Riparian Zone Soil Research Articles

Occurrence Characteristics of Microplastics in Multi-environmental Media and Bellamya aeruginosa of Manao River

Microplastic pollution poses threats to aquatic ecosystems and human health. In this study, in order to investigate the characteristics of microplastic occurrence in different environmental media, the abundance, particle size, shape, color, and composition types of microplastics in the water column, sediment, riparian zone soil, and the benthic snail Bellamya aeruginosa of the Manao River were analyzed using field sampling, microscopic observation, and Fourier infrared spectroscopy. The results showed that the average abundance of microplastics in the surface water of the Manao River was (5.9±0.26) n·L-1; the abundance of microplastics in the upper sediment (by dry weight) was (1.35±0.1) n·g-1, and that in the lower sediment (by dry weight) was (0.93±0.12) n·g-1. The abundance of microplastics in the near riparian zone soil (by dry weight) was (0.68±0.16) n·g-1, and that in the far riparian zone soil (by dry weight) was (0.69±0.14) n·g-1, and the abundance of microplastics in the B. aeruginosa was (2.06±0.25) n·g-1. The analysis results showed that the abundance of microplastics in the upper and lower sediments were positively correlated; the abundance of microplastics in B. aeruginosa was positively correlated with the abundance of microplastics in the upper and lower sediments, respectively; and the abundance of microplastics in the near and far riparian zone soils were also correlated. Most of the microplastics within each environmental medium and B. aeruginosa were <0.1 mm in size, mainly in the form of fibers and fragments, mainly blue and black in color, and mainly composed of polypropylene (PP) and polyethylene (PE). It was found that microplastics in riparian zone soils mainly originated from the fragmentation and decomposition of agricultural plastic films. The results of this study shed light on the accumulation of microplastics in macrobenthic organisms through the investigation of microplastics in multi-environmental media and in the B. aeruginosa, which helps us to understand the potential ecological risk of microplastics in a comprehensive manner.

Impacts of Acetochlor on Nitrogen-Cycling-Related Microbial Communities in Riparian Zone Soils

The riparian zone has a proven ability to reduce agricultural nonpoint-source nitrogen pollution. However, prior studies have only assessed nitrification and denitrification and their influencing factors, such as hydrology, climate, vegetation, and soil physicochemical properties, and overlooked the role of pesticide accumulation, which is an important nonpoint-source anthropogenic pollutant. This study investigated the response of the soil microbial nitrogen cycle in riparian zones to 60 days of acetochlor (ACE) exposure at doses of 0.5, 2.5, and 5.0 mg/kg. The results showed that ACE inhibited the transformation of soil NH3-N, NO3−-N, and NO2−-N and also decreased potential nitrification and denitrification rates by affecting the respective enzyme activities and related microbial communities. Metagenomic sequencing revealed that the expression of functional genes associated with NO3−-N transformation processes, including denitrification, dissimilatory nitrate reduction to ammonium, and assimilatory nitrate reduction, declined the most. The recommended field dose (0.5 mg/kg) showed a slight effect on soil microbial nitrogen transformation and the related microbial communities, whereas doses 5 and 10 times the recommended dose were highly inhibitory. This is a novel study exploring the effects of ACE on the microbial nitrogen cycle in riparian soils, also suggesting that pesticide accumulation in riparian zones could affect the health of aquatic ecosystems.

Hydrological connectivity affects nitrogen migration and retention in the land‒river continuum

Land use change and excessive nitrogen (N) loading threaten the health of receiving water bodies worldwide. However, the role of hydrological connectivity in linking watershed land use, N biogeochemistry and river water quality remain unclear. In this study, we investigated 15 subwatersheds in the Jiulong River watershed (southeastern China) during a dry baseflow period in 2018, combined with 3‒year (2017–2019) nutrient monitoring in 5 subwatersheds to explore river N dynamics (dissolved nutrients, dissolved gases and functional genes) and their controlling factors at three hydrological connectivity scales, i.e., watershed, hydrologically sensitive areas (HSAs) and riparian zone. The results show that land use at HSAs (less than 20% of watershed area) and watershed scales contributed similarly to river N variation, indicating that HSAs are hotspots for transporting land N into river channels. In particular, the agricultural land was the main factor affecting river nitrate and nitrous oxide (N2O) concentrations, while the built–up land significantly affected river ammonium and nitrite. At the riparian zone scale, soils and sediments substantially influenced river N retention processes (i.e., nitrification and denitrification). Management and protection measures targeting HSAs and riparian zones are expected to efficiently reduce river N loading and improve water quality.

