Community-level physiological profiling

Enhanced retention of hydrophobic pesticides in subsurface soils using organic amendments

The rapid global population growth since the early 2000s has significantly increased the demand for agricultural products, leading to widespread pesticide use, particularly organophosphorus pesticides (OPPs). This extensive application poses severe environmental risks by contaminating air, soil, and water resources. To protect groundwater quality, it is crucial to understand the transport and fate of these pesticides in soil and sediment. This study investigates the effects of hydrochars and biochars derived from sugar beet shreds (SBS) and Miscanthus×giganteus (MIS) on the retardation and biodegradation of OPPs in alluvial Danube sandy soil. The research is novel in its approach, isolating native OPP-degrading bacteria from natural alluvial sandy soil, inoculating them onto chars, and reapplying these bioaugmented chars to the same soil to enhance biodegradation and reduce pesticide leaching. The amendment of chars with immobilized Bacillus megaterium BD5 significantly increased bacterial abundance and activity. Metabarcoding of the 16S rRNA gene revealed a dominance of Proteobacteria (48.0-84.8 %) and Firmicutes (8.3-35.6 %). Transport modeling showed retardation coefficients (Rd) for OPPs ranging from 10 to 350, with biodegradation rates varying between 0.05 % and 75 %, indicating a positive correlation between retardation and biodegradation. The detection of biodegradation byproducts, including derivatives of phosphin, pyridine, and pyrazole, in the column leachate confirmed that biodegradation had occurred. Additionally, principal component analysis (PCA) revealed positive correlations among retardation, biodegradation, specific surface area (SSA), aldehyde/ketone groups, and bacterial count. These findings demonstrate the potential of biochar and hydrochar amendments to enhance OPP immobilization in contaminated soils, thereby reducing their leaching into groundwater. This study offers a comprehensive approach to the remediation of pesticide-contaminated soils, advancing both our fundamental understanding and the practical applications of environmental remediation techniques.

Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity

Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.

Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region

Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.

Structural and functional spatial dynamics of microbial communities in aerated and non-aerated horizontal flow treatment wetlands

A multiphasic study using structural and functional analyses was employed to investigate the spatial dynamics of the microbial community within five horizontal subsurface flow treatment wetlands (TWs) of differing designs in Germany. The TWs differed in terms of the depth of media saturation, presence of plants (Phragmites australis), and aeration. In addition to influent and effluent water samples, internal samples were taken at different locations (12.5 %, 25 %, 50 %, and 75 % of the fractional distance along the flow path) within each system. 16S rRNA sequencing was used for the investigation of microbial community structure and was compared to microbial community function and enumeration data. The microbial community structure in the unaerated systems was similar, but different from the aerated TW profiles. Spatial positioning along the flow path explained the majority of microbial community dynamics/differences within this study. This was mainly attributed to the availability of nutrients closer to the inlet which also regulated the fixed biofilm/biomass densities. As the amount of fixed biofilm decreased from the inlet to the TW outlets, structural diversity increased, suggesting different microbial communities were present to handle the more easily utilized/degraded pollutants near the inlet vs. the more difficult to degrade and recalcitrant pollutants closer to the outlets. This study also confirmed that effluent water samples do not accurately describe the microbial communities responsible for water treatment inside a TW, highlighting the importance of using internal samples for investigating microbial communities in TWs. The results of this study reinforce an existing knowledge gap regarding the potential for TW design modifications which incorporate microbial community spatial dynamics (heterogeneity). It is suggested that utilizing step-feeding could allow for improved water treatment within the same areal footprint, and modifications enhancing co-metabolic processes could assist in improving the treatment of more difficult to degrade or recalcitrant compounds such as micropollutants.

Effects of Different Native Plants on Soil Remediation and Microbial Diversity in Jiulong Iron Tailings Area, Jiangxi

