Community Metabolic Profiles Research Articles

Analysis of Microbial Communities Associated with Bioremediation Systems for Thiocyanate-Laden Mine Water Effluents

During the processing of refractory gold ores, cyanide (CN-) and residual sulphur species react to form an effluent stream containing thiocyanate (SCN-) and residual CN-. The release of SCN- and CN- containing effluent water to the environment is prohibited, necessitating effective treatment prior to discharge and/or reuse of contaminated plant water. Biologically mediated effluent remediation processes have been developed for commercial use, to remediate SCN- containing effluents, with the aim of enabling recycling of process water and improving the quality of effluent water prior to disposal. Bioremediation processes to treat these effluents rely on a complex consortium of microorganisms to metabolise the SCN- resulting in the production of ammonium that is in turn removed by conversion to nitrite and subsequent denitrification. Increasingly, genomic methods are being used to investigate processes in wastewater treatment to identify key microbial species and, thereby, inform the rationale design and operation of these bioremediation systems. The microbial ecology of laboratory-based SCN- degrading bioprocesses have been investigated, using genome resolved metagenomics, to provide detailed information on the community composition and metabolic profile of abundant microbial community members. Our on-going research is focused on developing a greater understanding of the heterotrophic and autotrophic populations of microorganisms within the SCN- degrading community as well as the role of the component members in SCN- destruction. We are interested in the formation of microbial biofilm and the spatial distribution of key microorganisms within the resulting biofilm communities. This information is being used to inform further rational development of SCN- degradation processes for treatment of contaminated wastewater effluents.

Bacillus licheniformis affects the microbial community and metabolic profile in the spontaneous fermentation of Daqu starter for Chinese liquor making

Chinese liquor is produced from spontaneous fermentation starter (Daqu) that provides the microbes, enzymes and flavors for liquor fermentation. To improve the flavor character of Daqu, we inoculated Bacillus licheniformis and studied the effect of this strain on the community structure and metabolic profile in Daqu fermentation. The microbial relative abundance changed after the inoculation, including the increase in Bacillus, Clavispora and Aspergillus, and the decrease in Pichia, Saccharomycopsis and some other genera. This variation was also confirmed by pure culture and coculture experiments. Seventy-three metabolites were identified during Daqu fermentation process. After inoculation, the average content of aromatic compounds were significantly enriched from 0.37mg/kg to 0.90mg/kg, and the average content of pyrazines significantly increased from 0.35mg/kg to 5.71mg/kg. The increase in pyrazines was positively associated with the metabolism of the inoculated Bacillus and the native genus Clavispora, because they produced much more pyrazines in their cocultures. Whereas the increase in aromatic compounds might be related to the change of in situ metabolic activity of several native genera, in particular, Aspergillus produced more aromatic compounds in cocultures with B. licheniformis. It indicated that the inoculation of B. licheniformis altered the flavor character of Daqu by both its own metabolic activity and the variation of in situ metabolic activity. Moreover, B. licheniformis inoculation influenced the enzyme activity of Daqu, including the significant increase in amylase activity (from 1.3gstarch/g/h to 1.7gstarch/g/h), and the significant decrease in glucoamylase activity (from 627.6mgglucose/g/h to 445.6mgglucose/g/h) and esterase activity (from 28.1mgethylcaproate/g/100h to 17.2mgethylcaproate/g/100h). These effects of inoculation were important factors for regulating the metabolism of microbial communities, hence for improving the flavor profile Daqu.

Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils

Landfills are always the most important part of solid waste management and bear diverse metabolic activities involved in element biogeochemical cycling. There is an increasing interest in understanding the microbial community and activities in landfill cover soils. To improve our knowledge of landfill ecosystems, we determined the microbial physiological profiles and communities in three landfill cover soils (Ninghai: NH, Xiangshan: XS, and Fenghua: FH) of different ages using the MicroResp(TM), phospholipid fatty acid (PLFA), and high-throughput sequencing techniques. Both total PLFAs and glucose-induced respiration suggested more active microorganisms occurred in intermediate cover soils. Microorganisms in all landfill cover soils favored L-malic acid, ketoglutarate, and citric acid. Gram-negative bacterial PLFAs predominated in all samples with the representation of 16:1ω7, 18:1ω7, and cy19:0 in XS and NH sites. Proteobacteria dominated soil microbial phyla across different sites, soil layers, and season samples. Canonical correspondence analysis showed soil pH, dissolved organic C (DOC), As, and total nitrogen (TN) contents significantly influenced the microbial community but TN affected the microbial physiological activities in both summer and winter landfill cover soils.

The effect of biochar loading rates on soil fertility, soil biomass, potential nitrification, and soil community metabolic profiles in three different soils

Biochar is increasingly being used as a soil amendment to both increase soil carbon storage and improve soil chemical and biological properties. To better understand the shorter-term (10 months) impacts of biochar on selected soil parameters and biological process in three different textured soils, a wide range of loading rates was applied. Biochar derived from eucalypt green waste was mixed at 0, 2.5, 5, 10 % (wt/wt) with a reactive black clay loam (BCL), a non-reactive red loam (RL) and a brown sandy loam (BSL) and placed in pots exposed to the natural elements. After 10 months of incubation, analysis was performed to determine the impacts of the biochar rates on the different soil types. Also, microbial biomass was estimated by the total viable counts (TVC) and DNA extraction. Moreover, potential nitrification rate and community metabolic profiles were assayed to evaluate microbial function and biological process in biochar-amended soils. The results showed that biochar additions had a significant impact on NH4 and NO3, total C and N, pH, EC, and soil moisture content in both a soil type and loading-dependent manner. In the heavier and reactive BCL, no significant impact was observed on the available P and K levels, or the total exchangeable base cations (TEB) and CEC. However, in the other lighter soils, biochar addition had a significant effect on the exchangeable Al, Ca, Mg, and Na levels and CEC. There was a relatively limited effect on microbial biomass in amended soils; however, biochar additions and its interactions with different soils reduced the potential nitrification at the higher biochar rate in the two lighter soils. Community metabolic profile results showed that the effect of biochar on carbon substrate utilization was both soil type and loading dependent. The BCL and BSL showed reduced rates of substrate utilization as biochar loading levels increased while the opposite occurred for the RL. This research shows that biochar can improve soil carbon levels and raise pH but varies with soil type. High biochar loading rates may also influence nitrification and the function and activity of microbial community in lighter soils.

Indoor Heating Drives Water Bacterial Growth and Community Metabolic Profile Changes in Building Tap Pipes during the Winter Season.

The growth of the bacterial community harbored in indoor drinking water taps is regulated by external environmental factors, such as indoor temperature. However, the effect of indoor heating on bacterial regrowth associated with indoor drinking water taps is poorly understood. In the present work, flow cytometry and community-level sole-carbon-source utilization techniques were combined to explore the effects of indoor heating on water bacterial cell concentrations and community carbon metabolic profiles in building tap pipes during the winter season. The results showed that the temperature of water stagnated overnight (“before”) in the indoor water pipes was 15–17 °C, and the water temperature decreased to 4–6 °C after flushing for 10 min (“flushed”). The highest bacterial cell number was observed in water stagnated overnight, and was 5–11 times higher than that of flushed water. Meanwhile, a significantly higher bacterial community metabolic activity (AWCD590nm) was also found in overnight stagnation water samples. The significant “flushed” and “taps” values indicated that the AWCD590nm, and bacterial cell number varied among the taps within the flushed group (p < 0.01). Heatmap fingerprints and principle component analyses (PCA) revealed a significant discrimination bacterial community functional metabolic profiles in the water stagnated overnight and flushed water. Serine, threonine, glucose-phosphate, ketobutyric acid, phenylethylamine, glycerol, putrescine were significantly used by “before” water samples. The results suggested that water stagnated at higher temperature should be treated before drinking because of bacterial regrowth. The data from this work provides useful information on reasonable utilization of drinking water after stagnation in indoor pipes during indoor heating periods.

