Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type.

UNLABELLED: This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols. IMPORTANCE: This work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale.

The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyse bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on ß-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower ß-diversity and narrower breadth compared with distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of ß-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region was likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity.

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.

The genus Sediminibacterium comprises species present in diverse natural and engineered environments. Here, we report for the first time the genome sequences of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a valuable model for the study of substrate-dependent autoaggregation.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks.

Bacterial indicator of agricultural management for soil under no-till crop production.

The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non-sustainable agricultural practices in the Pampa region.

Performance of planar and cylindrical carbon electrodes at sedimentary microbial fuel cells.

This paper presents data obtained using an indigenous microbial community contained in anaerobic sediments (mud) collected from the shore of the Río de La Plata River (South America). After the sedimentary microbial fuel cells were assembled the evolution of current and power vs. time was studied. Two types of commercially available graphite materials were used as electrodes, which differ mainly in shape and size. In some experiments, an external carbon source (acetate) increased the power generation rate. The maximum power density observed in the aforementioned condition was 19.57 ± 0.35 and 8.72 ± 1.39 mW/m(2) using rod and graphite disk electrodes, respectively. The better performance of the rod electrodes can be explained, at least in part, by an enhanced rate of mass transport by radial diffusion. DGGE fingerprints were used to study the electrogenic community growing over the electrodes.

[Impact of the recent advances in the analysis of microbial communities on the control of the wastewater treatment process]. / Impacto de los recientes avances en el análisis de comunidades microbianas sobre el control del proceso de tratamiento de efluentes.

One of the main functions of environmental biotechnology is to address the study of microbial communities that provide essential services to society. Beyond the similarities with industrial and agricultural microbiology, the unique features exhibited by environmental biotechnology, such as process objectives, biomass characteristics and type and mode of feeding (substrates), allow a clear distinction from the other related disciplines. Recent advances in microbial ecology, ecophysiology, genomics and process engineering are herein reviewed to illustrate how the integration of the new knowledge can help overcome the shortcomings of classic microbiological analyses to understand, predict and optimize the performance of wastewater treatment.

Impacto de los recientes avances en el análisis de comunidades microbianas sobre el control del proceso de tratamiento de efluentes / Impact of the recent advances in the analysis of microbial communities on the control of the wastewater treatment process

Una de las funciones principales de la biotecnología ambiental es ocuparse del estudio de comunidades microbianas que proveen servicios esenciales para la sociedad. Más allá de las similitudes que presenta con la microbiología industrial y la agrícola, la biotecnología ambiental presenta peculiaridades, tales como los objetivos de proceso, las características de la biomasa y el tipo y modo de alimentación (sustratos), que la distinguen claramente de las otras disciplinas relacionadas. En este artículo se reseñan recientes avances en la ecología microbiana, la ecofisiología, la genómica y la ingeniería de procesos, para ilustrar cómo la integración de los nuevos conocimientos permite superar las limitaciones del análisis microbiológico clásico para entender, predecir y optimizar el funcionamiento de los procesos de tratamiento de efluentes.

One of the main functions of environmental biotechnology is to address the study of microbial communities that provide essential services to society. Beyond the similarities with industrial and agricultural microbiology, the unique features exhibited by environmental biotechnology, such as process objectives, biomass characteristics and type and mode of feeding (substrates), allow a clear distinction from the other related disciplines. Recent advances in microbial ecology, ecophysiology, genomics and process engineering are herein reviewed to illustrate how the integration of the new knowledge can help overcome the shortcomings of classic microbiological analyses to understand, predict and optimize the performance of wastewater treatment.

Diversity of nitrifying bacteria in a full-scale petroleum refinery wastewater treatment plant experiencing unstable nitrification.

We have investigated bacterial populations relevant to nitrification in a full-scale activated sludge plant receiving wastewater from a petroleum refinery showing unstable nitrification. Inhibition of ammonia oxidation was related to phenol concentration according to a model of non-competitive inhibition. While the number of ammonia-oxidizing bacteria (AOB) did not correlate with nitrification performance, the total number of nitrite-oxidizing bacteria (NOB) dropped considerably during periods of nitrite accumulation or no nitrification. Diversity of nitrifiers in the sludge of the full-scale facility was examined at a time of full nitrification with the construction of clone libraries of ammonia monooxygenase (amoA) gene and of the 16S rRNA gene of NOB. Nucleotide sequences of amoA gene belonged to one dominant population, associated with Nitrosomonas europaea, and to a minor population related to the Nitrosomonas nitrosa lineage. The majority of sequences retrieved in the NOB-like clone library also clustered within a single operational taxonomic unit. The high dominance of Nitrobacter over Nitrospira and the low diversity of nitrifying bacteria observed in this wastewater treatment plant might account for the increased risk of failure in the presence of disturbances.

Bacterial taxa abundance pattern in an industrial wastewater treatment system determined by the full rRNA cycle approach.

The description of the diversity and structure of microbial communities through quantification of the constituent populations is one of the major objectives in environmental microbiology. The implications of models for community assembly are practical as well as theoretical, because the extent of biodiversity is thought to influence the function of ecosystems. Current attempts to predict species diversity in different environments derive the numbers of individuals for each operational taxonomic unit (OTU) from the frequency of clones in 16S rDNA gene libraries, which are subjected to a number of inherent biases and artefacts. We show that diversity of the bacterial community present in a complex microbial ensemble can be estimated by fitting the data of the full-cycle rRNA approach to a model of species abundance distribution. Sequences from a 16S rDNA gene library from activated sludge were reliably assigned to OTUs at a genetic distance of 0.04. A group of 17 newly designed rRNA-targeted oligonucleotide probes were used to quantify by fluorescence in situ hybridization, OTUs represented with more than three clones in the 16S rDNA clone library. Cell abundance distribution was best described by a geometric series, after the goodness of fit was evaluated by the Kolmogorov-Smirnov test. Although a complete mechanistic understanding of all the ecological processes involved is still not feasible, describing the distribution pattern of a complex bacterial assemblage model can shed light on the way bacterial communities operate.

Replicability of dominant bacterial populations after long-term surfactant-enrichment in lab-scale activated sludge.

Bacterial communities were examined in replicate lab-scale activated sludge reactors after a period of several months of enrichment with non-ionic nonylphenol ethoxylate (NPE) surfactants. Four sequential batch reactors were fed with synthetic sewage, two of which received additionally NPE. Small subunit rDNA-derived denaturing gel gradient electrophoresis (DGGE) profiles and 16S rDNA clone libraries were dominated by clones of Gammaproteobacteria class. Sequences of the other codominant rDNA phylotypes observed only in DGGE from NPE-amended reactors were, respectively, associated with the Group III of the Acidobacteria phylum. Intriguingly, 16S rRNA content from abundant Gammaproteobacteria cells was unexpectedly low. In addition to Acidobacteria, rRNA-derived DGGE profiles were dominated by members of the order Burkholderiales (of the Betaproteobacteria) and of the genus Sphingomonas (a member of the Alphaproteobacteria). Specific oligonucleotide probes for the selected ribotypes were designed and applied for quantitative real time polymerase chain reaction and fluorescence in situ hybridization, confirming their dominance in treated reactors. The parallel abundance of unique phylotypes in replicate reactors implies a distinctive selection of dominant organisms, which are better adapted to specialized niches in the highly selective environment.