Soil microbiome feedback to climate change and options for mitigation.

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO2 and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

Topsoil microbial community structure responds to land cover type and environmental zone in the Western Pacific region.

Soil encompasses diverse microbial communities that are essential for fundamental ecosystem functions such as biogeochemical cycling. To better understand underlying biogeochemical processes, it is necessary to know the structure of soil archaeal and bacterial communities and their responses to edaphic and climate variables within and across various land cover types (LCTs) and environmental zones (ENZs). Here we sampled eighty-nine sites across five ENZs and four LCTs within the Western Pacific region. Through leveraging the second-generation sequencing of topsoil samples, we showed that α-diversity (taxonomic diversity) of archaea strongly varied within LCTs, whereas bacterial α-diversity was significantly controlled by both LCT and ENZ. Soil archaea and bacteria showed global niche differentiation associated with contrasting diversity responses to latitude and differential responses of microbial diversity patterns to edaphic and climate variables within LCTs and ENZs. In contrast to α-diversity, microbial ß-diversity (the compositional dissimilarity between sites) was majorly governed by ENZs, particularly for archaea (P < 0.01). Our results highlight the importance of LCTs and ENZs for understanding soil microbial contributions to nutrient dynamics and ecosystem resilience under land-use intensification and climate change.

Modeling Nitrogen Dynamics in a Waste Stabilization Pond System Using Flexible Modeling Environment with MCMC.

This study presents an approach for obtaining realization sets of parameters for nitrogen removal in a pilot-scale waste stabilization pond (WSP) system. The proposed approach was designed for optimal parameterization, local sensitivity analysis, and global uncertainty analysis of a dynamic simulation model for the WSP by using the R software package Flexible Modeling Environment (R-FME) with the Markov chain Monte Carlo (MCMC) method. Additionally, generalized likelihood uncertainty estimation (GLUE) was integrated into the FME to evaluate the major parameters that affect the simulation outputs in the study WSP. Comprehensive modeling analysis was used to simulate and assess nine parameters and concentrations of ON-N, NH3-N and NO3-N. Results indicate that the integrated FME-GLUE-based model, with good Nash-Sutcliffe coefficients (0.53-0.69) and correlation coefficients (0.76-0.83), successfully simulates the concentrations of ON-N, NH3-N and NO3-N. Moreover, the Arrhenius constant was the only parameter sensitive to model performances of ON-N and NH3-N simulations. However, Nitrosomonas growth rate, the denitrification constant, and the maximum growth rate at 20 °C were sensitive to ON-N and NO3-N simulation, which was measured using global sensitivity.

Effect of salinity on adsorption and desorption of paraquat in Pak Phanang river sediment, Thailand.

Batch experiments were conducted to study the effect of salinity (0-30 g L(-1)) on adsorption and desorption of paraquat (1, 1'-dimethyl-4, 4'-dipyridylium dichloride), one of the most widely used herbicides in the world, in sediment of Pak Phanang River Basin, Thailand. Sediments from five locations were used in the studies (two from freshwater sites and three sites under saline environment). The adsorption capacity (K(f)) of the sediments was positively correlated with CEC (r = 0.81**) and clay content (r = 0.70*). Paraquat adsorption by sediment was faster under fresh water (0 g L(-1)) versus saline conditions (10 and 20 g L(-1)). The adsorption coefficient (K(f)) at low salinity (0 g L(-1)) was 17,302 whereas the K(f) at 10 and 20 g L(-1) were 5,344 and 4,263, respectively. Paraquat desorption was greater at higher salinity, which is similar to the salinity of estuarine or seawater. Approximately 12-31 % of sorbed paraquat in fresh water and saline sediment (7.67 and 7.98 mg kg(-1)) were released when leaching with 20 g L(-1) salinity. The amount of paraquat released was in proportion to the amount sorbed. Results show that increases in salinity resulting from salt water intrusion from the lower estuary into the Pak Phanang River Basin would result in release of adsorbed paraquat from sediment into the water column.

Manganese doped zinc sulfide quantum dots for detection of Escherichia coli.

A novel biocompatible chitosan passivated manganese doped zinc sulfide (Mn doped ZnS) nanophosphor has been synthesized through a simple aqueous precipitation reaction. Upon excitation with ultraviolet light, the quantum dots (QDs) emit an orange luminescence peaking at 590 nm, which is visible to the naked eye. These chitosan coated Mn doped ZnS QDs can have potential applications in bio-labeling, particularly in fluorescence-based imaging. One of the envisioned applications of these QDs is in improving the conventional, organic dye-reliant Fluorescence in situ Hybridization (FISH) technique, a widely used method for microbial detection. Here we demonstrate that the chitosan-capped Mn doped ZnS QDs are suitable for this purpose.

Molecular techniques in ecohealth research toolkit: facilitating estimation of aggregate gastroenteritis burden in an irrigated periurban landscape.