Influence of long-term irrigation with treated papermaking wastewater on soil ecosystem of a full-scale managed reed wetland

A large-scale managed reed wetland in Yancheng Biosphere Reserve of China has been irrigated by treated papermaking wastewater (TPW) for approximately 8 to 12 years. This report details the risk evaluation of long-term TPW irrigation on the soil and its microbial viability, providing important perspective on the suitability of TPW reuse for irrigation. An extensive field survey was employed for assessing the impacts of long-term TPW irrigation of reed fields (F1 to F6), as compared to river water irrigated field, on soil physicochemical properties, accumulation of heavy metals (Cu, Cd, Pb), soil enzyme activities (i.e., urease, invertase, catalase, and polyphenol oxidase), and soil microbial community metabolic profiles. The results revealed that long-term TPW reuse for irrigation resulted in a slight increase of pH value, while a remarkable increase was identified regarding to soil organic carbon, as expected from the organic carbon content of the wastewater, but was not proportional to the time of irrigation. TPW irrigation caused a remarkable increase in soil electrical conductivity and resulted in soil salinization, having strong correlation with the duration of irrigation. Soil salinization increase in irrigated area was mainly due to the high sodium content of the wastewater applied for irrigation. Furthermore, soil enzymes displayed significantly increased activities (except for catalase) in the irrigated fields, while the microbial ability of utilizing carbon source was enhanced. The diversity of microbial communities was boomed due to the increase of soil organic matter, as evidenced by the calculated diversity indices. However, a remarkable increase of heavy metals was also identified regarding Cd and Pb concentrations, which may pose potential risks to human health. The input of excessive pollutants and nutrients will disrupt the equilibrium mechanism of the wetland ecosystem. Although long-term TPW irrigation may increase the soil fertility and microbial activity, heavy metals (i.e., Cd and Pb) in wastewater can be accumulated in the soil. Furthermore, alkaline TPW caused an increase in soil salinity. Therefore, more cautions should be exercised in the reuse of TPW for irrigation.

Effect of organic and conventional practices on carbon-substrate utilisation by the soil microbial community in a ‘Cripps Pink’/M7 apple orchard

Changes in microbial community metabolic profiles potentially can be used to identify differences in soil characteristics caused by dissimilar orchard floor management practices. The impacts of orchard floor management practices on the microbial community metabolic diversity (CMD) were examined in apple orchard soils subjected to two conventional (CON) and three organic (ORG) orchard floor management practices. The CMD, as indicated by carbon (C) substrate utilisation (BIOLOG™ system), was determined in composite soil samples (0–15 cm) from the tree rows. The CON treatments reduced, and ORG treatments increased, C-source utilisation and, hence, CMD. Among the CON treatments, C-source utilisation in summer was favoured by winter cover crops in work rows, controlled with herbicide in spring, compared to uncontrolled weed-covered work rows. Orchard soils under ORG regimes more closely resembled soils of natural ecosystems in that they were better able to sustain CMD, and possibly afford a better option to sustain critical ecosystem functions than under CON management, which relies heavily on synthetic agrochemical usage.

Microbial community and functional diversity associated with different aggregate fractions of a paddy soil fertilized with organic manure and/or NPK fertilizer for 20 years

