciliates dominates both photic and deep waters on the New England shelf. Marine Ecology Progress Series, 526: 1-9
Dunthorn M., et al. Ciliates – microbes with complex morphologies and their ambiguous early fossil record. Marine Micropaleontology, 119: 1-6
2014
Santoferrara L., Guida S., Zhang H., McManus G. De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PLoS ONE 9: e101418
Santoferrara L., Grattepanche J.D., Katz L., McManus G. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environmental Microbiology, 16: 2752-2763 pdf
Grattepanche J.D., Santoferrara L., McManus G., Katz L. Diversity of diversity: conceptual and methodological differences in biodiversity estimates of bacteria and eukaryotic microbes. Trends in Microbiology, 8: 432-437
Grattepanche J.D., Santoferrara L., Andrade J., Oliverio A., McManus G., Katz L. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and by DGGE in temperate coastal waters. Aquatic Microbial Ecology, 71: 211-221
2013
Santoferrara L., McManus G., Alder V. Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea). Protist, 164: 24-36 pdf
McManus G., Santoferrara L. Tintinnids in microzooplankton communities. In: Biology and Ecology of Tintinnid Ciliates. Models for Marine Plankton. Dolan J.R., Agatha S., Coats D.W.C., Montagnes D.J.S., Stoecker D.K. (eds.). Wiley/ Blackwell, Oxford, pp. 198-213 pdf
2012
Santoferrara L., McManus G., Alder V. Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small and large subunit rRNA genes. Journal of Eukaryotic Microbiology, 59: 423-426 pdf
Santoferrara L., Alder V. Abundance and diversity of tintinnids (planktonic ciliates) under contrasting levels of productivity in the Argentine Shelf and Drake Passage. Journal of Sea Research, 71: 25-30 pdf
2011 and before
Santoferrara L., Gomez M. I., Alder V., 2011. Bathymetric, latitudinal and vertical distribution of protozooplankton in a cold-temperate shelf (southern Patagonian waters) during winter. Journal of Plankton Research, 33: 457-468 pdf
Cuevas L., Alder V., Santoferrara L., 2009. Nanoplancton. In: Manual de métodos para el estudio de sistemas planctónicos marinos. Alder V. and Morales C. (eds.). EUDEBA, Buenos Aires, pp. 65-93
Santoferrara L., Alder V., 2009. Morphological variability, spatial distribution and abundance of Helicostomella species (Ciliophora, Tintinnina) in relation to environmental factors (Argentine shelf; 40-55ºS). Scientia Marina, 73: 701-716 pdf
Santoferrara L., Alder V., 2009. Abundance trends and ecology of planktonic ciliates of the south-western Atlantic (35-63° S): A comparison between neritic and oceanic environments. Journal of Plankton Research, 31: 837-851 pdf
Friedman L., Messina M., Santoferrara L., Santillán M., Mangano A., Franco M., 2006. Characterization of Bordetella bronchiseptica strains using phenotypic and genotypic markers. Veterinary Microbiology, 117: 313-320