Assessment of microbial hazards associated with certain environmental matrices, livelihood strategies, and food handling practices are constrained by time-consuming conventional microbiological techniques that lead to health risk assessments of narrow geographic or time scope, often targeting very few pathogens. Health risk assessment based on one or few indicator organisms underestimates true disease burden due a number of coexisting causative pathogens. Here, we employed molecular techniques in a survey of Cryptosporidium parvum, Giardia lamblia, Campylobacter jejuni, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio cholera, and Rotavirus A densities in canal water with respect to seasonality and spatial distribution of point-nonpoint pollution sources. Three irrigational canals stretching across nearly a 150-km(2) periurban landscape, traditionally used for agricultural irrigation but function as vital part of municipal wastewater stabilization in recent years, were investigated. Compiled stochastic data (pathogen concentration, susceptible populations) and literature-obtained deterministic data (pathogen dose-response model parameter values) were used in estimating waterborne gastroenteritis burden. Exposure scenarios include swimming or fishing, consuming canal water-irrigated vegetables, and ingesting or inhaling water aerosols while working in canal water-irrigated fields. Estimated annual gastroenteritis burden due individual pathogens among the sampling points was -10.6log(10) to -2.2log(10) DALYs. Aggregated annual gastroenteritis burden due all the target pathogens per sampling point was -3.1log(10) to -1.9log(10) DALYs, far exceeding WHO acceptable limit of -6.0log(10) DALYs. The present approach will facilitate the comprehensive collection of surface water microbiological baseline data and setting of benchmarks for interventions aimed at reducing microbial hazards in similar landscapes worldwide.

Zinc oxide nanorod mediated visible light photoinactivation of model microbes in water.

The inactivation of model microbes in aqueous matrix by visible light photocatalysis as mediated by ZnO nanorods was investigated. ZnO nanorods were grown on glass substrate following a hydrothermal route and employed in the inactivation of gram-negative Escherichia coli and gram-positive Bacillus subtilis in MilliQ water. The concentration of Zn(2+) ions in the aqueous matrix, bacterial cell membrane damage, and DNA degradation at post-exposure were also studied. The inactivation efficiencies for both organisms under light conditions were about two times higher than under dark conditions across the cell concentrations assayed. Anomalies in supernatant Zn(2+) concentration were observed under both conditions as compared to control treatments, while cell membrane damage and DNA degradation were observed only under light conditions. Inactivation under dark conditions was hence attributed to the bactericidal effect of Zn(2+) ions, while inactivation under light conditions was due to the combined effects of Zn(2+) ions and photocatalytically mediated electron injection. The reduction of pathogenic bacterial densities by the photocatalytically active ZnO nanorods in the presence of visible light implies potential ex situ application in water decontamination at ambient conditions under sunlight.

Evolution of N-converting bacteria during the start-up of anaerobic digestion coupled biological nitrogen removal pilot-scale bioreactors treating high-strength animal waste slurry.

Animal wastes have been successfully employed in anaerobic biogas production, viewed as a pragmatic approach to rationalize energy costs in animal farms. Effluents resulting from that process however are still high in nitrogen such that attempts were made to couple biological nitrogen removal (BNR) with anaerobic digestion (AD). The demand for organic substrate in such system is partitioned between the anaerobic metabolism in AD and the heterotrophic denitrification cascade following the autotrophic nitrification in BNR. Investigation of underlying N-converting taxa with respect to process conditions is therefore critical in optimizing N-removal in such treatment system. In this study, a pilot-scale intermittently aerated BNR bioreactor was started up either independently or in series with the AD bioreactor to treat high-strength swine waste slurry. The compositions of NH(3)-oxidizing bacteria (AOB), NO(2)(-)-oxidizing bacteria (NOB) and denitrifiers (nosZ gene) were profiled by polymerase chain reaction-capillary electrophoresis/single strand conformation polymorphism (PCR-CE/SSCP) technique and clone library analysis. Performance data suggested that these two process configurations significantly differ in the modes of biological N-removal. PCR-CE/SSCP based profiling of the underlying nitrifying bacteria also revealed the selection of distinct taxa between process configurations. Under the investigated process conditions, correlation of performance data and composition of underlying nitrifiers suggest that the stand-alone BNR bioreactor tended to favor N-removal via NO(3)(-) whereas the coupled bioreactors could be optimized to achieve the same via a NO(2)(-) shortcut.

N-removal performance and underlying bacterial taxa of upflow filter bioreactor system under different dissolved oxygen and internal recycle conditions.

