Biology subjects

Hatt, J. K.

Publications and source records attributed to Hatt, J. K..

3 recordsLinked to original sources

bioRxiv2021

Novel municipal sewage-associated bacterial genomes and their potential in source tracking

Little is known about the genomic diversity of raw municipal wastewater (sewage) microbial communities, including to what extent sewage-specific populations exist and how they can be used to improve source attribution and partitioning in sewage-contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) as inoculum in multiple controlled laboratory mesocosms to simulate sewage contamination events and followed these perturbed freshwater microbial communities with metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inoculum yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster under the well-aerated incubation conditions. Notably, a portion of these populations show decay patterns similar to common markers, Enterococcus and HF183. Comparisons against MAGs from different sources such as human and animal feces, revealed low cross-reactivity, indicating how genomic collections could be used to sensitively identify sewage contamination and partition signal among multiple sources. Overall, our results indicate the usefulness of metagenomic approaches for assessing sewage contamination in waterbodies and provides needed methodologies for doing so.

microbiology↗

bioRxiv2021

Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking

Fecal material in the environment is a primary source of pathogens that cause waterborne diseases and affect over a billion people worldwide. Microbial source tracking (MST) assays based on single genes (e.g., 16S rRNA) do not always provide the resolution needed to attribute fecal contamination sources. In this work, we used dialysis bag mesocosms simulating a freshwater habitat that were spiked separately with cow, pig, or human feces to monitor the decay of host-specific fecal signals over time with metagenomics, traditional qPCR, and culture-based methods. Sequencing of the host fecal communities used as inocula recovered 79 non-redundant metagenome-assembled genomes (MAGs) whose abundance patterns showed that the majority of the fecal community signal was not detectable in the mesocosm metagenomes after four days. Several MAGs showed high host specificity, and thus are promising candidates for biomarkers for their respective host type. Traditional qPCR methods varied in their correlation with MAG decay kinetics. Notably, the human-specific Bacteroides assay, HF183/BFDRev, consistently under-estimated fecal pollution due to not being present in all hosts and/or primer mismatches. This work provides new insights on the persistence and decay kinetics of host-specific gut microbes in the environment and identifies several MAGs as putative biomarkers for improved MST. SYNOPSISWe track cow, pig, and human fecal pollution in lake water over time with metagenomics and benchmark these novel protocols against standard culture-based and qPCR tests for water quality monitoring.

microbiology↗

bioRxiv2021

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size ([~]15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (non-core) genes showed low in situ coverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept. Significance StatementThe pangenomes of bacterial species, i.e., the number of non-redundant genes carried by members of the species, can be enormous based on the genome sequencing of isolates from various sites around the globe and different years. However, to what extent this pattern of gene diversity applies to natural bacterial populations, i.e., strains co-occurring in the same site, and the value of this diversity for population adaptation during environmental transition remains unclear. This study showed that while the pangenome of a natural population can be similarly large, only a small fraction of the pangenome appears to be functionally important when conditions change. Taken together, these results provided quantitative insights into the extent and functional significance of the accessory pangenome of a natural, species-like population.

microbiology↗