Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation

A comparative study: impact of chemical and biological fungicides on soil bacterial communities

Soil microbial communities play key roles in agroecosystems, particularly in processes like organic matter decomposition and nutrient cycling. However, human activities can negatively impact their community structure and, consequently, soil function. SoilGard and Ridomil are effective methods for controlling carrot cavity spots caused by Pythium spp., but their effects on bacterial taxonomic and metabolic function shifts are not well understood. This study aims to investigate the comparative impact of the chemical fungicide Ridomil and the biological fungicide SoilGard on the bacterial communities in soils cultivated with carrots. Our results showed that both SoilGard and Ridomil significantly impacted soil bacterial diversity, but their effects were distinct and time-dependent. Ridomil had an immediate negative effect on soil bacterial diversity two weeks after treatment, whereas SoilGard was initially less disruptive but showed delayed negative consequences 12 weeks after treatment, particularly when combined with Pythium inoculation. Ridomil treatment led to an increase in Proteobacteria, especially the Pseudomonas population, as confirmed by both MiSeq and qPCR data. In contrast, SoilGard depleted the Mycobacterium population at 12 weeks after treatment. Furthermore, the results of community-level physiological profiling using Biolog Ecoplates showed significant differences in substrate-level diversity between Ridomil and SoilGard-treated samples, indicating a shift in the metabolic activity of bacterial communities. Ridomil-treated samples showed the lowest metabolic activity of bacterial communities, based on the diversity and richness of carbon source utilization, compared to control. Overall, this research highlights the distinct and time-dependent effects of biological and chemical fungicides on soil bacterial communities when applied at recommended doses.

In-depth assessment of microbial communities in the full-scale vertical flow treatment wetlands fed with raw domestic wastewater

A multiphase study was proposed to examine microbial communities linked to the nitrogen cycle in the first stage of four full-scale French vertical flow treatment systems. To this end, denaturing gradient gel electrophoresis (DGGE) was performed for structural assessment and quantitative PCR (qPCR) to enumerate the abundance of ammonia-oxidizing (AOB). 16S rRNA sequencing was used to assess the taxonomic profile followed by putative assessment of functional genes. The samples were collected under different conditions, such as operational time (presence/absence of sludge layer on the surface of the filters), season (winter and summer), sampling depth (0, 15 and 30 cm) and operation cycle (rest and feed periods). A structural disparity was noted in the upper layers, whereas higher similarity at 30 cm was observed highlighting the effect of organic matter on bacterial diversity. The 7th rest day was highlighted by an apparent decline in the microbial community abundance. Additionally, qPCR indicated that the largest amount of AOB was found at 30 cm depth and during the feeding period. From the taxonomic profile, Mycobacterium, Acinetobacter, Flavobacterium, and Nitrospira were the most abundant genre found in all systems. The functional prediction results showed predicted genes linked to the denitrification process. The results suggested that operating time and season were responsible for the pattern of the microbial community behavior. This study allowed us to further understand the bacterial dynamics and to advance the idea of design modifications made in the first stage of the classical French system to improve nitrogen removal are promising.

Assessing the role of microbial communities in the performance of constructed wetlands used to treat combined sewer overflows

Combined sewer overflows are contaminated with various micropollutants which pose risk to both environmental and human health. Some micropollutants, such as carbamazepine and sulfamethoxazole, are very persistent and difficult to remove from wastewater. Event loaded vertical-flow constructed wetlands (retention soil filters; RSFs) have proven to be effective in the treatment of combined sewer overflows for a wide range of pollutants. However, little is known about how microbial communities contribute to the treatment efficiency, specifically to the reduction of micropollutants. To the best of our knowledge, this is the first study attempting to close this gap. Microbial communities in pilot-scale RSFs were investigated, which showed explicit grouping of metabolic activity at different filter depths with some differential abundance of identified genera. The highest microbial activity was found in the top layer of 0.75 m deep filters, whereas homogeneous activity dominated in a 0.50 m deep filter, indicating oxygen availability to be a limiting factor of the metabolic activity in RSFs. The removal efficiencies of all investigated organic trace substances were correlated to the utilization of specific carbon sources. Most notable is the correlation between the carbon source glucose-1-phosphate and the removal of metoprolol. The strongest correlations for other substances were the removal of diclofenac to the utilization of the carbohydrate i-erythritole; bisphenol A to carbohydrate α-d-lactose, and 1-H-benzotriazole to carbonic acid D-galacturonic acid. Those results are supported by positive correlations of specific microbial genera with both the utilization of the above mentioned carbon sources and the removal efficiency for the respective micropollutants. Most notable is correlation of Tetrasphaera and the removal of benzotriazole and diclofenac.

