Date of Degree


Document Type


Degree Name



Earth & Environmental Sciences


Jeffrey Bird


Gregory O'Mullan

Committee Members

Hari Pant

Alexander Kolker

Subject Categories

Biogeochemistry | Environmental Microbiology and Microbial Ecology | Environmental Sciences | Soil Science | Terrestrial and Aquatic Ecology


Methane, carbon dioxide, biogeochemistry, estuaries, combined sewage overflows, wetland soils


Coastal megacities deposit significant amounts of carbon (C), nitrogen (N) and other pollutants into surrounding waters. These inputs, including wastewater and surface water runoff, may affect estuarine and adjacent wetland biogeochemical cycles, microbial production and ultimately greenhouse gas (GHG) efflux. In many megacities pollutant loading is typically greatest after periods of precipitation when the volume of wastewater and storm water runoff exceeds local sanitation capacity, resulting in the discharge of raw sewage into adjacent waters. These combined sewage overflow (CSO) events have received considerable attention primarily due to their potential impact on human health and eutrophication. However, whether these events alter GHG dynamics in the surrounding waterbody remains largely understudied and therefore unconstrained.

To better understand estuarine GHG production and connect it to urban drivers, I quantified carbon dioxide (CO2) and methane (CH4) surface concentrations and efflux in combination with a suite of biogeochemical parameters including anthropogenic indicators from the Hudson River Estuary (HRE). The HRE has overlaying salinity and “urban” gradients with the most densely populated areas located at both the southern brackish (New York City [NYC], NY, USA) and northern fresh (Albany, NY, USA) termini. Sampling was conducted from urban mid-channel sites, suburban/rural mid-channel sites, urban embayments and natural tributaries (both likely delivery areas of C and N), as well directly from CSO discharge. I further explored the impact of anthropogenic inputs through a series of laboratory incubation experiments which quantified potential CO2 and CH4 production rates following C and N additions with sampled soils/sediments of varied salinities and histories of pollutant loading.

In the largely hypoxic and anoxic environments (wetland soils, embayment sediments and the water column) of urban estuaries, facultative and obligate heterotrophic microbial communities utilize electron acceptors that yield less energy from the oxidation of organic C molecules relative to aerobic environments. These thermodynamic constraints result in reduced growth in microbial communities and thus lower demand for N. The ratio of methanogenesis (CO2 and CH4 byproducts) to sulfate reduction (CO2 byproduct), two dominant estuarine alternative metabolic pathways, is correlated to salinity due to the resupply of sulfate from ocean waters and the higher energy yield from sulfate reduction. However, anaerobic soil and sediment environments with high concentrations likely support multiple metabolic pathways simultaneously. In urban estuaries on-going C and N loading from runoff and wastewater may result in greater rates of methanogenesis than would be predicted based on the salinity gradient alone.

We hypothesize that microbial activity in these anaerobic ecosystems (estuary sediments and wetland soils) is limited by the availability of labile C which provides electron donors to support microbial metabolism. The addition of C from urban inputs will result in both hotspots (poorly flushed sewage delivery areas) and hot moments (following sewage additions) of GHG production in the HRE. We predict these large point sources of C will result in greater CO2 and CH4 surface concentrations in urban surface waters (notably embayments with reduced tidal circulation), relative to suburban/rural areas. GHG concentrations will also be positively correlated to indicators of anthropogenic loading, such as dissolved organic C (DOC), dissolved organic N (DIN) and fecal indicator bacteria (FIB) values. C additions as acetate (but not nitrate [NO3-] nor ammonium [NH4+]) will enhance both CO2 and CH4 production rates in slurry incubation experiments with all sampled soils and sediments of varied salinities sampled across the HRE.

Sampling surface waters from the HRE from 2013-2014 (n=10 sampling cruises) yielded many key findings including: (1) the HRE was a source of both CO2 (35 ± 4 mmol CO2 m-2 day-1) and CH4 (191 ± 26 µmol CH4 m-2 day -1) from all sites and almost all (>99%) time points; (2) methane (CH4) but not carbon dioxide (pCO2) mid-channel surface values were significantly greater in urban vs. less developed areas (regardless of salinity); (3) urban embayments (Flushing Bay, Gowanus Canal and Newtown Creek) had the greatest GHG values quantified through the HRE and (4) surface water salinity, oxygen saturation, fecal-indicator bacteria, nitrate concentrations and temperature best explained the variance in pCO2 (r2=0.85) and CH4 (r2=0.41) concentrations in multiple regression analyses, producing robust predictive power for both GHGs. Our multifaceted HRE data set demonstrated that urban inputs enhance GHG concentrations in surrounding estuarine waters. Enhanced production was localized primarily in tributaries and embayments, hotspots of activity. These likely hot spots of CH4 production “bleed” into surrounding waters resulting in elevated CH4 surface concentrations in urban mid-channel vs. suburban/rural sites.