Microbial communities are sensitive to fertilizations, and the response of microbial communities to different fertilization regimes in bulk soils has been studied. However, it is unclear how microbial communities performance in soil aggregates. We determined the composition and functional diversity of the microbial community within different aggregate size fractions of a paddy soil fertilized with organic manure (OM) or/and mineral NPK fertilizer (NPK/NPKO) for 20 years, along with a control (no fertilizer, NoF). Soils were sampled in late December 2010 from a long-term experimental site established from an uncultivated wasteland in 1990. Five aggregate fractions, i.e., large macroaggregates (>2 mm), macroaggregates (1–2 mm), small macroaggregates (0.25–1 mm), microaggregates (0.053–0.25 mm), and non-aggregated silt and clay particles (<0.053 mm), respectively, were obtained by wet sieving. Microbial community composition was estimated based on phospholipid fatty acids (PLFAs) analysis. Microbial functional diversity was evaluated using the community level physiological profile method by Biolog Eco-microplate. The PLFA signature analysis revealed that microbial biomass tended to decrease with decreasing aggregate size. The application of fertilizer significantly increased the microbial biomass of large macroaggregates relative to the NoF treatment, but there was no significant difference among aggregates of the three fertilization treatments. Average well color development (AWCD) as well as all the functional diversity indices was almost highest in large macroaggregates and microaggregates of NoF, OM, and NPK treatments and in microaggregates of NPKO treatment, while all of them were lowest in silt and clay particles. NPKO treatment led to the greatest microbial functional diversity. AWCD values and McIntosh index (U) of most aggregates under the NPK treatment were significantly increased. The OM treatment did not significantly affect microbial functional diversity associated with different aggregate fractions. Aggregate fractions and fertilization significantly affected microbial community composition and functional diversity. Soil organic C and carbon to nitrogen (C/N) ratio dominated microbial community composition and metabolic profile associated with different aggregates, respectively.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas.

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Characterization of enriched aerotolerant cellulose-degrading communities for biofuels production using differing selection pressures and inoculum sources

Ethanol production from direct cellulose fermentation has mainly been described as a strictly anaerobic process. The use of air-tolerant organisms or consortia for this process would reduce the need for prereduction of the medium and also permit continuous feed of aerobic feedstock. To this end, moderately thermophilic (60 °C) consortia of fermentative, cellulolytic bacteria were enriched from 3 distinct environments (manure, marsh, and rotten wood) from a farm in southeast Saskatchewan, Canada. Community phenotypic and metabolic profiles were characterized. Selection methods included direct plating under an aerobic atmosphere and repeated passaging; the methods were designed to select for robust, stable aerotolerant cellulose-degrading communities. Several of the isolated communities exhibited an increase in total cellulose degradation and total ethanol yield when compared with a monoculture of Clostridium thermocellum DSMZ 1237. Owing to stringent selection conditions, low diversity enrichments were found, and many appeared to be binary cultures via density gradient gel electrophoresis analysis. On the basis of 16S rRNA gene sequencing, aerobic conditions selected for a mix of organisms highly related to C. thermocellum and Geobacillus species, while anaerobic conditions led to the development of consortia containing strains related to C. thermocellum with strains from either the genus Geobacillus or the genus Thermoanaerobacter. The presence of a Geobacillus-like species appeared to be a prerequisite for aerotolerance of the cellulolytic enrichments, a highly desired phenotype in lignocellulosic consolidated bioprocessing.

