Biology subjects

Hatt, J.

Publications and source records attributed to Hatt, J..

11 recordsLinked to original sources

bioRxiv2025

Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input

Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced [[~]5 Gbp/sample] shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station, even when including previously determined samples from other ocean basins. However, a community level pangenome style gene content analysis revealed [~]54% of predicted gene sequences to be station specific within our GoM samples. Of the 154 high-quality MAGs recovered, 145 represent novel species compared to NCBI genomes and TARA MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin ([~]6% of total detected) were relatively abundant at 600m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearsons r [≥] 0.5) or negatively (Pearsons r [≤] -0.5) correlated with depth including beta-lactamases, dehydrogenase, and CoA-associated oxidoreductases. Taken together our results reveal substantial novel genome and gene diversity across the GoMs water column, and testable hypotheses for some of the diversity patterns observed. IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths and what the impact of freshwater input by major rivers may be on these communities remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2000m. Comparison to similar data from other ocean basins highlight the unique diversity harbored by the GoM, which could be driven by more substantial input by the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute toward its more complete characterization.

microbiology↗

bioRxiv2024

Promiscuous and unbiased recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean

Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species usually show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria), which play a major role in carbon cycling, are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up [~]20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a newly developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR-11 appears to be more promiscuous compared to other prokaryotic species and has facilitated the spreading of adaptive mutations within the species, further promoting the high intra-species diversity observed. These results implicate rampant, genome-wide homologous recombination as the mechanism that underlies the evolution of SAR11 into discrete species. SignificanceDistinguishing "species" is a pressing issue in microbiology, partly because the mechanisms that create and maintain clusters of genetically similar microbes are sparsely documented for natural populations. By leveraging high quality single-cell genomic data and a novel method for assessing homologous recombination, we show that rampant homologous recombination maintains species-level clusters of genomes for the most abundant order of marine bacteria, suggesting that these genomes may be evolving sexually to a much greater extent than previously thought. Therefore, our results identify a mechanism explaining the evolution of species in a major microbial group and have implications for understanding microbial diversity and the species concept more broadly.

microbiology↗

bioRxiv2024

Microbial species exist and are maintained by ecological cohesiveness coupled to high homologous recombination.

Recent analyses of metagenomes and genomes have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars). To advance the species concept the underlying genetic or ecological mechanisms that maintain these discrete units need to be elucidated. By analyzing closely related isolate genomes from the same or related samples we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on higher similarity in abundance patterns of genomes of the same vs. different units, while recombination frequency was shown to have two times or more impact on sequence evolution than point mutation. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or selection-driven recombination, but not their synergistic effect, as the mechanism of unit cohesion. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results have strong implications for how to identify and regulate microbial species and genomovars of clinical or environmental importance and answer an important question for microbiology: what a species is. SIGNIFICANCEA highly pressing issue to resolve toward advancing the species concept for microbes (i.e., "what a species is") is to elucidate the underlying mechanisms for creating and maintaining species- and intraspecies-level gaps in diversity, or simply "clusters". In this study, we provide a novel methodology and the appropriate data to elucidate these mechanisms, and thus provide a mechanistic explanation of how the evolution of species- and strain-level clusters takes place. Specifically, our results show that several bacteria may be evolving and speciating much more sexually than previously thought, even under conditions of no strong positive selection for DNA exchange (i.e., neutral conditions). These results have major implications for better understanding and modeling microbial diversity on the planet.

microbiology↗

bioRxiv2023

Low-troposphere microbial communities differ between dry-air and rainfall but do not show strong seasonal patterns in Metro Atlanta, Southeast USA