A high-throughput assay to quantify protein hydrolysis in aerobic and anaerobic wastewater treatment processes

Proteins, an important fraction of the organic matter in wastewater, typically enter a treatment facility as high molecular weight components. These components are degraded by extracellular protein hydrolytic enzymes, denoted as proteases. Adequate protein hydrolysis monitoring is crucial, since protein hydrolysis is often a rate-limiting step in wastewater treatment. However, current monitoring tools lack a high sample throughput and reliable quantification. Here, we present an improved assay for high-throughput protein hydrolysis rate measurements in wastewater treatment applications. A BODIPY FL casein model substrate was implemented in a microplate format for continuous fluorescent quantification. Case studies on a conventional and a high-rate aerobic municipal wastewater treatment plant and a lab-scale, two-stage, anaerobic reactor provided proof-of-concept. The assay presented in this study can help to obtain monitoring-based process insights, which will in turn allow improving biological performance of wastewater treatment installations in the future. KEY POINTS: • Protein hydrolysis is a crucial step in biological wastewater treatment. • Quantification of the protein hydrolysis rate enables in-depth process knowledge. • BODIPY FL casein is a suitable model substrate for a protein hydrolysis assay. • High sample throughput was obtained with fluorescent hydrolysis quantification. Graphical abstract.

Community level physiological profiling of microbial electrochemical-based constructed wetlands

The performance of constructed wetlands (CW) can be enhanced through the use of microbial electrochemical technologies like METland systems. Given its novelty, uncertainties exist regarding processes responsible for the pollutant removal and microbial activity within the systems. Genetic characterization of microbial communities of METlands is desirable, but it is a time and resource consuming. An alternative, is the functional analysis based on community-level physiological profile (CLPP), which allows to evaluate the diversity of microbial communities based on the carbon consumption patterns and derived indexes (average well color development - AWCD -, richness, and diversity). This study aimed to characterize the microbial community function of laboratory-scale METlands using the CLPP method. It encompassed the analysis of planted and non-planted set-ups of two carbon-based electroconductive materials (Coke-A and Coke-LSN) colonized with electroactive biofilms, and compared to Sand-filled columns. Variations in the microbial metabolic activity were found to depend on the characteristics of the material rather than to the presence of plants. Coke-A systems showed lower values of AWCD, richness, and diversity than Sand and Coke-LSN systems. This suggests that Coke-A systems provided more favorable conditions for the development of relatively homogeneous microbial biofilms. Additionally, typical parameters of water quality were measured and correlations between utilization of carbon sources and removal of pollutants were established. The results provide useful insight into the spatial dynamics of the microbial activity of METland systems.

Development and evaluation of a mechanistic model to assess the fate and removal efficiency of hydrophobic organic contaminants in horizontal subsurface flow treatment wetlands

A mechanistic model for assessing the fate and removal efficiency of hydrophobic organic contaminants in horizontal subsurface flow treatment wetlands was developed and evaluated using empirical concentration data from Singapore's Lorong Halus Treatment Wetland. This treatment wetland consists of a series of horizontal subsurface flow reed beds. The model, calibrated for the Lorong Halus Treatment Wetland, provided an adequate description of the concentrations of nine neutral organic substances in water, rhizomes and emergent vegetation in the wetland. The model was applied to investigate the sensitivity of the contaminant removal efficiency to environmental conditions and physicochemical properties of contaminants that enter the wetland. The water-budget of the wetland was found to exhibit an important influence on both the mass-removal efficiency and reduction of contaminant concentrations that can be achieved through wetland treatment. The model illustrated that removal pathways of organic contaminants in the wetland varied as a function of the properties of the contaminants. The mass-removal efficiency of the treatment wetland was greatest for chemicals with a log K_OW between 3.0 and 5.0 and log K_AW > -1.0. Removal of contaminants through volatilization was found to be greatest for substances with a log K_OW between 3 and 5 and log K_AW > 0. Transpiration flux in vegetation was found to be most important for substances with a log K_OW between 4.5 and 5.5 and a log K_AW between -5.0 and 0.0. Biotransformation rates of the contaminants in the wetland media play a crucial role in the removal of contaminants from wastewater. The model provides a tool for assessing the removal capacity of treatment wetlands for neutral organic contaminants and evaluating trade-offs in the design and operation of a horizontal subsurface flow treatment wetland.

Community-Level Physiological Profiling for Microbial Community Function in Broiler Ceca

Poultry production is a major agricultural output worldwide. It is known that the gut health of broilers is essential for their growth and for providing wholesome products for human consumption. Previously, the microbial diversity of broiler ceca was studied at the genetic level. However, the functional diversity and metabolic activity of broiler cecal bacterial communities are not fully investigated. Recently, the EcoPlates™ from Biolog, Inc. have been used for characterizing bacterial communities from various environments. In this study, we applied these plates to physiologically profile cecal bacterial communities in broilers. The ceca were aseptically excised from 6-week-old broilers, and their contents were suspended in phosphate buffered saline. The cultures in the EcoPlates™ were incubated at 42 °C for 5 days in an OmniLog^® system. Responses of the bacterial communities to the various chemicals as carbon sources were measured on formazan production. The results show sigmoidal growth curves with three phases in all 12 cecal samples. Cecal bacterial communities could not use 11 carbon substrates for carbon sources; instead, they used pyruvic acid methyl ester, glycogen, glucose-1-phosphate and N-acetyl-D-glucosamine most frequently. Each bacterial community metabolized various numbers of the substrates at different rates among broilers. In the future, modification of the culture conditions to mimic the gut environment is needed. More investigations on the effects of nutrients, Salmonella or Campylobacter on physiological functions of cecal bacterial communities will provide insights into the improvement of animal well-being, saving production expenditures for producers and providing safer poultry products for human consumption.