Phytoremediation is an important solution to heavy metal pollution in soil. However, the impact of plants on microbial communities in contaminated soil also requires attention. Community-level physiological profiling (CLPP) based on the Biolog™ EcoPlate and high-throughput sequencing were used to study the soil microbial community in this article. The rhizosphere and bulk soil samples of six native species were collected from the iron mine tailings on Jiulong Mountain, Jiangxi Province. According to the average well color development (AWCD), all plants improved the activity and diversity of the contaminated soil microbial community to varying degrees. Cunninghamia lanceolate is considered to have good effects and led to the appearance of Cunninghamia lanceolata > Zelkova schneideriana > Toona ciliata > Alnus cremastogyne > Cyclobalanopsis myrsinifolia > Pinus elliottii. The Shannon–Wiener diversity index and principal component analysis (PCA) show that the evenness and dominance of soil microbial communities of several plants are structurally similar to those of uncontaminated soil (UNS). The results of high-throughput sequencing indicated that the bacterial community diversity of C. lanceolata, A. cremastogyne, and P. elliottii is similar to UNS, while fungal community diversity is different from UNS. C. lanceolata has a better effect on soil nutrients, C. myrsinifolia and P. elliottii may have a better effect on decreasing the Cu content. The objective of this study was to assess the influence of native plants on microbial communities in soils and the soil remediation capacity. Mortierellomycota was the key species for native plants to regulate Cu and microbial community functions. Native plants have decisive influence on microbial community diversity.

Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes

Microbial mixed cultures are gaining increasing attention as biotechnological production systems, since they offer a large but untapped potential for future bioprocesses. Effects of secondary metabolite induction and advantages of labor division for the degradation of complex substrates offer new possibilities for process intensification. However, mixed cultures are highly complex, and, consequently, many biotic and abiotic parameters are required to be identified, characterized, and ideally controlled to establish a stable bioprocess. In this review, we discuss the advantages and disadvantages of existing measurement techniques for identifying, characterizing, monitoring, and controlling mixed cultures and highlight promising examples. Moreover, existing challenges and emerging technologies are discussed, which lay the foundation for novel analytical workflows to monitor mixed-culture bioprocesses.

Patterns in utilization of carbon sources in soil microbial communities contaminated with mine solid wastes from San Luis Potosi, Mexico

In San Luis Potosí, Mexico, the exploitation of minerals has historically been carried out as an activity that has left in its path environmental liabilities, with high concentrations of heavy metals. These metals have undergone weathering by rain and wind and have moved closer to inhabited locations as is the case of Cerro de San Pedro (CSP) and Villa de la Paz (VDP). The objective of this study is to show the biological alteration of soils due to the presence of heavy metals and metalloids like Cadmium (Cd), Copper (Cu), Lead (Pb) and Arsenic (As) and to find the relationship between contamination and risk indexes. Soil samples were obtained from sites with historical records of mining activity and their surroundings. Several analyses were performed, such as pH levels, organic matter, electrical conductivity, clays, heavy metals and As. Moreover, Community Level Physiological profiling (CLPP) were conducted. The obtained evidence showed high levels of contamination by As and heavy metals in both sites (CSP: 6485.1 mg/Kg of Pb and pH of 4.4; VDP: 7188.2 mg/Kg of As and pH of 7.8). According to the Metal Pollution Index (MPI), 607.0 in CSP and 1050.5 in VDP, presented a high environmental risk, apart from, risk to human health (SQGQI) 35.8 in CSP and 131.5 in VDP. At the same time, CLPPs showed that microbiological communities were selective in taking up substrate groups, in the following order: Carbohydrates > Polymers > Carboxylic acids > Amino acids > Amines/Amides. However, a positive correlation in CSP was only found between both indexes and Amines/Amides (r = 0.46, p < 0.05), and in VDP the D-Galactonic acid-γ-Lactone with the MPI (r = 0.49, p < 0.05), and with the SQGQI (r = 0.45, p < 0.05). Although this behavior was not homogeneous, it was possible to find negative correlations between both indexes and the AWCD with other substrates, influenced by the physicochemical characteristics presented in each studied site. Consequently, according to our findings, a combined effect between the physicochemical characteristics, As, and heavy metals took place, on the metabolic activity, causing alterations to soil functions.

Bacterial Community Assessed by Utilization of Single Carbon Sources in Broiler Ground Meat after Treatment with an Antioxidant, Carnosine, and Cold Plasma

ABSTRACT

Contaminated poultry meat is a major source of human foodborne illnesses. Many interventions have been developed to reduce and/or eliminate human foodborne pathogens in poultry products; however, treatments with cold plasma or carnosine or their combination have not been extensively investigated. In this study, the bacterial microflora of poultry meat samples after treatments with cold plasma and carnosine were characterized with EcoPlates in the OmniLog system. The plates were incubated at 25°C for 7 days in the OmniLog chamber, and bacterial growth was monitored by recording formazan production every 30 min at an optical density of 590 nm. The kinetics of lag, log, and stationary phases of bacterial growth followed the Gompertz sigmoidal model but with different inflection times and asymptotes at the log phase and the stationary phase, respectively. Results indicated that treatment of poultry meat samples with cold plasma technology and carnosine could inhibit growth of the bacteria in the treated meat samples. Of 31 chemicals tested, phenylethylamine, α-d-lactose, d,l-α-glycerol phosphate, 2-hydroxybenzoic acid, γ-hydroxybutyric acid, α-ketobutyric acid, and d-malic acid could not be metabolized by bacteria in the meat samples. Future research is required to determine whether these seven chemicals that inhibited growth of bacteria in these meat samples can be used as food preservatives for extending the shelf life of these products. Whether the bacterial flora can be an indicator of effectiveness for meat samples treated with cold plasma, carnosine, or both needs further study.

