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Background: Leptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disease is incomplete, which may convolute leptospirosis diagnosis, prevention, and epidemiology. Methodology/Principal findings: We collected environmental samples from 22 sites in Puerto Rico during three sampling periods over 14-months (Dec 2018-Feb 2020); 10 water and 10 soil samples were collected at each site. Samples were screened for DNA from potentially pathogenic Leptospira using the lipL32 PCR assay and positive samples were sequenced to assess genetic diversity. One urban site in San Juan was sampled three times over 14 months to assess persistence in soil; live leptospires were obtained during the last sampling period. Isolates were whole genome sequenced and LipL32 expression was assessed in vitro. We detected pathogenic Leptospira DNA at 15/22 sites; both soil and water were positive at 5/15 sites. We recovered lipL32 sequences from 83/86 positive samples (15/15 positive sites) and secY sequences from 32/86 (10/15 sites); multiple genotypes were identified at 12 sites. These sequences revealed significant diversity across samples, including four novel lipL32 phylogenetic clades within the pathogenic P1 group. Most samples from the serially sampled site were lipL32 positive at each time point. We sequenced the genomes of six saprophytic and two pathogenic Leptospira isolates; the latter represent a novel pathogenic Leptospira species likely belonging to a new serogroup. Conclusions/Significance: Diverse and novel pathogenic Leptospira are widespread in the environment in Puerto Rico. The disease potential of these lineages is unknown but several were consistently detected for >1 year in soil, which could contaminate water. This work increases understanding of environmental Leptospira diversity and should improve leptospirosis surveillance and diagnostics. Author summary: Leptospirosis is a common zoonotic disease worldwide, but more prevalent in the tropics. Cases are more common following severe weather events, possibly due to flooding, which may more readily distribute soil and/or water contaminated with Leptospira spp., the disease agents. Human cases increased following the 2017 hurricanes that ravaged Puerto Rico (Maria and Irma), prompting environmental sampling of soil and water to assess the presence, abundance, and possible persistence of pathogenic leptospires in these environments. The goal was to better understand these potential reservoirs of human and animal disease. Diverse and novel groups of pathogenic Leptospira were abundant and widespread in soil and water in Puerto Rico and sometimes were consistently detected in these environments for >1 year. However, most groups we identified have not previously been described from humans and/or other animals, so the disease potential of these novel organisms is unknown. The results of this study reveal a tremendous amount of previously uncharacterized Leptospira diversity in soil and water in Puerto Rico. The description and characterization of these novel types improves our understanding of the genus Leptospira, and will aid in the development of improved diagnostics and preventative tools to advance public health outcomes. [ABSTRACT FROM AUTHOR]