Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater

Anthropogenic pollution gradient along a mountain river affects bacterial community composition and genera with potential pathogenic species

Mountain regions in Poland are among the most frequently visited tourist destinations, causing a significant anthropogenic pressure put on the local rivers. In this study, based on numbers of 9 microorganisms, content of 17 antibiotics and 17 physicochemical parameters, we determined a pollution gradient in six sites along Białka, a typical mountain river in southern Poland. The E.coli/Staphylococcus ratio varied evidently between polluted and non-polluted sites, indicating that the possible utility of this parameter in assessing the anthropogenic impact on river ecosystems is worth further investigation. Then, using next generation sequencing, we assessed the changes in bacterial community structure and diversity as a response to the pollution gradient. Proteobacteria and Bacteroidetes were the most abundant phyla in the majority of samples. Actinobacteria were the most abundant in the most pristine (groundwater) sample, while Firmicutes and Verrucomicrobia were more prevalent in polluted sites. Bacterial diversity at various levels increased with water pollution. Eleven bacterial genera potentially containing pathogenic species were detected in the examined samples, among which Acinetobacter, Rhodococcus, and Mycobacterium were the most frequent. At the species level, Acinetobacter johnsonii was most prevalent potential pathogen, detected in all surface water samples, including the pristine ones. Two bacterial taxa-genus Flectobacillus and order Clostridiales showed very distinct variation in the relative abundance between the polluted and non-polluted sites, indicating their possible potential as biomarkers of anthropogenic impact on mountain river waters.

Tracking down carbon inputs underground from an arid zone Australian calcrete

Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwater systems. However, despite the growing concerns related to increasing anthropogenic pressure and effects of global change to groundwater environments, our understanding of the dynamics regulating subterranean carbon flows is still sparse. We traced carbon composition and transformations in an arid zone calcrete aquifer using a novel multidisciplinary approach that combined isotopic analyses of dissolved organic carbon (DOC) and inorganic carbon (DIC) (δ13CDOC, δ13CDIC, 14CDOC and 14CDIC) with fluorescence spectroscopy (Chromophoric Dissolved OM (CDOM) characterisation) and metabarcoding analyses (taxonomic and functional genomics on bacterial 16S rRNA). To compare dynamics linked to potential aquifer recharge processes, water samples were collected from two boreholes under contrasting rainfall: low rainfall ((LR), dry season) and high rainfall ((HR), wet season). Our isotopic results indicate limited changes and dominance of modern terrestrial carbon in the upper part (northeast) of the bore field, but correlation between HR and increased old and 13C-enriched DOC in the lower area (southwest). CDOM results show a shift from terrestrially to microbially derived compounds after rainfall in the same lower field bore, which was also sampled for microbial genetics. Functional genomic results showed increased genes coding for degradative pathways-dominated by those related to aromatic compound metabolisms-during HR. Our results indicate that rainfall leads to different responses in different parts of the bore field, with an increase in old carbon sources and microbial processing in the lower part of the field. We hypothesise that this may be due to increasing salinity, either due to mobilisation of Cl- from the soil, or infiltration from the downstream salt lake during HR. This study is the first to use a multi-technique assessment using stable and radioactive isotopes together with functional genomics to probe the principal organic biogeochemical pathways regulating an arid zone calcrete system. Further investigations involving extensive sampling from diverse groundwater ecosystems will allow better understanding of the microbiological pathways sustaining the ecological functioning of subterranean biota.

Phenanthrene removal and response of bacterial community in the combined system of photocatalysis and PAH-degrading microbial consortium in laboratory system

This work aimed to study the removal of phenanthrene, change of bacterial community and microbial functions through combined photocatalysis and biodegradation under ultraviolet (UV) and visible light illumination. Results showed that phenanthrene removal was enhanced in combined system irradiated by UV and visible light. High-throughput sequencing of 16S rRNA gene manifested that alpha diversity (richness, evenness and diversity) got promoted and data of relative abundance reported that Planococcaceae as the dominant bacteriawas replaced by Pseudomonadaceae, with some other functional bacteria quickly acclimatizing. Difference analysis indicated that top fifteen genera were generally different significantly (p < 0.001) among two distinct samples, particularly for Pseudomonas on relative abundance. Functional features' regulation suggested that the bacterial community not only protected itself well but also participated in degrading phenanthrene. Selecting suitable degrading microbial consortium from natural environment and understanding deeply on performance of bacterial community contribute to assemble effective and directional combined system.

