Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms

Assessment of seasonal and annual patterns in phosphorus content in a monitored catchment through a partitioning approach based on hydrometeorological data

High amounts of phosphorus (P) in rivers come mainly from two sources: fertilizers washed off from agricultural and urban areas by runoff water (non-point sources) and urban and industrial development which are translated in P discharges from wastewater treatment plants (WWTP). This work analyses the content of P in water for nearly 40 years inquiring into the origin of the sources, based on the hypothesis of runoff generation from the detection of river streamflow increases during the P contribution episode and the previous precipitation. For this purpose, the Guadaira River, which is located in the South of Spain and has a drainage surface of 1524 km2, was selected. In this watershed agricultural land use converges with numerous human activities resulting in high pressures on water quality. We found 40% of the P contribution episodes found seem to come from the runoff generated after the heaviest rainfall events, which normally occur between November and May. The remaining 60% of the P contribution episodes were found to be linked to point sources, which become more relevant from June to September, reaching the highest concentration values (6-17 mg/L). The results highlight that the target phosphate concentration value of 0.34 mg PO4/L imposed by the national legislation for a good state following the Water Framework Directive 2000/60/EC is exceeded by 96% of the measurements during the period from 1981 to 2022. On a monthly basis, PO4 loads showed a linear relationship with river streamflow (R2 = 0.94). However, on field measurements scale, a potential relationship between both variables was found, which changed according to the improvement in the wastewater treatment and facilities for 1982-1994, 1995-2017 and 2018-2022. In these three periods, different significant decreasing trends of the P content were found, mainly marked by the setup of each individual WWTP.

Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.

Ammonium concentration in stream sediments resulting from decades of discharge from a wastewater treatment plant

A study of ammonium pollution in the sediments of a stream that receives wastewater treatment plant (WWTP) discharge has been carried out. It is urgently necessary to find environmental indicators that can help prevent and detect potential contamination of water, as water is an increasingly scarce resource. To understand the behaviour of ammonium ions introduced by a historical (50-year) contamination process, vertical boreholes were drilled in the stream banks to depths between 30 and 120 cm. Moisture, pH, ammonium (soluble and exchangeable), and clay fraction content were analysed. The variation profile of these parameters was evaluated as a function of depth to determine factors related to the distribution of ammonium in several locations along the stream banks. The ammonium concentration was asymmetrically distributed among samples collected in near-surface locations, with ammonium concentrations between 0.3048 mmol/kg soil and 0.0007 mmol/kg soil. Ammonium was typically concentrated at sediment depths of 30-40 cm, which also exhibited the highest clay fraction content. High positive correlations were detected (r > 0.8; p < 0.0001) among the different ammonium variables (exchanged and dissolved species). No contamination effect was observed below 60-70 cm depth, which was due to ammonium retention in a natural barrier layer of clayey sediment. The clays in our study area (previously identified as smectite, a 2:1 sheet silicate) were able to control the contamination by retaining ammonium in the interlayers, which retarded nitrification. It is suggested that clay could serve as a geo-indicator of ammonium pollution evolution.

Wastewater treatment plant effluent inputs influence the temporal variability of nutrient uptake in an intermittent stream

Wastewater treatment plant (WWTP) effluents alter water chemistry and in-stream nutrient uptake rates of receiving freshwaters, thus changing the magnitude and fate of the nutrients exported. In Mediterranean regions, the dilution capacity of receiving streams can vary strongly over time due to the seasonal occurrence of floods and droughts, causing temporal variability of nutrient uptake. We assessed the temporal patterns and the controlling factors of net nutrient uptake in an intermittent Mediterranean stream receiving WWTP effluent inputs. We compiled the longitudinal concentration profiles of ambient dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) along a 800 m reach on 47 sampling dates between 2001 and 2017, encompassing a wide range of hydrological conditions. We estimated net nutrient uptake in the receiving stream. In 72% of the dates, high rates of net ammonium uptake co-occurred with net releases of either nitrate or nitrite. This pattern suggests that the receiving stream has a high nitrification capacity. Conversely, 75% of the dates did not show any longitudinal pattern in SRP concentration, suggesting that uptake and release processes for this element were either counterbalanced or both occurred at very low rates. Finally, net ammonium uptake was low when the stream had a low dilution capacity (< 40%) and ammonium concentration was high. Overall, we demonstrate that consideration of the receiving stream’s dilution capacity is imperative to the management of freshwaters to guarantee an adequate dilution of WWTP effluent inputs and avoid saturation of in-stream nutrient uptake capacity under low flow conditions in urban landscapes.

Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers

Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.

Seasonal and spatial distribution and assembly processes of bacterioplankton communities in a subtropical urban river

The ecological functions of core and non-core bacteria are gradually being identified, yet little is known about their responses to environmental changes and assembly processes, especially in urban river ecosystems. Here, we investigated bacterioplankton communities over 1 year in an urban section of the Ganjiang River, China. The results revealed that the alpha- and beta-diversity of bacterioplankton communities had no significant spatial differences along the urbanization gradient, but they presented distinct seasonal variations. The bacterioplankton communities were comprised of a few core taxa (11.8%) and a large number of non-core taxa (88.2%), of which the non-core taxa were the most active component responsible for community dynamics. Most non-core taxa (76.84%) belonged to non-typical freshwater bacteria, implying that they are more likely to derive from allochthonous inputs than the core taxa. Variance partitioning analyses showed that air temperature, flow rate and water chemistry together explained 58.2 and 38.9% of the variations of the core taxa and non-core taxa, respectively. In addition, the relative importance of temperature and water chemistry on the bacterioplankton communities prevailed over that of flow rate alone. This means that deterministic processes and stochastic processes simultaneously control the bacterioplankton community assembly, with deterministic processes contributing more than stochastic processes.

River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs

The sensitivity and spatial recovery of river sediment biofilms along 1 km after the input of two wastewater treatment plants (WWTPs) located in two river reaches with different degrees of anthropogenic influence were investigated. First, at the upper reach, we observed an inhibition of some microbial functions (microbial respiration and extracellular enzyme activities) and strong shifts in bacterial community composition (16S rRNA gene), whereas an increase in microbial biomass and activity and less pronounced effect on microbial diversity and community composition were seen at the lower reach. Second, at the lower reach we observed a quick spatial recovery (around 200 m downstream of the effluent) as most of the functions and community composition were similar to those from reference sites. On the other hand, bacterial community composition and water quality at the upper reach was still altered 1 km from the WWTP effluent. Our results indicate that biofilms in the upstream sites were more sensitive to the effect of WWTPs due to a lower degree of tolerance after a disturbance than communities located in more anthropogenically impacted sites.

Combined effects of urban pollution and hydrological stress on ecosystem functions of Mediterranean streams

Urban pollution and hydrological stress are common stressors of stream ecosystems, but their combined effects on ecosystem functioning are still unclear. We measured a set of functional processes and accompanying environmental variables in locations upstream and downstream of urban sewage inputs in 13 streams covering a wide range of water pollution levels and hydrological variability. Sewage inputs seriously impaired stream chemical characteristics and led to complex effects on ecosystem functioning. Biofilm biomass accrual, whole-reach nutrient uptake and metabolism (ecosystem respiration) were generally subsidized, whereas organic matter decomposition and biofilm phosphorus uptake capacity decreased with increasing pollutant concentrations. Hydrological stress affected stream ecosystem functioning but its effect was minor compared to the effects of urban pollution, due to the large inter-site variability of the streams. Changes appeared mainly linked to the concentration of pharmaceutically active compounds, followed by other chemical characteristics and by hydrology. The results point to the need to further improve sewage treatment, especially as climate change will stress riverine organisms and reduce the dilution capacity of the receiving streams.

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)

Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH₄⁺) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R² = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH₄⁺ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.

