The microbiome of urban waters

More than 50% of the world’s population lives in urban centers. As collection basins for landscape activity, urban waters are an interface between human activity and the natural environment. The microbiome of urban waters could provide insight into the impacts of pollution, the presence of human health risks, or the potential for long-term consequences for these ecosystems and the people who depend upon them. An integral part of the urban water cycle is sewer infrastructure. Thousands of miles of pipes line cities as part of wastewater and stormwater systems. As stormwater and sewage are released into natural waterways, traces of human and animal microbiomes reflect the sources and magnitude of fecal pollution and indicate the presence of pollutants, such as nutrients, pathogens, and chemicals. Non-fecal organisms are also released as part of these systems. Runoff from impervious surfaces delivers microbes from soils, plants and the built environment to stormwater systems. Further, urban sewer infrastructure contains its own unique microbial community seemingly adapted to this relatively new artificial habitat. High microbial densities are conveyed via pipes to waterways, and these organisms can be found as an urban microbial signature imprinted on the natural community of rivers and urban coastal waters. The potential consequences of mass releases of non-indigenous microorganisms into natural waters include creation of reservoirs for emerging human pathogens, altered nutrient flows into aquatic food webs, and increased genetic exchange between two distinct gene pools. This review highlights the recent characterization of the microbiome of urban sewer and stormwater infrastructure and its connection to and potential impact upon freshwater systems. [Int Microbiol 18(3):141-149 (2015)]Keywords: urban freshwaters · infrastructure and sanitation · next generation sequencing · human health · aquatic food web

Diversity of Estrogen Degrading Microorganisms in Las Vegas Wash and Lake Mead, Nevada, USA

Endocrine disrupting chemicals (EDCs) are a subject of intense research as more studies reveal their persistence in the environment and detrimental effects on wildlife. Steroid hormones, including the natural and synthetic estrogens estrone (E1), 17-beta-estradiol (E2) and 17- alpha-ethinyl estradiol (EE2), are among the most bioactive and have been detected at low concentrations in waterways downstream from wastewater treatment plants. Las Vegas Wash, a stream flowing into Lake Mead and fed primarily by treated wastewater, provides a unique experimental system in which to study the role microorganisms play in the fate and dispersal of these compounds in surface waters

Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 1496-1503, doi:10.1128/AEM.02456-15.The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineating host-microbial associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macro-organisms, but it remains unclear how specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA gene amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). The interspecific abundance-occupancy relationship—where widespread taxa tend to be more abundant than narrowly distributed taxa—among operational taxonomic units (OTUs) was investigated within and among host species. In a separate analysis, specialists OTUs that were highly abundant in a single host and rare in all other hosts were identified using a multinomial model without excluding under-sampled OTUs a priori. We also show that intestinal microbes in humans and other vertebrates studied follow a similar interspecific abundance-occupancy relationship compared to plants and animals, as well as microbes in ocean and soil environments; but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest bacterial taxa can be shared among diverse vertebrate hosts in ways similar to those of ‘free-living’ bacteria

Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 1496-1503, doi:10.1128/AEM.02456-15.The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineating host-microbial associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macro-organisms, but it remains unclear how specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA gene amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). The interspecific abundance-occupancy relationship—where widespread taxa tend to be more abundant than narrowly distributed taxa—among operational taxonomic units (OTUs) was investigated within and among host species. In a separate analysis, specialists OTUs that were highly abundant in a single host and rare in all other hosts were identified using a multinomial model without excluding under-sampled OTUs a priori. We also show that intestinal microbes in humans and other vertebrates studied follow a similar interspecific abundance-occupancy relationship compared to plants and animals, as well as microbes in ocean and soil environments; but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest bacterial taxa can be shared among diverse vertebrate hosts in ways similar to those of ‘free-living’ bacteria

Baseline microbial characterizations of an imperiled aquatic diversity hotspot: Ash Meadows National Wildlife Refuge

Located in the discharge zone of the Death Valley Flow System, Ash Meadows National Wildlife Refuge is a spring-fed desert oasis and biodiversity hotspot about 90 miles northwest of Las Vegas. These critical wetlands are potentially threatened by groundwater pumping, exotic species invasions, and climate change. Although a major component of the lower food web, very little is known about the microbial makeup of this ecosystem. As a first step towards understanding the microbial and biogeochemical aspects of this system, a detailed molecular-based characterization of microbial communities, baseline chemistry, and physical characteristics of various springs of Ash Meadows will be conducted over the summer of 2009. Specifically, springs will be compared using DNA extraction followed by PCR amplification of the 16s rRNA gene, DNA fingerprinting, cultivation, and flow cytometric cell counting

Long distance microbial transport in air: Global change implications

The first manifestations of global change will most likelv be observed in the Earth\u27s atmosphere. Changing wind patterns, for example, may effect the long distance dispersal of microor-g anisms. The overall objective of this research is to correlate molecular assessments of microbial community structure from cloud water and snow samples, obtained from DRI\u27s Storm Peak Laboratory atop Mt. Werner in Colorado, with atmospheric data and calculated air mass back trajectories. Our activities for summer of 2009 will be a focused proof-of-concept exercise to determine if intact microbial DNA and viable cells can be recovered from cloud water and alpine snow samples. Specific methods employed will include DNA extraction and PCR amplification of the bacterial 16s rRNA gene, community fingerprinting (T-RFLP), flow cytometric cell counting, and dilution plate counting

