Detection of Salmonella in the intestine of Hypostomus plecostomus from the upper San Marcos River, Texas.

The prevalence of salmonellae in the intestines of the invasive suckermouth catfish Hypostomus plecostomus was assessed in the San Marcos River, just down-stream of its spring-fed headwaters. In 2014, H. plecostomus, sediment, and water samples were collected during 15 sampling events. A combination of semi-selective enrichment and quantitative polymerase chain reaction (qPCR) revealed the presence of salmonellae in 45% of the fish intestines across the entire year, with a prevalence range of 13-100% per sampling event. Repetitive element sequence-based PCR (rep-PCR) and multi-locus sequence typing (MLST) revealed a high diversity of salmonellae from fish intestine samples at individual sampling times, single or multiple presence of rep-PCR patterns and serotypes within individual fish, and identical rep-PCR patterns and serotypes for different fish within and across sampling events. Overall, 15 serotypes were identified by MLST, with a diversity range between one and seven serotypes per sampling event. Some serotypes were retrieved only once, while others were detected more frequently. A few serotypes were retrieved at several sampling times, nearly evenly distributed over the entire sampling period. Prevalence and diversity were independent of precipitation events, indicating the potential presence of environmental strains that are capable of long-term persistence in the environment.

Diversity of Frankia in soil assessed by Illumina sequencing of nifH gene fragments.

Targeted Illumina sequencing of nitrogenase reductase (nifH) gene fragments and analyses of pair-end reads through a modified QIIME pipeline were used to assess the diversity of the actinomyceteous genus Frankia in three soils. Soils were vegetated with host or non-host plants, and included locations in Illinois (ABA, host), Colorado (CoMt, non-host), and Wisconsin (FMWI, non-host). After filtering, seven unique sequences were recovered for soil ABA, six for CoMt, and four sequences for FMWI. These sequences were included in a Bayesian topology anchored by published sequence data from pure cultures of Frankia. Sequences from all three soils showed affinities to Frankia strains from both the Alnus and Elaeagnus host infection groups. Reads representing Casuarina-infective strains were not detected. Four sequences from soil CoMt and five sequences from soil ABA did not cluster, at 97% similarity, into a shared OTU that contained a cultured relative. These results demonstrate that targeted Illumina sequencing provides an efficient and economical method for assessing haplotype diversity of ecofunctional genes (e.g. nifH) at the genus level in microorganisms that perform important ecosystem functions.