HIGHLIGHTS

Emerging environmental contaminants (silver nanoparticles) altered the catabolic capability and metabolic fingerprinting of microbial communities

Microbial community functional diversity enhances the degradation of organic matter and pollutants in the environment, but there is a growing concern that these ecosystem services may be altered by the introduction of emerging environmental contaminants including silver nanoparticles (AgNPs) into aquatic systems. We added 0, 25, 50, 75, 100, and 125 mg L^-1 (nominal concentrations) of citrate-AgNP and polyvinylpyrrolidone-AgNP (PVP-AgNP) each to freshwater sediment and examined their antimicrobial effects on microbial communities using community-level physiological profiling. The results showed that citrate-AgNP decreased the overall microbial catabolic activity by 80% from 1.16 ± 0.02 to 0.23 ± 08 while PVP-AgNP decreased the catabolic activity by 51% from 1.25 ± 0.07 to 0.61 ± 0.19 at 125 mg L^-1. Citrate-AgNP and PVP-AgNP caused a statistically significant reduction in substrate richness and substrate diversity that decreased microbial functional diversity. AgNPs decreased microbial catabolic capability and functional diversity at concentrations ranging from 0.12 ± 0.04 to 0.43 ± 0.07 mg Ag kg^-1 which are lower than the predicted concentrations in freshwater sediment. To our knowledge, this is the first study to demonstrate inhibition of microbial functional diversity by citrate-AgNP and PVP-AgNP in a pathogen impaired stream. Citrate-AgNP caused greater inhibition of carbon substrate utilization but amino acids, carbohydrates, and carboxylic acids were the most affected carbon groups which led to a shift in the metabolic fingerprint pattern of the microbial community. AgNPs decreased the catabolic capability and the ability of the microbial community to degrade organic matter and a variety of pollutants in the environment.

The interactive effects of titanium dioxide nanoparticles and light on heterotrophic bacteria and microalgae associated with marine aggregates in nearshore waters

Titanium dioxide nanoparticles (n-TiO₂) are emerging contaminants and the ecological impact of these materials to the nearshore environment is largely unknown. The reactivity of n-TiO₂ increases with light exposure, and the photocatalytic effects have been shown on cultures of bacteria and microalgae in the laboratory. The purpose of this study was to assess the response of natural bacterial and microalgal communities associated with marine aggregates to n-TiO₂ under conditions similar to those found in the photic zone of nearshore waters. Nano and bulk TiO₂ particles were incorporated into marine aggregates over 4 days under two light conditions: 6:18 and 0:24 (hours light:dark). The abundance and metabolic response of heterotrophic bacteria and viability of microalgae associated with aggregates were assessed. Although the proportion of living microalgae was unchanged, the abundance, total metabolic activity and functional diversity of heterotrophic bacteria were significantly altered by irradiated n-TiO₂.

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.

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.

Shifts in metabolic patterns of soil bacterial communities on exposure to metal engineered nanomaterials

The explosive growth in nanomaterial use will bring about their increased release into terrestrial ecosystems. Metal engineered nanomaterials (ENMs) that gain entry into these environments may alter the composition and activities of resident natural bacterial communities. To assess changes in community level physiological profiles (CLPP) of microbial communities in soils exposed to metal ENMs, Biolog EcoPlates were used in this exploratory comparative study. The CLPP is a rapid screening technique to characterise functional differences among heterotrophic microbial communities based on variable substrate utilization. The impacts of three metal ENMs, silver, titanium dioxide and zinc oxide, on bacterial communities were investigated using three soil types from Maharashtra, India. Metabolic diversity of bacterial communities was impacted in the soils in presence of silver and zinc oxide, but not in presence of titanium dioxide nanoparticles. Diversity indices, viz., Shannon's index, Evenness index and Simpson's index also showed significant differences in the presence of silver and zinc oxide nanoparticles. Principal component analysis revealed changes in metabolic profiles in the presence of silver nanoparticles. This study also shows that testing ecotoxicity of nanoparticles using readily culturable bacteria is a practical approach.