Characterization and risk assessment of metals in surface sediments and riparian zone soils of Liaohe River, China

Characterization and risk assessment of metals in surface sediments and riparian zone soils were studied in Liaohe River, northeast China. Surface sediment and riparian soil samples were collected from 24 monitoring sites along 538 km of Liaohe River. Metal concentrations and enrichment factors of Zn, Cr, Pb, Cu, Ni, and As were analyzed. Potential sources of metal contaminants along with ecological risk assessment and health risk via ingestion, inhalation, and dermal contact for residents were also assessed. Metal concentrations followed the order Cr > Zn > Cu > Ni > As > Pb in surface sediments, and Cr > Zn > Cu > Ni > Pb > As in riparian zone soils. The degree of metal pollution in Liaohe River sediments and riparian soils was considered moderate and is showing signs of recovery compared to historical concentrations reported previous studies. Enrichment factors also indicated metal pollution was not severe in both riparian and river sediments and were mainly derived from natural sources. Children had significantly higher health risks along the Liaohe River, and oral ingestion was the dominant exposure pathway. The major non-carcinogenic metal was Cr, and As was the main carcinogenic metal. Although carcinogenic and non-carcinogenic health risks of metals were considered low for both children and adults along the Liaohe River, future monitoring of metal contaminants, especially for As and Cr is recommended.

The Ecological Relationship of Groundwater–Soil–Vegetation in the Oasis–Desert Transition Zone of the Shiyang River Basin

Groundwater is an important ecological water source in arid areas. Groundwater depth (GWD) is an important indicator that affects vegetation growth and soil salinization. Clarifying the coupling relationship between vegetation, groundwater, and soil in arid areas is beneficial to the prevention of environmental problems such as desertification and salinization. Existing studies lack research on the water–soil–vegetation relationship in typical areas, especially in shallow groundwater areas. In this study, the shallow groundwater area in Minqin, northwest China, was taken as study area, and vegetation surveys and soil samples collection were conducted. The relationships between vegetation fractional coverage (VFC) and GWD, soil salinity, soil moisture, and precipitation were comprehensively analyzed. The results showed low soil salinity in the riparian zone and high soil salinity in other shallow-buried areas with salinization problems. Soil salinity was negatively correlated with VFC (R = −0.4). When soil salinity &gt;3 g/kg, VFC was less than 20%. Meanwhile, when GWD &gt;10 m, VFC was usually less than 15%. In the areas with soil salinity &lt;3 g/kg, when GWD was in the range of 4–10 m, VFC was positively correlated with soil moisture content (R = 0.99), and vegetation growth mainly depended on surface soil water, which was significantly affected by precipitation. When GWD was less than 4 m, VFC was negatively correlated with GWD (R = −0.78), and vegetation growth mainly relied on groundwater and soil water. There are obvious ecological differences in the shallow-buried areas in Minqin. Hence, it is reasonable to consider zoning and grading policies for ecological protection.

A global meta-analysis shows soil nitrogen pool increases after revegetation of riparian zones