Wastewater treatment plant effluent inputs induce large biogeochemical changes during low flows in an intermittent stream but small changes in day-night patterns

Wastewater treatment plant (WWTP) effluents alter stream water chemistry and metabolic activity. Yet, essential aspects influencing the biogeochemical response of receiving streams such as hydrology and diel oscillations of light and temperature remain largely unexplored. We measured day vs night water chemistry and in-stream net nutrient uptake velocity (V_f) in an intermittent forested stream, upstream and downstream of a WWTP effluent under contrasting hydrological conditions. The WWTP effluent negatively influenced stream water chemistry, especially during the dry period. Despite large diel oscillations in light inputs, day-night differences in nutrient and oxygen concentrations were small, suggesting that heterotrophic respiration drove stream metabolism with a minor contribution of gross primary production. The magnitude of V_f was similar between day and night at the two reaches. Yet, at the downstream reach, in-stream net DIN uptake occurred more often at night, and values of V_f for ammonia and nitrite indicated enhanced in-stream nitrification. The two reaches showed a small capacity to retain DIN and soluble reactive phosphorus from the water column. Positive values of in-stream net nutrient uptake (i.e. uptake > release) occurred mostly during the dry period, highlighting that in-stream biogeochemical processing can contribute to improve water quality in streams receiving point-sources effluents in regions with low water availability.

Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China

Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 10⁸ gene copies (g-soil⁻¹) to 2.23 × 10⁸ gene copies (g-soil⁻¹) and 5.45 × 10⁸ gene copies (g-soil⁻¹) to 3.30 × 10⁷ gene copies (g-soil⁻¹), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3−, Temp, and NH\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.

Niche partitioning of microbial communities in riverine floodplains

Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor β (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.

Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river

Background

In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems.

Methods

Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm² and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR.

Results

We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and antibiotic resistance.

The flux and impact of wastewater infrastructure microorganisms on human and ecosystem health

Wastewater infrastructure is designed, in part, to remove microorganisms. However, many microorganisms are able to colonize infrastructure and resist treatment, resulting in an enormous flux of microorganisms to urban adjacent waters. These urban-associated microorganisms are discharged through three primary routes 1) failing infrastructure, 2) stormwater, and 3) treated wastewater effluent. Bacterial load estimates indicate failing infrastructure should be considered an equivalent source of microbial pollution as the other routes, but overall discharges are not well parameterized. More sophisticated methods, such as machine learning algorithms and microbiome characterization, are now used to track urban-derived microorganisms, including targets beyond fecal indicators, but development of methods to quantify the impact of these microbes/genes on human and ecosystem health is needed.

The collaborative effect of Chlorella vulgaris-Bacillus licheniformis consortia on the treatment of municipal water

In this study, the effects of nutrient and dissolved organic matter removal, stress resistance (DNA methylation), and the algae-bacteria dynamic ratio of algal-bacterial consortia in actual municipal wastewater were investigated. Results indicate that the presence of a Chlorella vulgaris-Bacillus licheniformis consortium had profound effects. The removal rates of total nitrogen, ammonium, orthophosphate phosphorus and chemical oxygen demand were 88.82%, 84.98%, 84.87% and 82.25%, respectively. Protein-like substances, which are difficult to degrade in the natural water environment, were significantly degraded in actual municipal wastewater. Furthermore, the microbial diversity was measured. The algal-bacterial consortium did not disrupt the microbial in-situ diversity of the actual municipal wastewater under suitable conditions. The global nuclear DNA methylation level peaked at 7.80%. These results help to understand the effects of algal-bacterial consortia on nutrient and pollutant removal and adaptability in actual municipal wastewater.

Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4 +) pool size decreased, nitrate (NO3 -) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases - a hydrological scenario expected to become more important in the future.

Stream drying drives microbial ammonia oxidation and first-flush nitrate export

Stream microbial communities and associated processes are influenced by environmental fluctuations that may ultimately dictate nutrient export. Discharge fluctuations caused by intermittent stream flow are increasing worldwide in response to global change. We examined the impact of flow cessation and drying on in-stream nitrogen cycling. We determined archaeal (AOA) and bacterial ammonia oxidizer (AOB) abundance and ammonia oxidation activity in surface and deep sediments from different sites along the Fuirosos stream (Spain) subjected to contrasting hydrological conditions (i.e., running water, isolated pools, and dry streambeds). AOA were more abundant than AOB, with no major changes across hydrological conditions or sediment layers. However, ammonia oxidation activity and sediment nitrate content increased with the degree of stream drying, especially in surface sediments. Upscaling of our results shows that ammonia oxidation in dry streambeds can contribute considerably (~50%) to the high nitrate export typically observed in intermittent streams during first-flush events following flow reconnection. Our study illustrates how the dry channels of intermittent streams can be potential hotspots of ammonia oxidation. Consequently, shifts in the duration, spatial extent and severity of intermittent flow can play a decisive role in shaping nitrogen cycling and export along fluvial networks in response to global change.