Additional FB sampling following dry weather (n=8), wet weather (n=10) and during CSO flow (n=2) demonstrated that: (1) CSO discharge was a source of FIBs, DOC, DIN, CH4 and CO2, however; (2) except for FIBs, the concentrations of these analytes in surface waters were not significantly different following dry or wet weather. The reasons that DOC, NH4+ and GHGs were not significantly different between wet and dry weather conditions in FB are likely multifaceted, but we posit that the regular CSO inputs of sewage pollutants into FB over many years has created a permanent ‘hot spot,’ with elevated labile C and N levels compared with their natural state. “Permanent” elevated production from urban embayments was validated by soil slurry incubations (3) which demonstrated significantly enhanced CH4 (10X) and CO2 (1.8X) production rates following input of acetate C over timescales (>14 days) longer than the frequency between CSO events in NYC. Our combined data demonstrates that CSO events are both a direct source of CH4 and CO2 and potential indirect source of these GHGs via enhanced in situ microbial production from C additions. When these values are scaled to NYCs total CSO discharge (6.33 x 10-5 million metric tons of CO2e) or potential production from embayments (1.92 million metric tons CO2e) we find that total CO2e production via these pathways represents up to 0.0001 and 4%, respectively, of NYCs total GHG footprint.

Soil slurry incubations with Iona Island Marsh (II; 0-6 mg L-1), Piermont Marsh (PM; 0-12 mg L-1) and Saw Mill Creek Marsh (SM; 17-27 mg L-1) wetland soils demonstrated that: (1) C (as acetate), but not N (NO3- or NH4+), additions significantly enhanced CH4 (>150X) and CO2 (>1.7X) production rates; and (2) CH4 production in slurry experiments was correlated to salinity (r2=0.81) except for FB (20-28 mg L-1) sediments which produced more total C-CH4 day-1 than SM soils with similar salinity but with a history of less anthropogenic inputs. Contextual sequencing data also showed (3) that each wetland site had dissimilar methanogenic and sulfate reducing communities, which were not impacted by treatments revealing that the enhancement of GHG production was driven by alterations in microbial activity, not abundance. Lastly, (4) enhanced production, estuarine soils and sediments mineralized less than 20% of C additions as GHGs indicating wetland soils and embayment sediments are sinks of anthropogenic C. The differences observed in CH4 production lead to much higher estimates of the global warming potentials (CO2 equivalents) from these soils/sediments with added acetate (1784 ± 830, 1289 ± 263, 245 ± 27 and 605 ± 216 µg C day-1 g-1 dry soil C for II, PM, SM and FB, respectively) compared with unamended soils (109 ± 12, 157 ± 16, 164 ± 17 and163 ± 39 µg C day-1 g-1 of dry soil C for II, PM, SM and FB respectively) during the incubation period. Given these data, C pollution from megacities have the potential to increase GHG production from the environment across salinity gradients, with soils/sediments (FB) most exposed “primed” for higher production rates.

These data address significant knowledge gaps in the fields of both estuarine and soil science. It has long been posited that anthropogenic inputs including wastewater treatment from coastal megacities enhance GHG production, concentrations and efflux in estuarine waters. This potential loading mechanism has been utilized to explain supersatured GHG concentrations in estuaries worldwide. My studies pioneer the linkage of FIB explicitly to both CH4 and CO2 values on the scale of an entire tidal estuary. The soil incubations were also, to my knowledge, the first C addition experiments in temperate wetland soils. Enhanced production via urban inputs demonstrated here likely occurs in areas such as tributaries and embayments (CSO discharge sites) that have historically received less research attention. For example, a large area fraction (34%) of the HRE is shallow (feet) and these shallow areas receive the largest delivery of both urban and terrestrial inputs and have received almost no research attention examining estuarine GHG dynamics. Consequently, GHG released from estuaries is almost certainty significantly underestimated. C additions from wastewater treatment including CSOs alters the environment, likely removes typical controls for microbial production in anaerobic soils/sediments, resulting in permanent “hotspots” or GHG production and efflux, akin to agricultural systems. Overall, these data demonstrate that CSO discharge is likely a relevant management concern beyond the well-recognized human health (fecal contact) and ecosystem impacts (eutrophication) and warrants substantial further study.