The composition and seasonal patterns of airborne bacterial and fungal communities and how these are affected by atmospheric conditions (e.g., dry vs. rain), origin of air masses, and presence of air pollutants remain understudied, despite their obvious importance for public health. To provide insights into these questions, monthly dry air and rain samples were collected at the Environmental Science and Technology building rooftop on Georgia Techs campus (Metro Atlanta) between June 2017 and November 2019. The sampling included the remnants of Hurricane Irma and a Saharan dust event in 2020. Amplicon sequencing of the V4 region of the 16S rRNA gene and the fungal nuclear ribosomal internal transcribed spacer (ITS) region showed that spore-forming bacteria and widespread fungi were enriched in dry samples, while photosynthetic bacteria and wood-decaying fungi were more abundant in rain samples, demonstrating the effect of sample type on bioaerosol composition. Further, higher relative abundance of fungal human pathogens and allergens were identified in the dry-air and Saharan dust samples, including Alternaria alternata and Cladosporium cladosporioides. Bacterial and fungal species richness and composition appeared to be relatively consistent between seasons for both sample types. Accordingly, sample type and seasonality explained [~]14% and [~]8.5% of the microbial diversity between samples, respectively, while presence of air pollutants and three-day back trajectory data were not significant. Collectively, our data indicates that dry air might represent a higher public health risk and provides a reference point for the long-term monitoring of airborne microbial communities in an urban Southeast US setting. ImportanceIn the atmosphere, or in the air we breathe, bioaerosols are always present. Bioaerosols are biological particles (alive or dead) suspended in the air, being bacteria and fungi the most abundant. In addition, bioaerosols can potentially contribute to weather/climate patterns. Although and unfortunately, a clear biodiversity pattern from different atmospheric events (air, rain, snow, etc.) remains to be discovered, especially in urban areas, where bioaerosols can also have implications for public health. The role of airborne microbes and their diversity patterns in the atmosphere constitutes a significant gap in our understanding of their interactions with health, climate, and other ecosystems compared to other environments. Our research provides the first reference point for long-term monitoring of airborne microbial communities in an urban Southeast US setting. This research contributes novel knowledge about public health and insights for integrating biological information into weather and climate prediction models.

microbiology↗

bioRxiv2021

Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions

The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that "naturalized" populations of E. faecalis exist in the extraenteric environment in a viable but not culturable (VBNC) state. The extent to which these naturalized or VBNC E. faecalis can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and qPCR counts. However, the enteric isolates exhibited a spike in rRNA:rDNA ratios between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential expression of genes thought to be related to habitat adaptation in the accompanying mesocosm metatranscriptomes when compared between environmental and enteric isolates. Overall, our results provide novel information on how rRNA levels may vary over different metabolic states (i.e., alive vs. VBNC) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring. IMPORTANCEEnterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, some species within this group can enter an inactive, viable but not culturable (VBNC) state that make it difficult to accurately quantify during routine monitoring. Furthermore, lower-risk, environmental enterococci strains may also confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested here; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher risk) fecal pollution because rRNA levels significantly decreased after one week in all isolates.

microbiology↗

bioRxiv2020

Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs

Geothermal springs are barely affected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 (two to four samples per year) from the Thermopyles sulfur geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples, while grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, especially in comparison to other surface water systems in Greece, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed - in addition- that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate and/or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, driving presumably the corresponding stability in community structure.

microbiology↗

bioRxiv2020

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling

The phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity when compared to temperate grasslands or agricultural soils. Unlike temperate soils, LEF soils showed little stratification with depth in the first 0-30cm, with ~45% of community composition differences explained solely by location. The relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest compared to temperate soils (20% vs. 0.1-0.3% of bacterial genomes in each soil type harbored the gene, respectively). Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities, and should facilitate future ecological modeling efforts. ImportanceTropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two critical greenhouse gases for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from 3 distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.

microbiology↗

bioRxiv2019

Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

Indigenous microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enters the natural environment through natural seeps or accidental oil spills, but the interactions among microbes and with their chemical environment during oil biodegradation are highly complex and poorly understood. Genome-resolved metagenomics have the potential to help in unraveling these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oiled environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we present a curated, comprehensive, and searchable database that documents microbial populations in oiled ecosystems on a global scale, along with underlying physicochemical data, geocoded via GIS to reveal geographic distribution patterns of the populations. Analysis of the ~2,000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats e.g., specialization to coastal sediments vs. water-column vs. deep-sea sediments. Over 95% of the recovered MAGs represented novel and uncultured species underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oiled ecosystems are members of the rare biosphere in non-oiled samples, except for the Gulf of Mexico (GoM) which appears to be primed for oil biodegradation. GROS should facilitate future work toward a more predictive understanding of the microbial taxa and their activities that control the fate of oil spills as well as serve as a model approach for building similar resources for additional environmental processes and omic data of interest.