Sustainable management of riparian zone soils is required to ensure the health of natural ecosystems and maintenance of soil nitrogen (N) pools and soil N cycling. However, the effect of revegetation type and age on soil N pools remains poorly understood. This study compiled data from published articles to understand the effects of revegetation types and age on soil total N (TN) and soil inorganic N (NH4+-N, and NO3−-N) using a meta-analysis. We extracted 645 observations from 52 published scientific articles. The revegetation of riparian zones led to a significant increase of soil TN (mean effect size: 11.5%; 95% CI: 3.1% and 20.6%). Woodland increased soil TN significantly by 14.0%, which was associated with the presence of N fixing species and high litter inputs. Soil NH4+-N concentration significantly increased (mean effect size: 20.1%; 95% CI: 15.1% and 25.4%), whereas a significant decrease in soil NO3−-N (mean effect size: − 21.5%; 95% CI: − 15.0% and − 27.5%) was observed. Of the revegetation types considered in this paper, NO3−-N concentration in soil followed the order: grassland < shrubland < woodland, suggesting that woodland might be more efficient in soil NO3−-N retention than grassland. The high plant N uptake and accelerated NO3−-N leaching in grassland could be related to the decreased soil NO3−-N in grassland compared with other revegetation types. Revegetation significantly decreased soil moisture by (mean effect size: − 7.9%; 95% CI: − 3.3% and − 12.2%) compared with the control, which might be associated with the selection of exotic species as dominant vegetation in the riparian zone. Soil TN increased in revegetation ages between 10 and 40 years following revegetation and was related to increased soil organic carbon inputs within those ages following the establishment. This study provides insight into influence of different vegetation types and age on soil N pools and soil moisture. This study also highlights the importance of revegetation in riparian zones to increase soil TN.

Lack of methane hotspot in the upstream dam: Case study in a tributary of the Three Gorges Reservoir, China

River damming has seen a growing trend in demand worldwide and the impounded reaches are considered hotspots of greenhouse gas emissions. However, it remains unclear how the spatial distribution of C-gas in sediments and methane (CH4) emissions of dammed tributary changes under different operation periods of the Three Gorges reservoir (TGR). We measured CH4 and carbon dioxide (CO2) concentrations in sediment and CH4 emissions from a dammed river of the TGR, and evaluated the effect of damming on the spatial variability of carbon in the sediment and on CH4 flux. It was found that damming led to a distinct spatial pattern of total organic carbon (TOC) in the sediment, which resulted in higher CH4 and CO2 in upstream sediment compared to the downstream. During the TGR impounding period, the upstream CH4 diffusive flux (0.253–0.427 mg m−2 h−1) across the water-air interface was higher than in the downstream (0.093 mg m−2 h−1), which was consistent with the spatial variation of CH4 in the sediments. However, the CH4 emission was predominantly by ebullition and the flux in the downstream (169.173 mg m−2 h−1) was significantly higher than upstream (12.23–123.05 mg m−2 h−1) in the discharging period. This can be attributed to a sharp increase in TOC in downstream sediment due to riparian zone soil erosion on both banks, which was caused by periodic large fluctuation in the water level, and a shallow water depth in the downstream. This study adds to our understanding of effects of the TGR's operation on CH4 emissions from a dammed tributary and suggests that the water level fluctuation of tributaries which has direct influence on ebullition and methane oxidation caused by manipulation of the TGR should not be overlooked.

Insight into the Mechanism of Feammox in the Surface Soils of a Riparian Zone

Anaerobic ammonium oxidation coupled to iron (Ⅲ) reduction (termed Feammox) is a recently discovered pathway of nitrogen cycling. However, little is known about the pathways of N transformation via the Feammox process in riparian zones. In this study, evidence of Feammox in the riparian zone soil layers (0-20 cm) was demonstrated using the isotope tracing technique and a high-throughput sequencing technology. The results showed that Feammox occurred in the riparian zones in four different soil layers (A:0-5 cm, B:5-10 cm, C:10-15 cm, D:15-20 cm) and the Feammox rates ranged from 0.25 mg·(kg·d)-1 to 0.29 mg·(kg·d)-1. In the B soil sample, the Feammox rate was significantly higher than in the other soil samples (P<0.05). In addition, iron reducing bacteria played an essential role in the Feammox process, and Anaeromyxobacter and Geobacter were detected in all the soil samples. In the B soil sample, the abundance of iron reducing bacteria was significantly higher than in the other soil samples (P<0.05). Overall, the co-occurrence of ammonium oxidation and iron reduction suggest that Feammox can play an essential role in the pathway of nitrogen removal in riparian zones.

Denitrification Potential and Influencing Factors of the Riparian Zone Soils in Different Watersheds,Taihu Basin

In the recent decades, most rivers and lakes in the Taihu Basin have experienced degradation from an excess of nutrients. The presence of the nitrogen in water contributes to the increase of eutrophication. The riparian zones are associated with these watercourses and can effectively reduce any excess nitrogen. Soil denitrification is the most significant process in the transfer of nitrogen, which migrates from the terrestrial to the aquatic ecosystem. The relationship between soil denitrification and soil characteristics is well documented. However, the degree of soil denitrification and the main impact factors during different processes within the riparian zones due to gradual changes in the surroundings are not well understood. The present study selected four types of riparian soils that are contained in three different watersheds. The soil denitrification potential was determined within these soils using the acetylene block technique. The results indicate that, among the local factors studied, the soil denitrification potential increased with the intensity of anthropogenic activities, which varied significantly within the basin. This variation indicated a trend in the soil denitrification potential: cropland > woodland > grassland > bareland. Results suggest that soil moisture, nitrate-nitrogen concentration, and microbial biomass carbon concentration are the dominant factors that influence the riparian soil denitrification potential in the Tiaoxi watershed, while soil organic matter is the major factor for soil denitrification potential in the Hexi watershed and nitrate-nitrogen concentration is the dominant factor in the Tianmuhu watershed.

Denitrification potential of riparian soils in relation to multiscale spatial environmental factors: a case study of a typical watershed, China.

The objective of this study was to test the hypothesis that environmental regulators of riparian zone soil denitrification potential differ according to spatial scale within a watershed; consequently, a second objective was to provide spatial strategies for conserving and restoring the purification function of runoff in riparian ecosystems. The results show that soil denitrification in riparian zones was more heterogeneous at the profile scale than at the cross-section and landscape scales. At the profile scale, biogeochemical factors (including soil total organic carbon, total nitrogen, and nitrate-nitrogen) were the major direct regulators of the spatial distribution of soil denitrification enzyme activity (DEA). At the cross-section scale, factors included distance from river bank and vegetation density, while landscape-scale factors, including topographic index, elevation, and land use types, indirectly regulated the spatial distribution of DEA. At the profile scale, soil DEA was greatest in the upper soil layers. At the cross-section scale, maximum soil DEA occurred in the mid-part of the riparian zone. At the landscape scale, soil DEA showed an increasing trend towards downstream sites, except for those in urbanized areas.

Soil urease activity and bacterial ureC gene copy numbers: Effect of pH

Urea-N is ubiquitous in soils, having both natural and anthropogenic sources. The enzyme urease catalyzes its hydrolysis to NH3 and is produced by plants and many soil microorganisms, but there are growing concerns related to possible urea-induced eutrophication of surface waters proximate to agricultural fields. Agronomic research has focused on the relationship between urea hydrolysis and soil physical or chemical properties, rather than on direct measurements of the microbial community and its population diversity, especially using quantification of genes that code for urease. We quantified bacterial and archaeal 16S rRNA, fungal ITS, and bacterial ureC gene copies as a function of physical and chemical soil properties. Soils were sampled from A and B horizons along a toposequence that comprised an agricultural field, a grassed field border, and a forested riparian zone in the Chesapeake Bay watershed of Maryland. The riparian zone soils contained the highest total number of genes among both A- and B-horizon soils. The soils were then experimentally altered in the laboratory to achieve a range of pH values between 3.1 and 7.1. Soil pH was chosen as a variable because it varies both naturally and due to agronomic practices, and it influences microbial community structure and function. Archaeal 16S rRNA extracted from the pH-adjusted soils did not show a consistent pattern of increase or decrease with changes in pH, while ITS was greatest at low pH and bacterial 16S and bacterial ureC were greatest at high pH. We measured higher urea hydrolysis rates and gene copy numbers in A-horizon soils than in B-horizon soils, and found that urea hydrolysis rate was significantly correlated with gene copies of bacterial 16S, ureC, and increased pH. This suggests that liming acid soils increases urea hydrolysis rates in part by encouraging the growth of microorganisms capable of producing urease.

Effects of forested floodplain soil properties on phosphorous concentrations in two Chesapeake Bay sub-watersheds, Virginia, USA.

Aquatic ecosystems are known to undergo fluctuations in nutrient levels as a result of both natural and anthropogenic processes. Changes in both extrinsic and intrinsic fluvial dynamics necessitate constant monitoring as anthropogenic alterations exert new pressures to previously stable river basins. In this study, we analyzed stream water and riparian zone soil phosphorous (P) dynamics in two third-order sub-watersheds of the lower Chesapeake Bay in Virginia, USA. The Ni River is predominantly forested (70% forested), and Sugarland Run is a more human impacted (>45% impervious surfaces) sub-watershed located in the suburbs of Washington D.C. Total stream P concentrations were measured during both high and low flows and Mehlich-3 methods were used to evaluate potential P fluxes in riparian soils. The results show total stream P concentrations in Sugarland Run ranged from 0.002 to 0.20ppm, with an average of 0.054ppm. In contrast, the forested Ni River had typical stream P concentrations <0.01ppm. Total soil P was significantly higher in the more urbanized Sugarland Run basin (23.8 ± 2.1ppm) compared to the Ni River basin (16 ± 3.7ppm). Average stream bank erosion rates and corresponding cut-bank P flux rates were estimated to be 7.98cmyear(-1) and 361kg P year(-1) for Ni River and 9.84cmyear(-1) and 11,600kg P year(-1) for Sugarland Run, respectively. The significantly higher values of total P in the stream water and floodplain cut-banks of Sugarland Run suggests erosion and resuspension of previously deposited legacy sediments is an important processes in this human-impacted basin.

Nitrate contamination of groundwater in the western Po Plain (Italy): the effects of groundwater and surface water interactions

This study aims to investigate the physical and chemical effects of interactions between groundwater and surface water (GW–SW)—particularly in streams—on nitrate contamination. The effects of GW–SW interactions are briefly reviewed, with a particular emphasis on processes and environments that influence increases or decreases in nitrate concentration. Then, this paper analyses nitrate concentrations in groundwater and surface water in the western Po plain (Northwestern Italy); this analysis includes the nitrate concentration profiles across the shallow aquifer and intersecting the main streams on the plain. The investigation highlights how the concentration trends are similar, even when nitrate levels in rivers and groundwater are not comparable. The maximum nitrate concentrations in the surface water were generally measured in areas with high-nitrate levels in groundwater. An analysis of the nitrate concentration profiles highlighted the mutual influences of GW–SW. The most important streams on the plain (the Po River and Stura di Demonte River), both of them gaining streams, seem to reduce the nitrate concentrations of groundwater at a study scale. The proposed conceptual model indicates how the near-stream environment (the riparian zone, wetlands, hyporheic zone and shallow organic-rich soils in the near-stream environment) and the groundwater flow systems in shallow and deep aquifers, from the recharge zone to the streams, could dramatically affect the nitrate concentrations.

Urea Hydrolysis Rate in Soil Toposequences as Influenced by pH, Carbon, Nitrogen, and Soluble Metals.

A simultaneous increase in the use of urea fertilizer and the incidence of harmful algal blooms worldwide has generated interest in potential loss pathways of urea from agricultural areas. The objective of this research was to study the rate of urea hydrolysis in soil profile toposequences sampled from the Coastal Plain (CP) and Piedmont (PM) regions of Maryland to understand native urea hydrolysis rates (UHRs) as well as the controls governing urea hydrolysis both across a landscape and with depth in the soil profile. A pH-adjustment experiment was conducted to explore the relationship between pH and urea hydrolysis because of the importance of pH to both agronomic productivity and microbial communities. Soils were sampled from both A and B horizons along transects containing an agricultural field (AG), a grassed field border (GB), and a perennially vegetated zone adjacent to surface water. On average, the A-horizon UHRs were eight times greater than corresponding B-horizon rates, and within the CP, the riparian zone (RZ) soils hydrolyzed urea faster than the agricultural soils. The pH adjustment of these soils indicated the importance of organic-matter-related factors (C, N, extractable metals) in determining UHR. These results suggest that organic-matter-rich RZ soils may be valuable in mitigating losses of urea from neighboring fields. Additional field-scale urea hydrolysis studies would be valuable to corroborate the mechanisms described herein and to explore the conditions affecting the fate and transport of urea in agroecosystems.

Influence of streambank fencing and river access for cattle on riparian zone soils adjacent to the Lower Little Bow River in southern Alberta, Canada

Miller, J. J., Curtis, T., Chanasyk, D. S. and Willms, W. D. 2014. Influence of streambank fencing and river access for cattle on riparian zone soils adjacent to the Lower Little Bow River in southern Alberta, Canada. Can. J. Soil Sci. 94: 209–222. Cattle grazing in riparian pastures adjacent to rivers may increase soil compaction and increase soil nutrients, such as N and P. We conducted a 4-yr study with sampling in 3 yr (2009, 2010, 2012) of riparian zone soils adjacent to fenced and unfenced reaches of the Lower Little Bow River in southern Alberta. We examined the effect of grazing, access of cattle to the river (access versus no-access), and distance (0.25, 1, 2, 4, 6, 8, 10 m) from the river on surface soil bulk density, volumetric water content, NH4-N, NO3, and soil test P. Penetration depth was also measured in 2012. The three grazing treatments consisted of one fenced reach (ungrazed treatment), one unfenced and grazed reach with high cattle impact (high-impact grazed treatment), and one unfenced and grazed reach with low cattle impact (low-impact grazed treatment). We hypothesized that soil compaction would be greater, soil nutrients would be enriched, and soil water content would be lower for grazed compared with ungrazed treatments, and that this same trend would occur for access compared with no-access locations. The soil properties in our study were generally significantly (P≤0.05) influenced by grazing, access, and distance from the riverbank. However, treatment effects were generally dependent on two- or three-way interactions with the other factors. Soil bulk density in 2009 and 2012 was 8 to 20% greater at access compared with no-access locations within 2 m of the riverbank, suggesting soil compaction by cattle was confined close to the wetter riverbank soils. Most soil properties generally supported our hypothesis of greater soil compaction and nutrient enrichment for unfenced compared with fenced reaches, as well as for access compared with no-access locations. The exceptions were soil water content and soil test P results that did not support the grazing hypothesis, and soil water content and NH4-N results that did not support the cattle-access hypothesis.

Source and age of dissolved and gaseous carbon in a peatland–riparian–stream continuum: a dual isotope (14C and δ13C) analysis

Radiocarbon isotopes are increasingly being used to investigate the age and source of carbon released from peatlands. Here we use combined 14C and δ13C measurements to determine the isotopic composition of soil and soil decomposition products [dissolved organic carbon (DOC), CO2 and CH4] in a peatland–riparian–stream transect, to establish the isotopic signature and potential connectivity between carbon pools. Sampling was conducted during two time periods in 2012 to investigate processes under different temperature, hydrological and flux conditions. Isotopic differences existed in the peatland and riparian zone soil organic matter as a result of the riparian depositional formation. The peatland had a mean radiocarbon age of 551 ± 133 years BP, with age increasing with depth, and δ13C values consistent with C3 plant material as the primary source. In contrast the riparian zone had a much older radiocarbon age of 1,055 ± 107 years BP and showed no age/depth relationship; δ13C in the riparian zone was also consistent with C3 plant material. With the exception of DOC in September, soil decomposition products were predominately >100 %modern with 14C values consistent with derivation from organic matter fixed in the previous 5 years. Emissions of CO2 and CH4 from the soil surface were also modern. In contrast, CO2 and CH4 evaded from the stream surface was older (CH4: 310–537 years BP, CO2: 36 years BP to modern) and contained a more complex mix of sources combining soil organic matter and geogenic carbon. The results suggest considerable vertical transport of modern carbon to depth within the soil profile. The importance of modern recently fixed carbon and the differences between riparian and stream isotopic signatures suggests that the peatland (not the riparian zone) is the most important source of carbon to stream water.

A critical re-evaluation of the prediction of alkalinity and base cation chemistry from BGS sediment composition data

The model of Begum et al. (2010) that predicts alkalinity and Ca and Mg concentrations in river water from available sediment composition data has been critically re-evaluated using an independent validation data set. The results support the hypothesis that readily available stream water sediment elemental composition data are useful for prediction of mean and minimum concentrations of alkalinity and Ca and Mg in river water throughout the River Derwent catchment in North Yorkshire without requiring land-use data inputs as stream water sediment composition reflects all aspects of the riparian zone soil system, including land-use. However, it was shown for alkalinity prediction that rainfall exerts a significant dilution effect and should be incorporated into the model in addition to flow path-weighted sediments Ca% and Mg%. The results also strongly suggest that in catchments with substantial rough moorland land-use neutralization of organic acids consumes alkalinity and this fact should be considered in any future development of the model.

Denitrifier community size, structure and activity along a gradient of pasture to riparian soils

Forested riparian zones may protect waterways from receiving excess N from adjacent agricultural lands by immobilizing N in plants or microbes, or through denitrification. If denitrified, excess N is emitted either as harmful nitrous oxide or benign N2 gas. Therefore the size, structure and activity of the denitrifying community may play important roles in determining the net effect of riparian zones on the overall environmental impact of excess agricultural N. We assessed the size and structure of prokaryotic denitrifying communities, measured soil physiochemical characteristics and estimated denitrification along a gradient of grazed dairy pasture to forested riparian zone buffering the Manawatu River in New Zealand. We assessed denitrifier community structure by T-RFLP of the nirS and nosZ genes. We assessed denitrifier community size by quantitative PCR (qPCR) of these genes and total bacterial numbers by qPCR of the ribosomal polymerase (rpoB) gene. Strong gradients in microbial biomass, gene abundances and potential denitrification were primarily driven by differences in soil texture between pasture and riparian zones, with smaller scale patterns in soil properties emerging among slope positions with each zone. We found that nirS and nosZ communities responded strongly, though sometimes independently, to these gradients. nosZ abundance and community structure were significantly correlated to large scale patterns edaphic characters that distinguished pasture and riparian zone soils, but were not significantly correlated to denitrifier activity. By contrast, nirS abundance responded in a unimodal fashion to soil texture, leading to strong patterns of abundance and community structure associated with the different slope positions. Furthermore, nirS community structure was significantly correlated to denitrification rates and end-products. Finally, we found that the evenness of denitrifying communities was uncorrelated denitrification parameters and was negatively correlated to the proportional abundance of denitrifiers. Taken together, our data suggest that small numbers of genotypes become dominant and drive higher rates of denitrification in favourable ‘hotspots’ in the toe-slopes of pastures. Conversely, the low overall community evenness and low proportional abundance of complete denitrifiers in the riparian zone soils suggested a limited capacity for riparian buffers to remove excess N through denitrification and a propensity for incomplete denitrification to lead to N2O emissions. These results contribute to our understanding of the role of riparian zones determining the fate of excess agricultural N and highlight the importance of careful N management especially in pastures that occur on coarse textured soils.

Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples

Longer sequences of the bacterial 16S rRNA gene could provide greater phylogenetic and taxonomic resolutions and advance knowledge of population dynamics within complex natural communities. We assessed the accuracy of a Pacific Biosciences (PacBio) single molecule, real time (SMRT) sequencing based on DNA polymerization, a promising 3rd generation high-throughput technique, and compared this to the 2nd generation Roche 454 pyrosequencing platform. Amplicons of the 16S rRNA gene from a known isolate, Shewanella oneidensis MR1, and environmental samples from two streambed habitats, rocks and sediments, and a riparian zone soil, were analyzed. On the PacBio we analyzed ~500bp amplicons that covered the V1–V3 regions and the full 1500bp amplicons of the V1–V9 regions. On the Roche 454 we analyzed the ~500bp amplicons. Error rates associated with the isolate were lowest with the Roche 454 method (2%), increased by more than 2-fold for the 500bp amplicons with the PacBio SMRT chip (4–5%), and by more than 8-fold for the full gene with the PacBio SMRT chip (17–18%). Higher error rates with the PacBio SMRT chip artificially inflated estimates of richness and lowered estimates of coverage for environmental samples. The 3rd generation sequencing technology we evaluated does not provide greater phylogenetic and taxonomic resolutions for studies of microbial ecology.

Microbial Community Structure Across a Wastewater-Impacted Riparian Buffer Zone in the Southeastern Coastal Plain

Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.