土霉素对堆肥过程中酶活性和微生物群落代谢的影响

以猪粪和秸秆为试验材料，研究了土霉素对堆肥温度、种子发芽指数、C/N、纤维素酶、脲酶、过氧化氢酶以及微生物群落代谢的影响。结果表明，0 mg/kg（对照处理）的堆肥在第2天上升到 50 ℃以上，维持了 5 d，达到了无害化处理的要求。35 mg/kg土霉素处理（A1 处理）第4天升到 51.0 ℃，其高温期维持了 1 d。70 mg/kg 土霉素处理（A2 处理）第3天升到 50 ℃以上，高温期维持了 2 d。105 mg/kg 土霉素处理（A3 处理）和 140 mg/kg 土霉素处理（A4 处理）的温度在整个堆肥期间均未达到 50 ℃。在堆肥结束时各个处理的种子发芽指数均达到 80% 以上。CK（对照处理）、A1、A2、A3 和 A4 处理的 C/N 由 34.50 分别降为 16.64、16.07、19.48、18.45 和 19.83。堆肥的第1天，A1、A2、A3 和 A4 处理对纤维素酶活性的抑制率分别为 60.30%、21.30%、48.81% 和 76.05%，第3天，土霉素对纤维素酶活性起促进作用，在 4-30 d，A3、A4 处理对纤维素酶活性有抑制作用。在堆肥的前期（1-3 d），土霉素刺激脲酶活性，随着堆肥时间的延长，土霉素对脲酶活性由刺激变为抑制作用，在第18-30天 A3、A4 处理与 CK 相比有着显著的抑制作用。在堆肥第1天到第18天，土霉素基本上促进过氧化氢酶的活性，堆肥 18 d 之后土霉素对过氧化氢酶起着是抑制作用。用 Biolog（ECO Microplate）方法研究了土霉素对堆肥过程中微生物群落代谢的影响，结果表明，在升温期 CK 处理的平均颜色变化率AWCD（Average Well Color Development）在培养 60 h 之后大于其他处理，高温期 A2 处理的 AWCD 值最高，在降温期 CK 的 AWCD 值一直是最高的。对 Shannon 指数进行分析显示，堆肥的初始阶段土霉素降低微生物群落的功能多样性，随着时间的延长，土霉素增加微生物群落的功能多样性。对微生物利用六大类碳源分析表明，140 mg/kg 的土霉素浓度能够改变微生物利用碳源的种类。;An outdoor experiment was conducted to study the effect of oxytetraeyeline addition on composting temperature, seed germination index, ratio of carbon to nitrogen, cellulose, urease, catalase and microbial community metabolism during composting of pig manure mixed with wheat straw. The results showed that composting temperature was reached to 50 ℃ in the second day of composting and lasted for 5 days on treatment without addition of oxytetraeyeline (Control check,CK), which could meet the need of the requirement of harmlessness. The composting temperature was above 51.0 ℃ in the fourth day of composting with addition of 35 mg/kg oxytetracycline (A1 treatment), and the high temperature period maintained for 1 day. The temperature was above 50 ℃ in the third day of composting where 70 mg/kg oxytetracycline was added (A2 treatment), and the high temperature period only hold on for 2 days. The temperature could not reach to 50 ℃ over the whole time of composting on both A3 and A4 treatments where 105 mg/kg and 140 mg/kg of oxytetracycline were spiked respectively. The germination indices (<em>GI</em>) of seeds, which contained in the compost materials, were higher than 80% for all treatments at the end of the composting. The C/N ratios for all treatments were decreased from an initial value of 34.50 to 16.64, 16.07, 19.48, 18.45 and 19.83, respectively, when composting completed. Activities of cellulose on treatments those receiving oxytetracycline were inhibited by 60.30%, 21.30%, 48.81% and 76.05%, respectively, over CK treatment in the first day of the composting, and they were increased in the third day. Nevertheless, activities of cellulase were inhibited under A3 and A4 treatments compared with CK from day 4 to day 30. The activity of urease was increased by addition of oxytetracycline in the first 3 days, since then on, it was decreased. The higher concentrations of oxytetracycline (A3 and A4) had a significant inhibitory effect on activity of urease from day 18 to day 30. The catalase activity was enhanced generally by the addition of oxytetraeyeline from day 1 to day 18 compared to CK, from then on it was decreased over CK. The effect of oxytetracycline addition on microbial community metabolic profiles during composting was assayed with Biolog (ECO Microplate) method. The results showed that AWCD (Average Well Color Development) values of CK treatment were the highest after 60 h incubation during temperature raising period of the compost. The highest AWCD values were observed on A2 treatment during the high temperature period. AWCD values under CK were greater than other treatments over cooling period. Shannon index results suggested that the oxytetracycline addition could reduce the functional diversity of microbial communities in the initial stage of the composting, in contrast, it could increase the functional diversity of microbial communities at other stages of composting. The carbon source utilization data showed that the addition of 140 mg/kg of oxytetracycline could significantly change the types of carbon sources used by microorganisms.