Changes in infaunal assemblage structure influence nutrient fluxes in sediment enriched by mussel biodeposition

Although many studies have described the influence of bivalve aquaculture on the benthic environment, effects on benthic functional diversity are poorly known, as are links with ecosystem processes. We investigated the response of a benthic ecosystem in terms of taxonomic and functional diversity (infauna >500 μm), biogeochemical indicators (organic matter content, redox potential, sulfides level, bacteria) and metabolism (nutrient fluxes), subjected to various levels of mussel biodeposition as a general model of organic enrichment. Results show that local benthic conditions may recover fairly quickly depending on environmental conditions whereas modifications of the benthic community structure persist over a longer time scale with an impact on benthic ecosystem functioning. Fauna-mediated oxidation of the sediment likely increased nitrogen recycling through nitrification whereas binding and release of phosphorus to the water column seems to be driven by more complex processes. Results highlight the importance of species identity (ecological traits) on biogeochemical cycling and solute exchange across the sediment-water interface, with implications for the ecological functioning of exploited areas.

The effect of rosemary Extract and cold plasma treatments on bacterial community diversity in poultry ground meats

To provide safer food, many technologies have been used to preserve food. One such technology is cold plasma, which can reduce viable bacterial counts in various food matrices. However, bacterial communities in food matrices before and after cold plasma treatment have not been investigated. In this communication, the EcoPlates™ were used to physiologically profile bacterial communities from poultry ground meat treated with rosemary, cold plasma or both. The cultures in the plates were incubated at 25 °C for seven days in an OmniLog® system. Responses of the bacterial communities to 31 chemicals were measured on formazan production. The results show that the three parameters of the Gompertz growth curves were observed in all samples, 2-hydroxybenzoic acid could not be used, while pyruvic acid methyl ester was used for a carbon source by the bacterial communities from all meat samples, each bacterial community metabolized different numbers of chemical compounds at different rates, and reduction of bacterial functional diversity was observed in the poultry meat samples treated with cold plasma and rosemary. In the future, investigations on whether the physiological profiling in bacterial communities be used as an indicator for effectiveness of cold plasma treatment of meat samples.

Experimental evaluation on the applicability of necrobiome analysis in forensic veterinary science

Despite the wide usage of animals as models in forensic studies, the investigations of fundamental legal questions involving domesticated and nondomesticated animals were always given marginal attention compared to “human forensic,” and only recently the interest in the discipline is increasing. Our research focuses on the effect of the fur coat on the activity and development of microbial decomposers. In order to test this variable never assessed before, rabbit carcasses were used and results show that: (i) distinct and significant temporal changes in terms of metabolic activity and taxa distribution can be tracked over the decomposition process; (ii) the richness and the diversity of the bacterial communities does not significantly vary over time, but it does not mean that the species Operational Taxonomic Units (OTUs) do not change; (iii) the presence/absence of the fur on the carcasses does not significantly affect either the bacterial communities’ functional activity or the diversity intra‐ and intercommunity, neither at phylum nor at family resolution; (iv) the functional activity and the ecological diversity of the bacterial communities are significantly affected by the body region, while the relative abundance is not. Obtained data confirm previous observations and provide new insight in the Forensic Veterinary field in terms of equally using them in order to derive a statistical model for the PMI estimation. As a future perspective, a contribution to the Forensic Entomology approach will be given in legal investigations when domestic or wild animals are involved, regardless of the presence of a hair layer.

Physiological Diversity of Spitsbergen Soil Microbial Communities Suggests Their Potential as Plant Growth-Promoting Bacteria