Using Water Chemistry, Isotopes and Microbiology to Evaluate Groundwater Sources, Flow Paths and Geochemical Reactions in the Death Valley Flow System, USA

AbstractSprings of Ash Meadows and Furnace Creek (near or in Death Valley, CA) have nearly constant flow, temperature, chemistry, and similar δ2H and δ18O signatures. These factors indicate shared water sources and/or analogous geochemical reactions along similar flow paths. DNA-based (16S rRNA gene) microbial diversity assessments further illuminate these relationships. Whereas, all Ash Meadows springs share related archaeal populations, variations in carbon-14 (Crystal Spring) and strontium isotopes, Na+, SO2-, and methane concentrations (Big Spring), correspond with microbial differences within and between the two discharge areas. Similar geochemical signatures linking Ash Meadows and Furnace Creek springs appear to support a distinct end member at Big Spring in Ash Meadows, which is also supported by coincident enrichment in microbial methanogens and methanotrophs. Conversely, DNA libraries from a deep carbonate well (878 m) located between Ash Meadows and Furnace Creek (BLM-1), indicate no shared microbial diversity between Ash Meadows or Furnace Creek springs

A single genus in the gut microbiome reflects host preference and specificity

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.This study was funded by the NIH grant R01AI091829-01A1 to SLM

Sensitivity to grid resolution in the ability of a chemical transport model to simulate observed oxidant chemistry under high-isoprene conditions

Formation of ozone and organic aerosol in continental atmospheres depends on whether isoprene emitted by vegetation is oxidized by the high-NOx pathway (where peroxy radicals react with NO) or by low-NOx pathways (where peroxy radicals react by alternate channels, mostly with HO2). We used mixed layer observations from the SEAC4RS aircraft campaign over the Southeast US to test the ability of the GEOS-Chem chemical transport model at different grid resolutions (0.25°  ×  0.3125°, 2°  ×  2.5°, 4°  ×  5°) to simulate this chemistry under high-isoprene, variable-NOx conditions. Observations of isoprene and NOx over the Southeast US show a negative correlation, reflecting the spatial segregation of emissions; this negative correlation is captured in the model at 0.25°  ×  0.3125° resolution but not at coarser resolutions. As a result, less isoprene oxidation takes place by the high-NOx pathway in the model at 0.25°  ×  0.3125° resolution (54 %) than at coarser resolution (59 %). The cumulative probability distribution functions (CDFs) of NOx, isoprene, and ozone concentrations show little difference across model resolutions and good agreement with observations, while formaldehyde is overestimated at coarse resolution because excessive isoprene oxidation takes place by the high-NOx pathway with high formaldehyde yield. The good agreement of simulated and observed concentration variances implies that smaller-scale non-linearities (urban and power plant plumes) are not important on the regional scale. Correlations of simulated vs. observed concentrations do not improve with grid resolution because finer modes of variability are intrinsically more difficult to capture. Higher model resolution leads to decreased conversion of NOx to organic nitrates and increased conversion to nitric acid, with total reactive nitrogen oxides (NOy) changing little across model resolutions. Model concentrations in the lower free troposphere are also insensitive to grid resolution. The overall low sensitivity of modeled concentrations to grid resolution implies that coarse resolution is adequate when modeling continental boundary layer chemistry for global applications

Why do models overestimate surface ozone in the Southeast United States

Ozone pollution in the Southeast US involves complex chemistry driven by emissions of anthropogenic nitrogen oxide radicals (NOx  ≡  NO + NO2) and biogenic isoprene. Model estimates of surface ozone concentrations tend to be biased high in the region and this is of concern for designing effective emission control strategies to meet air quality standards. We use detailed chemical observations from the SEAC4RS aircraft campaign in August and September 2013, interpreted with the GEOS-Chem chemical transport model at 0.25°  ×  0.3125° horizontal resolution, to better understand the factors controlling surface ozone in the Southeast US. We find that the National Emission Inventory (NEI) for NOx from the US Environmental Protection Agency (EPA) is too high. This finding is based on SEAC4RS observations of NOx and its oxidation products, surface network observations of nitrate wet deposition fluxes, and OMI satellite observations of tropospheric NO2 columns. Our results indicate that NEI NOx emissions from mobile and industrial sources must be reduced by 30–60 %, dependent on the assumption of the contribution by soil NOx emissions. Upper-tropospheric NO2 from lightning makes a large contribution to satellite observations of tropospheric NO2 that must be accounted for when using these data to estimate surface NOx emissions. We find that only half of isoprene oxidation proceeds by the high-NOx pathway to produce ozone; this fraction is only moderately sensitive to changes in NOx emissions because isoprene and NOx emissions are spatially segregated. GEOS-Chem with reduced NOx emissions provides an unbiased simulation of ozone observations from the aircraft and reproduces the observed ozone production efficiency in the boundary layer as derived from a regression of ozone and NOx oxidation products. However, the model is still biased high by 6 ± 14 ppb relative to observed surface ozone in the Southeast US. Ozonesondes launched during midday hours show a 7 ppb ozone decrease from 1.5 km to the surface that GEOS-Chem does not capture. This bias may reflect a combination of excessive vertical mixing and net ozone production in the model boundary layer