Metabolic Sequences of Anaerobic Fermentation on Glucose-Based Feeding Substrates Based on Correlation Analyses of Microbial and Metabolite Profiling

Degradation processes in various biomasses are managed by complex metabolic dynamics created by diverse and extensive interactions and competition in microbial communities and their environments. It is important to develop visualization methods to provide a bird's-eye view when characterizing the entire sequential metabolic process in an environmental ecosystem. Here, we describe an approach for the visualization of the metabolic sequences in anaerobic fermentation ecosystems, characterizing the entire metabolic dynamics using a combination of microbial community profiles and metabolic profiles. By evaluating their time-dependent variation, we found that microbial community profiles and metabolite production processes were characteristically affected by the feeding of different glucose-based substrates (glucose, starch, cellulose), although the compositions of the major microbial community and the metabolites detected were likely to be similar in all experiments. This combinatorial approach to variation in microbial communities and metabolic profiles was used successfully to visualize metabolic sequences in anaerobic fermentation ecosystems, in addition to mining candidate microbiota for cellulose degradation. Thus, this approach provides a powerful tool for visualizing and evaluating metabolic sequences within the biomass degradation process in an environmental ecosystem. This is the first report to visualize the entire metabolic dynamic in an anaerobic fermentation ecosystem as metabolic sequences.

Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community

BackgroundThe Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H2 coupled to the reduction of halogenated organic compounds. Dehalococcoides spp. grow best in mixed microbial consortia, relying on non-dechlorinating members to provide essential nutrients and maintain anaerobic conditions.A metagenome sequence was generated for the dechlorinating mixed microbial consortium KB-1. A comparative metagenomic study utilizing two additional metagenome sequences for Dehalococcoides-containing dechlorinating microbial consortia was undertaken to identify common features that are provided by the non-dechlorinating community and are potentially essential to Dehalococcoides growth.ResultsThe KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes. The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined. Examination of specific metabolic pathways, including corrinoid synthesis, methionine synthesis, oxygen scavenging, and electron-donor metabolism identified the Firmicutes, methanogenic Archaea, and the ∂-Proteobacteria as key organisms encoding these pathways, and thus potentially producing metabolites required for Dehalococcoides growth.ConclusionsComparative metagenomics of the three Dehalococcoides-containing consortia identified that similarities across the three consortia are more apparent at the functional level than at the taxonomic level, indicating the non-dechlorinating organisms’ identities can vary provided they fill the same niche within a consortium. Functional redundancy was identified in each metabolic pathway of interest, with key processes encoded by multiple taxonomic groups. This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

Responses of microbial activity and community metabolic profiles to plant functional group diversity in a full-scale constructed wetland

Plant functional group diversity in terrestrial ecosystems can strongly influence microbial communities and ecological processes. This was tested in experimental communities containing 1, 2, 3 and 4 plant functional groups including C3 grasses, C4 grasses, legumes and forbs in a full-scale vertical flow constructed wetland (VFCW) fed with post-treated domestic wastewater. The spatial distribution of microbial activities, including basal respiration rate (BSR) and substrate induced respiration rate (SIR), and community-level physiological profiles (CLPP, basing on the BIOLOG Ecoplate technique), together with plant biomass production, were investigated. An increase in plant biomass production (1,208 g m −2) was only observed in the treatment with the highest plant functional group richness, and the BSR also followed a trend similar to plant biomass. The SIR was higher in all planted treatments than in the unplanted treatments, but did not differ significantly across plant functional group richness levels. Utilizations of both carbohydrates and amino acids and the diversity of substrate microbial community computed from average well color development in the Ecoplate followed the SIR dynamic pattern. The average utilization intensity of miscellaneous compounds was higher in all planted treatments than in the unplanted treatment, but decreased significantly with the plant functional group levels. The average utilizations of both polymers and amines/amides were significantly lower in all planted treatments than in the unplanted treatment, but did not differ significantly across the plant functional group levels. The principal components analysis showed that the metabolic profiles separated significantly unplanted treatment from the planted treatments, but did not separated these planted treatments from each other, appearing that the metabolic profiles of microbial community in our wetland only depended on the presence of plants but did not depended on the plant functional group level.