Biological N-removal treatment of piggery wastewater in the upflow anaerobic-anoxic-aerobic floating filter (UA(3)FF) bioreactor based on the concept of nitritation-denitritation was studied along with the changes in internal recycle ratio and dissolved oxygen concentration (DO). Consecutive changes in the recirculation ratio between the anoxic and aerobic reactors has resulted in abundance and composition shifts of N-cycling bacteria as well as other bacterial groups, reflecting different survival strategies across (bio/physico)chemical milieu. The DO concentration was optimized to achieve nitritation in the aerobic reactor and denitritation in the anoxic reactor. Optimal nitritation-denitritation (270 and 130 g NO(2) (-)-N produced or reduced/m(3) filter media/day) was obtained at DO of 1.0-1.5 mg/l, inter-reactor recirculation ratio of 1:1-2:1, HRT of 24 h, pH of 7.6 +/- 0.3, and temperature of 28 +/- 4 degrees C. Since only well known nitrifying and denitrifying taxa were found, nitritation-denitritation was likely carried out by these bacteria rather than the yet unidentified novel taxa. Archaeal nitrifiers recently discovered to be important in the global N-cycle were not detected.

GIS-based analysis of the fate of waste-related pathogens Cryptosporidium parvum, Giardia lamblia and Escherichia coli in a tropical canal network.

Urban canals play a major socio-economic role in many tropical countries and, particularly, Thailand. One of the overlooked functions that they perform is a significant attenuation of waste-related pathogens posing considerable health risk, as well as pollution attenuation in general. The study dealt with a comparison of three canals receiving: (i) municipal, (ii) mainly industrial and (iii) mainly agricultural wastewater, listed in order of progressively decreasing organic loading. The occurrence and fate of waterborne Cryptosporidium parvum, Giardia lamblia and Escherichia coli were monitored in the canals by both real-time PCR and conventionally for 12 months. The pathogens are etiological agents of an estimated 38% and 47% of diarrhea cases worldwide and in Thailand, respectively. The geographic information system (GIS) was used to evaluate and map point and, particularly, non-point pollution sources which allowed differentiating the canal sections in terms of predominant pathogen sources. The flowthrough canals, which can be viewed as waste stabilization ponds, were found to be efficiently removing the pathogens at the following generalized specific rates: 0.3 (C. parvum), 1.2 (G. lamblia), 1.8 (E. coli) log10/km.d in the dry season. The rates decreased in the rainy season for E. coli and G. lamblia, but increased for C. parvum which indicated different removal mechanisms. Data suggest that E. coli and G. lamblia were mainly removed through sedimentation and sunlight (UV) irradiation, while the likely mechanism for C. parvum was predation. Overall, the specific pathogen removal rates positively correlated with the canal organic loading rates in the rainy season. As an important result, an estimate of the municipal pollution mitigation by over 2280 km canals in the Greater Bangkok suggests that concomitant to the pathogens at least 36-95 tons of BOD5 is being removed daily, thereby saving the receiving Chao Phraya River and Bight of Bangkok, by far exceeding current, from major eutrophication problems.

Infection risk assessment of diarrhea-related pathogens in a tropical canal network.

A quantitative microbial risk assessment (QMRA) of Cryptosporidium, Giardia and diarrhegenic Escherichia coli (DEC) infection was performed using Monte Carlo simulations to estimate the human health risks associated with the use of canal water for recreational purposes, unrestricted and restricted irrigation in a tropical peri-urban area. Three canals receiving municipal, agricultural, and, predominantly, industrial wastewater were investigated. Identification of pathogenic protozoans revealed the major presence of Cryptosporidium hominis and both assemblages A and B of Giardia lamblia. The highest individual infection risk estimate was found to be for Giardia in an exposure scenario involving the accidental ingestion of water when swimming during the rainy season, particularly in the most polluted section, downstream of a large wholesale market. The estimated annual risks of diarrheal disease due to infection by the protozoan parasites were up to 120-fold greater than the reported disease incidence in the vicinity of the studied district and the entire Thailand, suggesting a significant host resistance to disease beyond our model's assumptions. In contrast, annual disease risk estimates for DEC were in agreement with actual cases of diarrhea in the study area.

IMS-free DNA extraction for the PCR-based quantification of Cryptosporidium parvum and Giardia lamblia in surface and waste water.

Extremely limited knowledge exists on the occurrence of protozoan pathogens in surface and waste water in the developing world. The article addresses one of the major reasons for this: prohibitively costly immunomagnetic separation (IMS) and commercial DNA extraction kits are required for the pathogen detection. As the presence of inhibitory substances critically impedes the polymerase chain reaction (PCR)-based detection of Cryptosporidium and Giardia in environmental samples, several direct DNA extraction methods based on the combination of physico-chemical means were evaluated in terms of reducing the impact of PCR inhibitors present in (oo)cyst-spiked water concentrates. Modifications that included the use of guanidine thiocyanate as a lysis agent and a sonication step were found to be more efficient in extracting DNA from (oo)cysts, while treatment with Chelex 100 chelating resin at post-lysis proved to be effective in the removal of the PCR inhibitors rather than the inclusion of the PCR facilitators during thermocycling. Direct DNA extraction protocol at a substantially reduced cost is proposed for the use in the PCR-based detection/quantification of the pathogens.