The objective of the study was to assess the physiological diversity and metabolic activity of the soil bacterial communities inhabiting Spitsbergen soils in search of bacterial abilities facilitating plant growth promotion. In the soil, the total number of culturable microorganisms, the number of their individual physiological groups (including Siderophore Synthesizing; SSB and Phosphate Solubilizing Bacteria; PSB), the dehydrogenase (DH) activity, and the ability to utilize sources of C, N, P (EcoPlate) were analysed. In bacterial isolates, siderophores production, ACC (1-aminocyclopropane-1-carboxylate) deaminase (ACCD) activity, IAA (indole-3-acetic acid) synthesis were examined. The isolates were applied to the seeds of Phaseolus coccineus regarding their germination and root length. The results showed differences between copio- and oligotrophic bacteria. A usually high number of SSB was accompanied by the raised number of PSB. A bigger number of SSB was connected with low values of Fe in the soil. High DH activity was assisted by greater number of copio- and oligotrophic bacteria, raised average well color development value, and N and C contents in the soil. Germination index was more alike relative seed germination than relative root growth. IAA concentration and ACCD activity were conversely related. Synthesis of siderophores was matched with ACCD activity and its high level was combined with elevated germination index. In spite of different localization of soil samples, some isolates proved similar traits of activity. Distinct affiliation of isolates and their various localizations were displayed. Among all isolates tested, some possessed one main trait of activity, but most of them had two or more significant features for potential plant growth stimulation. These isolates could be an important source of useful bacteria.

Impacts and fate of triclosan and sulfamethoxazole in intensified re-circulating vertical flow constructed wetlands

The impacts to microbial function, overall performance and eventual fate were assessed for triclosan (TCL) and sulfamethoxazole (SMX) in intensified (re-circulating) vertical subsurface flow (VSSF) constructed wetlands (CWs). The potential toxicity of each pharmaceutical to the intrinsic microbial communities was first assessed over a wide exposure range (0-1000 μg/l) via an ex-situ dose-response assay to estimate the concentration at which adverse effects were likely to occur. Based on these results an acute (7 day) in-situ exposures (500 μg/l) were then performed and impacts to the mesocosm systems monitored for 1 month via community-level physiological profiling (CLPP) alongside chemical oxygen demand (COD) removal rates and a range of water quality, and hydrological parameters. Despite the clear potential for negative impacts to microbial function from both compounds observed at 100 μg/l in the ex-situ dose-response test, no impacts were observed for the 500 μg/l in-situ exposure in the VSSF mesocosms. COD removal, water chemistry, plant health, and hydrological parameters did not significantly change in response to the in-situ exposure. In terms of fate, the removal efficiency for both TCL and SMX was high (>80%) after 1 h and complete removal (>99.7%) was observed after 168 h. Following the in-situ exposure, and subsequent one month effects-monitoring period, the mesocosms were decommissioned with the media biofilm spatially assessed for organic content as well as TCL and SMX concentrations. TCL and SMX were found to have persisted in the media and demonstrated spatial variation with an overall 2-20% and 5-6% recovered respectively. This suggests that biofilm bound TCL and SMX were biologically degraded in VSSF CWs, however may also accumulate in the biofilm if TCL and SMX are maintained in the influent. These results reinforce the robustness and potential of constructed wetlands for the treatment of pharmaceutical and personal care product (PPCP) contaminated wastewater.

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.

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China

Saline water irrigation can change soil environment, which thereby influence soil microbial process. Based on a field experiment, the shifts in soil microbial metabolic activities and community structures under five irrigation salinities were studied using Biolog and metagenomic methods in this study. The results demonstrated that microbial metabolic activities were greatly restrained in saline water irrigated soils, as average well color development (AWCD) reduced under all saline water irrigation treatments. Although no significant difference in carbon substrate utilization of all six categories was observed among Mild, Medium, High and Severe treatments, the consumption of sole carbon source was significantly varied. Especially, asparagine, galacturonic, putrescine and 4-benzoic acid played a decisive role in dominating the differences. Soil bacterial richness and diversity increased with irrigation salinity while the number of bacterial phyla decreased. Three significantly increased (Proteobacteria, Actinobacteria and Chloroflexi), two decreased (Planctomycetes, Bacteroidetes) and two irresponsive (Gemmatimonadetes and Acidobacteria) phyla were observed as the dominant groups in saline water irrigated soils. The results presented here could improve the understanding of the soil biological process under saline circumstance.

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.

Changes in dissolved organic matter composition and metabolic diversity of bacterial community during the degradation of organic matter in swine effluent

