biology Article Physiological and Phylogenetic Characterization of Rhodotorula diobovata DSBCA06, a Nitrophilous Yeast Enrico Civiero ID , Manuela Pintus, Claudio Ruggeri, Elena Tamburini ID , Francesca Sollai, Enrico Sanjust * ID and Paolo Zucca ID Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, SP 1 Km 0,700, 09042 Monserrato (CA), Italy; civieroenrico.81@gmail.com (E.C.); manuela.pintus@gmail.com (M.P.); rugg.claudio@gmail.com (C.R.); etamburini@unica.it (E.T.); sollai@unica.it (F.S.); pzucca@unica.it (P.Z.) * Correspondence: sanjust@unica.it; Tel.: +39-(0)70-675-4518 Received: 9 May 2018; Accepted: 27 June 2018; Published: 30 June 2018   Abstract: Agriculture and intensive farming methods are the greatest cause of nitrogen pollution. In particular, nitrification (the conversion of ammonia to nitrate) plays a role in global climate changes, affecting the bio-availability of nitrogen in soil and contributing to eutrophication. In this paper, the Rhodotorula diobovata DSBCA06 was investigated for growth kinetics on nitrite, nitrate, or ammonia as the sole nitrogen sources (10 mM). Complete nitrite removal was observed in 48 h up to 10 mM initial nitrite. Nitrogen was almost completely assimilated as organic matter (up to 90% using higher nitrite concentrations). The strain tolerates and efficiently assimilates nitrite at concentrations (up to 20 mM) higher than those previously reported in literature for other yeasts. The best growth conditions (50 mM buffer potassium phosphate pH 7, 20 g/L glucose as the sole carbon source, and 10 mM nitrite) were determined. In the perspective of applications in inorganic nitrogen removal, other metabolic features relevant for process optimization were also evaluated, including renewable sources and heavy metal tolerance. Molasses, corn, and soybean oils were good substrates, and cadmium and lead were well tolerated. Scale-up tests also revealed promising features for large-scale applications. Overall, presented results suggest applicability of nitrogen assimilation by Rhodotorula diobovata DSBCA06 as an innovative tool for bioremediation and treatment of wastewater effluents. Keywords: nitrogen; nitrite; bioremediation; wastewater; eutrophication 1. Introduction In the last decades, agriculture and intensive farming increased the use of inorganic fertilizers leading to huge health and economic benefits but also to severe input of polluting nitrogen compounds into the environment. Ammonium is the most easily assimilated inorganic nitrogen form. However, nitrification causes the loss of enormous amounts of nitrogen in the most oxidized forms (nitrite and nitrate), affecting global climate changes and increasing environmental pollution [1]. Enrichment of a water body with an excess amount of nutrients causes, for instance, eutrophication [2]. Nitrite is also toxic to humans, since it oxidizes the ferroheme in red blood cells and as a consequence prevents the oxygen carrying by hemoglobin [3]. Furthermore, nitrite can be transformed to genotoxic nitrosamines by some bacteria [4]. Industrialized countries counteracted the problem with laws restricting the use of simple ionic nitrogen compounds [5]. For instance, the European Commission issued the Nitrates Directive Biology 2018, 7, 39; doi:10.3390/biology7030039 www.mdpi.com/journal/biology