genomics↗

bioRxiv2019

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from agricultural activities such as Shiga Toxin-producing E. coli (STEC) in such sediments remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (~4 Gbp per library), we were unable to detect any pathogenic Escherichia coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low pathogen abundance. Further, no significant differences were detected in the abundance of human- or cow-specific gut microbiome sequences compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high baseline level of metagenomic reads encoding antibiotic resistance genes (ARGs) was found in all samples and was significantly higher compared to ARG reads in metagenomes from other environments, suggesting that these communities may be natural reservoirs of ARGs. Overall, our metagenomic results revealed that creek sediments are not a major sink for anthropogenic runoff and the public health risk associated with these sediment microbial communities may be low.\n\nIMPORTANCECurrent agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium, E. coli. However, the accuracy of these traditional methods (e.g., low quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

microbiology↗

bioRxiv2018

Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils

Multi-omic techniques can offer a comprehensive overview of microbial communities at the gene, transcript and protein levels. However, to what extent these levels reflect in situ process rates is less clear, especially in highly complex habitats such as soils. Here we performed microcosm incubations using soil from a site with a history of agricultural management. Microcosms, amended with isotopically labelled ammonium and urea to simulate a fertilization event, showed nitrification (up to 4.1 {+/-} 0.87 {micro}g N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+[->]NH2OH[->]NO2-[->]NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria (AOB) Nitrosomonas and Nitrosospira. In contrast, ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) nitrifiers showed stable gene expression during incubations but were generally more abundant (DNA level) than their Betaproteobacteria AOB counterparts. A strong relationship between nitrification activity and (mostly) betaproteobacterial ammonia monooxygenase (amoA; NH4+[->]NH2OH) and nitrite oxidoreductase (nxrA; NO2-[->]NO3-) transcript abundances revealed that mRNA levels quantitatively reflected measured activity and were generally more sensitive than the DNA level in the microcosm incubations. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing complex microbial communities and provide the molecular means to assess nitrification processes in soils.\n\nIMPORTANCEEven though the use of omic approaches has expanded our knowledge of the diversity of microbial communities in natural and engineered systems, it is less clear how well the use of whole community DNA-, RNA- or protein-based approaches reflect microbial activities. To this end, we directly compared the different levels of molecular information (i.e., DNA, RNA or proteins) in order to assess which level best correlated with isotope-based measurements of nitrification activity in agricultural soils after fertilization. This work reveals the strengths as well as the associated limitations of metagenomic, metatranscriptomic, and metaproteomic approaches in serving as reliable proxies for examining microbial activities in highly diverse environments like soils.

microbiology↗

bioRxiv2018

Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics

The Anones Lagoon, located in the island municipality of Vieques, Puerto Rico (PR), received extensive bombing during military practices by the US Navy for decades. After military activities ceased in 2003, the bombing range was designated as part of a larger Superfund site by US EPA. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PRs capital city). Consistent with selection under low anthropogenic impacts, Guaniquilla exhibited the highest degree of diversity with lower frequency of genes related to xenobiotics metabolism among the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique population genomes were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants. Collectively, these results provided new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and could serve as reference points to enhance bioremediation actions at this site and for assessing other similarly impacted sites.\n\nImportanceThis study represents the first assessment of the benthic microbial community in the Anones Lagoon in Vieques, Puerto Rico after the impact of intense pollution by bombs and unconventional weapons during military training exercises. Evaluating the microbial diversity of Anones, represents an opportunity to assess the microbial succession patterns during the active process of natural attenuation of pollutants. The culture-independent techniques employed to study these environmental samples allowed the recovery of almost complete genomes of several abundant species that were likely involved in the biodegradation of pollutants and thus, represented species responding to the strong selection pressure posed by military activities. Further, our results showed that natural attenuation has proceeded to a great extend ten years after the cease of military activities.

microbiology↗