Effects of plant diversity on microbial biomass and community metabolic profiles in a full-scale constructed wetland

There has been less understanding of relations of microbial community patterns with plant diversity in constructed wetlands. We conducted a single full-scale subsurface vertical flow constructed wetland (SVFCW, 1000 m 2) study focusing on domestic wastewater processing. This study measured the size and structure of microbial community using fumigation extraction and BIOLOG Ecoplate™ techniques, to examine the effects of macrophyte diversity on microbial communities that are critical in treatment efficiency of constructed wetlands. We also determined the relationship of plant diversity (species richness) with its biomass production under disturbance of the same wastewater supply. Linear regression analysis showed that plant biomass production strongly correlated with plant species richness ( R = 0.407, P < 0.001). Increase in plant species richness increased microbial biomass carbon and nitrogen ( R = 0.494, P < 0.001; R = 0.465, P < 0.001) and utilization of amino acids on Ecoplates ( R = 0.235, P = 0.03), but limited the utilization of amine/amides ( R = −0.338, P = 0.013). Principal components analysis (PCA) showed that the diversity and community-level physiological profiles (CLPP) of microbial community at 168 h of incubation strongly depended on the presence or absence of plant species in the SVFCW system, but not on the species richness. This is the first step toward understanding relations of plant diversity with soil microbial community patterns in constructed wetlands, but the effect of species diversity on microbial community should be further studied.

Changes in soil microbial community under willow coppice: The effect of irrigation with secondary-treated municipal wastewater

The effect of secondary-treated wastewater irrigation of a short-rotation willow coppice on soil microbial parameters was evaluated twice in 3 years using microbiological and biochemical properties. The soil metabolically active microbial biomass, basal respiration, N-mineralization, potential nitrification, alkaline and acid phosphatase and dehydrogenase activities were measured. The microbial community metabolic profile was determined with Biolog EcoPlates and bacterial community structure was assessed using denaturing gradient gel electrophoresis. After 2 years, a significant increase had occurred in soil microbial biomass, respiration and nitrogen mineralization activity both in the irrigated and in the non-treated plots. Wastewater irrigation increased the soil potassium concentration and enhanced the activity of alkaline phosphatase. Plant growth and irrigation affected the nitrogen mineralization activity—the increase was twice as high in the control plots as in the irrigated plots after 2 years. Potential nitrification, acid phosphatase activity and microbial community metabolic activity did not differ significantly ( P > 0.05) between the control and the irrigated plots during the study. The comparison of soil profiles indicated that the observed increases in the soil microbiological parameters were allocated to the upper 10 cm. The establishment of willow plants on the fields affected the microbial community structure, with an increased diversity and higher similarity among the planted plots after 2 years. From our results we conclude that the willow coppice affected the soil bacterial community structure and had a positive effect on soil biological activity. Irrigation with pre-treated wastewater affected soil chemical and biochemical properties.

Effects of fertilization and tillage on soil biological parameters

A short field assay was established to study the potential of soil biological parameters (i.e., soil enzymes, potentially mineralizable nitrogen, soil respiration, abundance of earthworms, and microbial community metabolic profiles) as early and sensitive indicators of the effects of agricultural practices (i.e., fertilization and tillage) on soil properties. The field assay consisted of growing a variety of forage corn for just 3 months under mineral and organic fertilization and conventional and no-tillage. In general, highest values of biological parameters were found in organically fertilized, no-tillage plots, while conventional tillage and mineral fertilization led to lower values. Values of potentially mineralizable N, basal respiration, substrate induced respiration, and earthworm abundance were 23.1, 35.3, 55.7, and 226.9% higher in organically fertilized, no-tillage plots than in inorganically fertilized, conventional tillage plots, respectively. Among the different soil enzymes studied (i.e., dehydrogenase, β-glucosidase, arylsulphatase, and acid phosphatase), dehydrogenase activity appeared most sensitive to the treatments. It was concluded that biological parameters have great value as early and sensitive indicators of changes in soil properties induced by different management strategies. On the contrary, conventional physicochemical parameters were not sensitive enough to detect the relatively subtle changes in soil properties caused by these management practices in the short-term.