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.

Characteristics of microbial community involved in early biofilms formation under the influence of wastewater treatment plant effluent

Effluents from wastewater treatment plants (WWTPs) containing microorganisms and residual nutrients can influence the biofilm formation. Although the process and mechanism of bacterial biofilm formation have been well characterized, little is known about the characteristics and interaction of bacteria, archaea and eukaryotes in the early colonization, especially under the influence of WWTP effluent. The aim of this study was to characterize the important bacterial, archaeal and eukaryotic species in the early stage of biofilm formation downstream of the WWTP outlet. Water and biofilm samples were collected 24 and 48hr after the deposition of bio-cords in the stream. Illumina Miseq sequencing of the 16S and 18S rDNA showed that, among the three domains, the bacterial biofilm community had the largest alpha and beta diversity. The early bacterial colonizers appeared to be "biofilm-specific", with only a few dominant operational taxonomic units (OTUs) shared between the biofilm and the ambient water environment. Alpha-proteobacteria and Ciliophora tended to dominate the bacterial and eukaryotic communities, respectively, of the early biofilm already at 24hr, whereas archaea played only a minor role during the early stage of colonization. The network analysis showed that the three domains of microbial community connected highly during the early colonization and it might be a characteristic of the microbial communities in the biofilm formation process where co-occurrence relationships could drive coexistence and diversity maintenance within the microbial communities.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams

Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent sources at six sites on two sampling dates on the chemical and microbial population regimes within the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. Effluent was observed to be a significant source of nutrients, human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources, which we hypothesize is controlled by distance from effluent source. Antecedent moisture conditions were observed to impact overall microbial community diversity, with higher diversity occurring after rainfall. Finally, the efficacy of using a subset of the microbial community including the orders of Bifidobacteriales, Bacteroidales, and Clostridiales to estimate the degree of influence due to sewage and fecal sources was explored and verified.

Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China

Microbial ecological information on the nitrogen removal processes in wastewater treatment plants (WWTPs) has been of considerable importance as a means for diagnosing the poor performance of nitrogen removal. In this study, the altitude-scale variations in the quantitative relationships and community structures of betaproteobacteria ammonia-oxidizing bacteria (βAOB) and nitrite-reducing bacteria containing the copper-containing nitrite reductase gene (nirK-NRB) and the cytochrome cd1-containing nitrite reductase gene (nirS-NRB) were investigated in 18 municipal WWTPs distributed along a 3660-masl altitude gradient in China. An altitude threshold associated with the proportions of NRB to total bacteria, NRB to βAOB and nirK-NRB to nirS-NRB was detected at approximately 1500m above sea level (masl). Compared with the stable proportions below 1500masl, the proportions exhibited a pronounced decreasing trend with increased altitude above 1500masl. Spearman correlation analysis indicated that the trend was significantly driven by altitude as well as multiple wastewater and operational variables. The community structure dissimilarity of βAOB, nirK-NRB and nirS-NRB showed significant and positive correlations with altitudinal distance between WWTPs. Redundancy analyses indicated that the variation in community structures above 1500masl were predominantly associated with wastewater, followed by operation and altitude. In summary, although the variations of nitrogen-removal bacterial community in WWTPs were driven dominantly by wastewater and operational variables, altitude was also an important variable influencing the quantitative relationships and community structures of nitrogen-removal bacteria in WWTPs particularly above 1500masl.

Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond

Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.

Influence of edaphic, climatic, and agronomic factors on the composition and abundance of nitrifying microorganisms in the rhizosphere of commercial olive crops

The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety.