Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil

Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.

Low levels of arsenic and cadmium in rice grown in southern Florida Histosols - Impacts of water management and soil thickness

Rice is planted as a rotation crop in the sugarcane-dominant Everglades Agricultural Area (EAA) in southern Florida. The Histosols in this area are unlike other mineral soils used to grow rice due to the high organic content and land subsidence caused by rapid oxidation of organic matter upon drainage. It remains unknown if such soils pose a risk of arsenic (As) or cadmium (Cd) mobilization and uptake into rice grain. Both As and Cd are carcinogenic trace elements of concern in rice, and it is important to understand their soil-plant transfer into rice, a staple food of global importance. Here, a mesocosm pot study was conducted using two thicknesses of local soil, deep (D, 50 cm) and shallow (S, 25 cm), under three water managements, conventional flooding (FL), low water table (LWT), and alternating wetting and drying (AWD). Rice was grown to maturity and plant levels of As and Cd were determined. Regardless of treatments, rice grown in these Florida Histolsols has very low Cd concentrations in polished grain (1.5-5.6 μg kg^-1) and relatively low total As (35-150 μg kg^-1) and inorganic As (35-87 μg kg^-1) concentrations in polished grain, which are below regulatory limits. This may be due to the low soil As and Cd levels, high soil cation exchange capacity due to high soil organic matter content, and slightly alkaline soil pH. Grain As was significantly affected by water management (AWD < FL = LWT) and its interaction effect with soil thickness (AWD-D ≤ AWD-S ≤ FL-D = LWT-S = LWT-D ≤ FL-S), resulting in as much as 62 % difference among treatments. Grain Cd was significantly affected by water management (AWD > FL > LWT) without any soil thickness impact. In conclusion, even though water management has more of an impact on rice As and Cd than soil thickness, the low concentrations of As and Cd in rice pose little health risk for consumers.

Changes in nitrogen and phosphorus within a decade in waters along a major canal and estuary in South Florida

The West Palm Beach-C51 (WPB-C51) canal connects Lake Okeechobee with Lake Worth Lagoon (LWL) in South Florida. This canal receives discharges from Lake Okeechobee and from agricultural and urbanized areas. The objectives of this research were to determine spatial and temporal differences and trends of N and P forms along the WPB-C51 canal and LWL for 2009-2019. Data were obtained from the South Florida Water Management District. Average total P (TP) and total N (TN) concentrations at studied stations ranged from 55 to 183 μg L^-1 and from 0.61 to 2.62 mg L^-1 , respectively. The TP and TN concentrations at LWL inflow were higher than the State of Florida's regulatory criteria (49 μg L^-1 and 0.66 mg L^-1 , respectively). The TP and TN concentrations generally declined from Lake Okeechobee to LWL; however, agricultural drainage was highest for soluble reactive P (SRP) and all N forms. Temporal trends showed predominantly increasing trends for concentrations of P forms. Total P and TN load rates increased by 0.005 and 0.032 t yr^-1 , respectively, at LWL inflow. Results suggest nutrient assimilation by plants and P precipitation along the WPB-C51 canal. Possible sources of SRP and N are fertilizers, nitrification, and organic matter mineralization. Increasing trends in P concentration are possibly due to legacy P and urbanization, and increases in TP and TN loads can be due to larger Lake Okeechobee discharges and higher nutrient concentrations. Results emphasize the need to implement strategies to minimize nutrient input into LWL to meet its water quality goals.

Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

Yuck! Plural Valuation of Constructed Wetland Maintenance for Decentralized Wastewater Treatment in Rural India

In 2012, an estimated 50% of rural households in India had a system of drainage for moving wastewater away from their homes, but 0.0% have access to safe, reuseable, treated wastewater. Constructed wetlands can provide decentralized wastewater treatment for rural villages and lead to multiple benefits, such as reusable water, reduced disease, and decreased environmental pollution. However, the maintenance of decentralized wastewater technologies is poorly understood. We used a case study design across four communities and six constructed wetlands to understand the social and cultural variables impacting the maintenance of constructed wetlands for decentralized wastewater treatment to provide agricultural irrigation water. Semi-structured interviews (n = 39) and focus groups (n = 4) were conducted with people from Telangana and Karnataka, India. Interviewees were classed into four groups: (1) Scientists, (2) Farmers, (3) Privileged Community Members, and (4) Socially Disadvantaged Community members. Inductive, constant comparison qualitative data analysis was used to develop a model for explaining the existing practice of wetland maintenance. Three themes emerged from the data: mental models of constructed wetland maintenance show plural valuation of ecosystem services, yuck as a leverage point for decreasing social cohesion in the community, and recommendations for improving maintenance through human-centered design. Based on the results, we propose a model for understanding how to incorporate the plural valuation of ecosystem services provided by constructed wetlands and human-centered design to support long-term adoption and maintenance of decentralized wastewater treatment technologies.

Capturing Flow-weighted Water and Suspended Particulates from Agricultural Canals During Drainage Events

The purpose of this study is to describe the methods used to capture flow-weighted water and suspended particulates from farm canals during drainage discharge events. Farm canals can be enriched by nutrients such as phosphorus (P) that are susceptible to transport. Phosphorus in the form of suspended particulates can significantly contribute to the overall P loads in drainage water. A settling tank experiment was conducted to capture suspended particulates during discrete drainage events. Farm canal discharge water was collected in a series of two 200 L settling tanks over the entire duration of the drainage event, so as to represent a composite subsample of the water being discharged. Imhoff settling cones are ultimately used to settle out the suspended particulates. This is achieved by siphoning water from the settling tanks via the cones. The particulates are then collected for physico-chemical analyses.

Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea

The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH3 concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.

Modeling of phosphorus loads in sugarcane in a low-relief landscape using ontology-based simulation

Water flow and P dynamics in a low-relief landscape manipulated by extensive canal and ditch drainage systems were modeled utilizing an ontology-based simulation model. In the model, soil water flux and processes between three soil inorganic P pools (labile, active, and stable) and organic P are represented as database objects. And user-defined relationships among objects are used to automatically generate computer code (Java) for running the simulation of discharge and P loads. Our objectives were to develop ontology-based descriptions of soil P dynamics within sugarcane- (Saccharum officinarum L.) grown farm basins of the Everglades Agricultural Area (EAA) and to calibrate and validate such processes with water quality monitoring data collected at one farm basin (1244 ha). In the calibration phase (water year [WY] 99-00), observed discharge totaled 11,114 m3 ha(-1) and dissolved P 0.23 kg P ha(-1); and in the validation phase (WY 02-03), discharge was 10,397 m3 ha(-1) and dissolved P 0.11 kg P ha(-). During WY 99-00 the root mean square error (RMSE) for monthly discharge was 188 m3 ha(-1) and for monthly dissolved P 0.0077 kg P ha(-1); whereas during WY 02-03 the RMSE for monthly discharge was 195 m3 ha(-1) and monthly dissolved P 0.0022 kg P ha(-1). These results were confirmed by Nash-Sutcliffe Coefficient of 0.69 (calibration) and 0.81 (validation) comparing measured and simulated P loads. The good model performance suggests that our model has promise to simulate P dynamics, which may be useful as a management tool to reduce P loads in other similar low-relief areas.

Long-term water quality trends after implementing best management practices in South Florida

A mandatory best management practices (BMP) program was implemented in the Everglades Agricultural Area (EAA) farms basin-wide in 1995 as required by the Everglades Forever Act to reduce P loads in drainage water reaching the Everglades ecosystem. All farms in the EAA basin implement similar BMPs, and basin wide P load reductions have exceeded the 25% reduction required by law; however, differences remain in water quality between subbasins. Our objective was to determine long-term trends in P loads in discharge water in the EAA after implementing BMPs for 7 to10 yr and to explore reasons for differences in the performance of the subbasins. Two monitoring datasets were used, one from 10 research farms and the second from the EAA basin inflow and outflow locations. Mann-Kendall trend analysis was used to determine the degree of change in water quality trends. A decreasing trend in P loads was observed in general on sugarcane (Saccharum officinarum L.) farms, while mixed crop farms showed either decreasing or insignificant trends. The insignificant trends are probably related to management practices of mixed crop systems. Decreasing trends in P loads were observed in the outflow of the EAA basin, S5A, and S8 subbasins from 1992 to 2002. Inflow water from Lake Okeechobee had increasing P concentration from 1992 to 2006 with the highest trend in the east side of the lake. This analysis indicated there may be other factors impacting the success of BMPs in individual farms including cropping rotations and flooding of organic soils. Elevated P concentrations in Lake Okeechobee water used for irrigation may pose a future risk to degrade water quality on farms in the EAA, especially in the S5A subbasin.

Tree-based modeling of complex interactions of phosphorus loadings and environmental factors

Phosphorus (P) enrichment has been observed in the historic oligotrophic Greater Everglades in Florida mainly due to P influx from upstream, agriculturally dominated, low relief drainage basins of the Everglades Agricultural Area (EAA). Our specific objectives were to: (1) investigate relationships between various environmental factors and P loads in 10 farm basins within the EAA, (2) identify those environmental factors that impart major effects on P loads using three different tree-based modeling approaches, and (3) evaluate predictive models to assess P loads. We assembled thirteen environmental variable sets for all 10 sub-basins characterizing water level management, cropping practices, soils, hydrology, and farm-specific properties. Drainage flow and P concentrations were measured at each sub-basin outlet from 1992-2002 and aggregated to derive monthly P loads. We used three different tree-based models including single regression trees (ST), committee trees in Bagging (CTb) and ARCing (CTa) modes and ten-fold cross-validation to test prediction performances. The monthly P loads (MPL) during the monitoring period showed a maximum of 2528 kg (mean: 103 kg) and maximum monthly unit area P loads (UAL) of 4.88 kg P ha(-1) (mean: 0.16 kg P ha(-1)). Our results suggest that hydrologic/water management properties are the major controlling variables to predict MPL and UAL in the EAA. Tree-based modeling was successful in identifying relationships between P loads and environmental predictor variables on 10 farms in the EAA indicated by high R(2) (>0.80) and low prediction errors. Committee trees in ARCing mode generated the best performing models to predict P loads and P loads per unit area. Tree-based models had the ability to analyze complex, non-linear relationships between P loads and multiple variables describing hydrologic/water management, cropping practices, soil and farm-specific properties within the EAA.

Pyrosequencing enumerates and contrasts soil microbial diversity

Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26,140 to 53,533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52,000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%-12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.

Energetics of arsenate sorption on amorphous aluminum hydroxides studied using flow adsorption calorimetry

Flow adsorption calorimetry was used to investigate the energetics of arsenate sorption on amorphous aluminum hydroxide (AHO) and its effect on surface charge and ion exchange. Arsenate sorption at pH 5.7 was exothermic and the molar heats of adsorption were quite variable, ranging from -3.0 to -66 kJ/mol. Repetitive exposure of the same sample to arsenate in the calorimeter showed that the AHO was able to regenerate a considerable amount of reactive surface over time periods as short as 15 to 20 min. The large variability in heats of arsenate adsorption and the ability to regenerate reactive surface is believed to result from the amorphous nature of the AHO used. Heats of Cl/NO3 exchange were much smaller and more consistent, ranging from about 3.0 to 6.0 kJ/mol. The molar ratio of exchangeable Cl:Al was about 6:1 for the AHO, indicating a highly porous material. At pH 5.7, arsenate sorption neutralized surface positive charge as measured by Cl/NO3 exchange. Only at the two highest loadings (>60,000 mg/kg) did arsenate sorption result in any negative surface charge as measured by Na/K exchange. These results showed that most of the arsenate was adsorbed by a mechanism that involved no increase in surface negative charge. The PZNC of the AHO decreased by about 1 pH unit when exposed to arsenate in the flow calorimeter. Exposure to arsenate in a batch system decreased the PZNC about 4 pH units. This difference in behavior between batch and flow systems was related to differences in the amount of arsenate adsorbed.

Specific conductance and ionic characteristics of farm canals in the everglades agricultural area

Specific conductance in farm canals of the Everglades Agricultural Area (EAA) in south Florida is an important water quality parameter that was categorized as a parameter of concern according to an observed frequency of >5% excursions over the Class III water quality criterion and needed to be addressed as a part of the Everglades Regulatory Program. This study was conducted to evaluate specific conductance in farm canals of the EAA. Specific conductance was monitored at 10 representative farms (a total of 12 pump stations) in the EAA using multi-parameter water quality data loggers, for periods ranging from 24 to 83 mo. Cation and anion concentrations were also determined. Nonparametric Mann-Kendall trend analyses and Sen's slope analysis of specific conductance were conducted to determine specific conductance trends. Mean specific conductance ranged from 0.74 to 1.68 dS m(-1) and only 2 of the 10 farms were above the State Class III water quality criterion of 1.275 dS m(-1). Statistically significant downward trends were observed at 3 of the 10 farms. Determination of ion compositions in grab samples at 8 of the 10 farms indicated that the major ions contributing to the increase in specific conductance in the EAA were Cl-, HCO3-, and Na+. Mean Na/Cl ratios in most of the EAA canals ranged from 0.57 to 0.78, whereas those of SO4/Cl ranged from 0.46 to 0.98. Investigation of historical data and literature indicates that elevated specific conductance in parts of the EAA is a natural phenomenon due to entrapment of connate seawater in the Everglades formation. Sulfur contributes minor increases in specific conductance in the EAA with probable sources from organic soil mineralization, ground water, Lake Okeechobee, and S fertilizers.