Bacterial community structure and metabolic profiles in a forest soil exhibiting spatially variable net nitrate production

High spatial heterogeneity in nitrification potentials has been observed in the top soils of a pine forest. In the present study the bacterial community structure, function and activity was determined in an acid forest soil and their relationships to spatial variation in net NO 3 − ‐ N production were analysed. The bacterial richness, determined by 16S rDNA DGGE fingerprinting showed more variation between samples from the same soil than the substrate utilisation patterns. Differences in microbial transformations such as NH 4 + ‐ N or NO 3 − ‐ N production were not correlated to bacterial diversity and community structure. Nonetheless, there was a positive significant correlation between N-mineralisation and nitrification, indicating that ammonium production is an important regulator of nitrification in this soil. The combined results showed that this forest soil contains a highly diverse bacterial community with a limited number of strongly dominant species, variable in space and a limited number of nitrifiers.

Functional and molecular responses of soil microbial communities under differing soil management practices

The effects of soil management on some microbiological properties and soil bacterial community structure were evaluated. Two field sites with the same soil type, located on the same geographic area adjacent to one other, have received different soil management practices and cultivation. One site has been subjected for 20 years to intensive horticulture under conventional tillage and irrigation with low quality salt-rich water; the second field site has been uncultivated for a long period and was turned to organic farming practices over the last 5 years and is currently cultivated with fruit orchard. Total bacterial counts, microbial ATP, microbial community metabolic (BIOLOG®) profiles, and DNA fingerprinting by PCR-DGGE were determined. Two-way ANOVA revealed that total bacterial counts were not significantly (P>0.3) affected by the two different management practices; ATP content was consistently and significantly (P<0.001) lower in salt-water irrigated soil than in organic soil at the three sampling times. The cluster analysis of community level physiological profiles indicated that microbial communities were much more uniform in organic soil than in irrigated one, suggesting that salt-water irrigation could have affected the size of the microbial population, its metabolic activities, as well as its composition. Molecular patterns fitted the BIOLOG® profile diversity. In particular, at any sampling time, PCR-DGGE patterns of bacterial DNA, extracted by an indirect method, significantly discriminated irrigated from organic soil samples. The PCR-DGGE patterns of total soil DNA, extracted by a direct method, showed a moderate to significant variation among irrigated and organic soil samples. Biochemical, microbiological and molecular data contributed to evidence a significantly different response of indigenous microflora to soil management by using saline water or organic farming.

Benthic microbial utilization of differential dissolved organic matter sources in a forest headwater stream

Streamside mesocosm experiments were conducted in a low-order forest watershed to directly examine responses by microbial communities on standardized substrates to different terrestrial and aquatic sources of dissolved organic matter (DOM). Community respiration (oxygen uptake), microbial density (colony-forming units on agar plates), leaf decomposition, and community metabolic profiles (metabolism patterns in sole carbon source utilization assays) were measured. Stream benthic microbial communities responded immediately and positively to increases in terrestrially derived DOM. Respiration activity and density estimates increased significantly, but there was no significant change in community metabolic profile. Responses were greater to DOM extracted from upper soil horizons than from deeper soils. Community respiration and bacterial abundance also increased in response to an aquatic DOM source, but were accompanied by a significant change in community metabolic profiles. Results provide direct experimental evidence that benthic microbial communities of forest headwater streams are able to rapidly utilize terrestrial DOM.