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress

The modification of rhizosphere microbial diversity and ecological processes are of rising interest as shifting in microbial community structure impacts the mutual role of host-microbe interactions. Nevertheless, the connection between host-microbial community diversity, their function under biotic stress in addition to their impact on plant performances is poorly understood. The study was designed with the aim to analyze the tripartite interactions among Chitiniphilus sp., Streptomyces sp. and their combination with indigenous rhizospheric microbial population of Bacopa monnieri for enhancing the plant growth and bacoside A content under Meloidogyne incognita stress. Overall, plants treated with the microbial combination recorded enhanced growth as illustrated by significantly higher biomass (2.0 fold), nitrogen uptake (1.8 fold) and bacoside A content (1.3 fold) along with biocontrol efficacy (58.5%) under nematode infected field. The denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S-rDNA revealed that microbial inoculations are major initiators of bacterial community structure in the plant rhizosphere. Additionally, the plants treated with microbial combination showed maximum diversity viz., Shannon's (3.29), Margalef's (4.21), and Simpson's (0.96) indices. Likewise the metabolic profiling data also showed a significant variation among the diversity and evenness indices upon microbial application on the native microflora. We surmise that the application of beneficial microbes in combinational mode not only helped in improving the microbial community structure but also successfully enhanced plant and soil health under biotic stress.

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant

To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water. Both microbial activity and bacterial diversity during the treatment process showed obvious spatial variation, with higher levels observed during the dry season and lower levels during the wet season. Clustering analysis and principal component analysis indicated dramatic shifts in the bacterial community after chlorination, suggesting that chlorination was highly effective at influencing the bacterial community. The bacterial community structure of finished water primarily comprised Pseudomonas, Citrobacter, and Acinetobacter, and interestingly showed high similarity to biofilms on granular activated carbon. Additionally, the abundance of bacterial communities was relatively stable in finished water and did not change with the season. A large number of unique operational taxonomic units were shared during treatment steps, indicating the presence of a diverse core microbiome throughout the treatment process. Opportunistic pathogens, including Pseudomonas, Acinetobacter, Citrobacter, Mycobacterium, Salmonella, Staphylococcus, Legionella, Streptococcus and Enterococcus, were detected in water including finished water, suggesting a potential threat to drinking-water safety. We also detected bacteria isolated from each treatment step using the pure-culture method. In particular, two isolates, identified as Mycobacterium sp. and Blastococcus sp., which belong to the phylum Actinobacteria, were obtained from finished water during the dry season. Together, these results provided evidence of spatial and temporal variations in DWTPs and contributed to the beneficial manipulation of the drinking water microbiome.

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen

Microbial degradation is an important pathway during the removal of pharmaceuticals in constructed wetlands (CWs). However, the effects of CW design, plant presence, and different plant species on the microbial community in CWs have not been fully explored. This study aims to investigate the microbial community metabolic function of different types of CWs used to treat ibuprofen via community-level physiological profiling (CLPP) analysis. We studied the interactions between three CW designs (unsaturated, saturated and aerated) and six types of mesocosms (one unplanted and five planted, with Juncus, Typha, Berula, Phragmites and Iris) treating synthetic wastewater. Results show that the microbial activity and metabolic richness found in the interstitial water and biofilm of the unsaturated designs were lower than those of the saturated and aerated designs. Compared to other CW designs, the aerated mesocosms had the highest microbial activity and metabolic richness in the interstitial water, but similar levels of biofilm microbial activity and metabolic richness to the saturated mesocosms. In all three designs, biofilm microbial metabolic richness was significantly higher (p < .05) than that of interstitial water. Both the interstitial water and biofilm microbial community metabolic function were influenced by CW design, plant presence and species, but design had a greater influence than plants. Moreover, canonical correlation analysis indicated that biofilm microbial communities in the three designs played a key role in ibuprofen degradation. The important factors identified as influencing ibuprofen removal were microbial AWCD (average well color development), microbial metabolic richness, and the utilization of amino acids and amine/amides. The enzymes associated with co-metabolism of l-arginine, l-phenyloalanine and putrescine may be linked to ibuprofen transformations. These results provide useful information for optimizing the operational parameters of CWs to improve ibuprofen removal.

The metabolic footprint of the airway bacterial community in cystic fibrosis

BACKGROUND

Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF.

METHODS

Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity.

RESULTS

Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity.

CONCLUSIONS

The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic footprint of the CF airway bacterial community. This method may be useful to study the CF microbial community over time and with changes in disease state.