In this study, an incubation experiment was conducted with effluent collected from the concentrated swine-feeding operations (CSFOs) located in Yujiang County of Jiangxi Province, China. The purpose of this study was to elucidate the relationships between the composition of dissolved organic matter (DOM) and the community-level physiological profiles (CLPPs) of microorganisms in swine effluent. For all samples examined, the concentrations of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were decreased by an average of 58.2 ± 30.4 and 49.2 ± 38.7 %, whereas total dissolved phosphorus (TDP) exhibited an average final accumulation of 141.5 ± 43.0 %. In the original samples, ammonium nitrogen accounted for 88.9 ± 4.9 % of the TDN, which was reduced to a final average of 83.9 ± 9.6 %. Two protein-like (tyrosine and tryptophan) and two humic-like (fulvic acids and humic acids) components were identified using a three-dimensional excitation-emission matrix. With the increase in incubation time, the relative concentrations of two protein-like components in effluent were reduced by an average of 83.2 ± 24.7 %. BIOLOG(™) ECO plates were used to determine the metabolic fingerprint of the bacterial community, and a shift in the utilization patterns of substrates was observed over the study period. Additionally, the Shannon-Wiener index of CLPP was ultimately reduced by an average of 43.5 ± 8.5 %, corresponding to the metabolic diversity of the bacterial community. The redundancy analysis identified significant relationships between environmental parameters and the CLPP of microorganisms. To a certain degree, the DOM compositions were linked with the substrate utilization patterns of the bacterial community during the degradation of organic matter in swine effluent.

Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China

We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables.

Microbial community functional change during vertebrate carrion decomposition

Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

Influence of long term irrigation with pulp and paper mill effluent on the bacterial community structure and catabolic function in soil

Microbial communities play a vital role in maintaining soil health. A multiphasic approach to assess the effect of pulp and paper mill effluent on both the structure and function of microbial soil communities is taken. Bacterial communities from agricultural soils irrigated with pulp and paper mill effluent were compared to communities form soils irrigated with well water. Samples were taken from fields in the state of Uttarakhand, India, where pulp and paper mill effluent has been used for irrigation for over 25 years. Comparisons of bacterial community structure were conducted using sequencing of the 16S rRNA gene from both isolates and clone libraries attained from the soil. Community-level physiological profiling was used to characterize the functional diversity and catabolic profile of the bacterial communities. The multiphasic approach using both physiological and molecular techniques proved to be a powerful tool in evaluating the soil bacterial community population and population differences therein. A significant and consistent difference in the population structure and function was found for the bacterial communities from soil irrigated with effluent in comparison to fields irrigated with well water. The diversity index parameters indicated that the microbial community in pulp and paper mill effluent irrigated fields were more diverse in both structure and function. This suggests that the pulp and paper mill effluent is not having a negative effect on the soil microbial community, but in fact may have a positive influence. In terms of soil health, this finding supports the continued use of pulp and paper mill effluent for irrigation. This is however only one aspect of soil health which was evaluated. Further studies on soil resistance and robustness could be undertaken to holistically evaluate soil health in this situation.

Effect of ciprofloxacin on microbiological development in wetland mesocosms

An understanding of how antibiotics and other "emerging contaminants" affect both water treatment systems and natural environments is of growing interest. Ciprofloxacin is a broad-spectrum antibiotic active against both Gram-positive and Gram-negative bacteria and has been extensively used over the past 20 years. The objective of this research was to study the effect of an antibiotic such as ciprofloxacin on the development, function and stability of bacterial communities in wetland systems. Four mesocosm wetlands planted with Phragmites australis were initially seeded with activated sludge from a waste water treatment plant and allowed to develop for a 1 week period, after which 2 of the 4 mesocosms were exposed to a ciprofloxacin concentration of 2 μg/mL for a 5 day period. The 4 mesocosms were then monitored for several microbiological and hydrological parameters over the course of 22 weeks. The bacterial community species distribution and catabolic capabilities were assessed via denaturing gradient gel electrophoresis (DGGE) and community level physiological profiling (CLPP), based on carbon utilization. DGGE results indicated that the ciprofloxacin decreased the total number of PCR-amplifiable DNA (bacteria) and the overall diversity of bacterial operational taxonomic units (OTUs). Through CLPP it was shown that the interstitial microbiological community was initially adversely affected by the ciprofloxacin, creating a temporary decrease in the activity and overall catabolic capabilities of the inherent wetland bacterial communities. However, after a 2-5 week recovery period the activities and catabolic capabilities of the bacterial communities exposed to ciprofloxacin returned to levels comparable to those found for bacterial communities not exposed to the ciprofloxacin. These findings suggest that ciprofloxacin exposure may have an adverse effect on the inherent bacterial communities in wetland systems initially reducing their ability to assimilate anthropogenic carbon-based compounds; however, normal functionality may resume after a 2-5 week period. It was also observed that plants in the ciprofloxacin-treated mesocosms did not adapt to the antibiotic presence, instead showing initial browning of above ground parts and eventual die-off. Reduced porosity, evapotranspiration, and overall hydrological mixing in the ciprofloxacin-treated mesocosms was observed.