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Acinetobacter sp. DW-1 immobilized on polyhedron hollow polypropylene balls and analysis of transcriptome and proteome of the bacterium during phenol biodegradation process

Phenol is a hazardous chemical known to be widely distributed in aquatic environments. Biodegradation is an attractive option for removal of phenol from water sources. Acinetobacter sp. DW-1 isolated from drinking water biofilters can use phenol as a sole carbon and energy source. In this study, we found that Immobilized Acinetobacter sp. DW-1cells were effective in biodegradation of phenol. In addition, we performed proteome and transcriptome analysis of Acinetobacter sp. DW-1 during phenol biodegradation. The results showed that Acinetobacter sp. DW-1 degrades phenol mainly by the ortho pathway because of the induction of phenol hydroxylase, catechol-1,2-dioxygenase. Furthermore, some novel candidate proteins (OsmC-like family protein, MetA-pathway of phenol degradation family protein, fimbrial protein and coenzyme F390 synthetase) and transcriptional regulators (GntR/LuxR/CRP/FNR/TetR/Fis family transcriptional regulator) were successfully identified to be potentially involved in phenol biodegradation. In particular, MetA-pathway of phenol degradation family protein and fimbrial protein showed a strong positive correlation with phenol biodegradation, and Fis family transcriptional regulator is likely to exert its effect as activators of gene expression. This study provides valuable clues for identifying global proteins and genes involved in phenol biodegradation and provides a fundamental platform for further studies to reveal the phenol degradation mechanism of Acinetobacter sp.

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.

Metagenomic Investigation of Viral Communities in Ballast Water

Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.

CoMeta: classification of metagenomes using k-mers

Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (k-mers) and fast program for indexing large set of k-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at https://github.com/jkawulok/cometa under a free GNU GPL 2 license.

Metagenomic analysis of the airborne environment in urban spaces

The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.

Census-based rapid and accurate metagenome taxonomic profiling

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.

Conclusion

CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.

A preliminary metagenomic study of puer tea during pile fermentation

BACKGROUND

Up to now, there has been no report on the taxonomic and functional analysis of the microbial community in fermenting puer tea by pyrosequencing. In this study, metagenomic pyrosequencing was first used in fermenting puer tea to delineate a relatively comprehensive overview of the microbial taxonomy while also preliminarily characterising the functional ontologies of microbial genes present in puer tea pile fermentation.

RESULTS

A total of 251 738 pyrosequencing reads (9197 contigs and 145 402 singletons) were generated by pyrosequencing. Taxonomic analysis revealed three dominant bacterial phyla, Actinobacteria (30.08%), Proteobacteria (24.47%) and Firmicutes (20.23%), and one dominant eukaryotic phylum, Ascomycota (15.21%) [corrected]. A total of 58 664 hits were categorised into 28 functional subsystems based on the SEED database. Moreover, two categories, 'metabolism of terpenoids and polyketides' and 'biosynthesis of other secondary metabolites', were selectively analysed and 69 enzyme genes were presented in 16 pathways.

CONCLUSION

The dominant microbes of puer tea fermentation were bacteria in the present study, and yeasts rather than moulds accounted for the overwhelming majority of Eukaryota. The analysis of functional genes and metabolic pathways will be helpful for further study of the mechanism of puer tea fermentation at molecular level.

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.

Distinctive microbial community structure in highly stratified deep-sea brine water columns

Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor

BACKGROUND

A solid-state anaerobic digestion method is used to produce biogas from various solid wastes in China but the efficiency of methane production requires constant improvement. The diversity and abundance of relevant microorganisms play important roles in methanogenesis of biomass. The next-generation high-throughput pyrosequencing platform (Roche/454 GS FLX Titanium) provides a powerful tool for the discovery of novel microbes within the biogas-generating microbial communities.

RESULTS

To improve the power of our metagenomic analysis, we first evaluated five different protocols for extracting total DNA from biogas-producing mesophilic solid-state fermentation materials and then chose two high-quality protocols for a full-scale analysis. The characterization of both sequencing reads and assembled contigs revealed that the most prevalent microbes of the fermentation materials are derived from Clostridiales (Firmicutes), which contribute to degrading both protein and cellulose. Other important bacterial species for decomposing fat and carbohydrate are Bacilli, Gammaproteobacteria, and Bacteroidetes (belonging to Firmicutes, Proteobacteria, and Bacteroidetes, respectively). The dominant bacterial species are from six genera: Clostridium, Aminobacterium, Psychrobacter, Anaerococcus, Syntrophomonas, and Bacteroides. Among them, abundant Psychrobacter species, which produce low temperature-adaptive lipases, and Anaerococcus species, which have weak fermentation capabilities, were identified for the first time in biogas fermentation. Archaea, represented by genera Methanosarcina, Methanosaeta and Methanoculleus of Euryarchaeota, constitute only a small fraction of the entire microbial community. The most abundant archaeal species include Methanosarcina barkeri fusaro, Methanoculleus marisnigri JR1, and Methanosaeta theromphila, and all are involved in both acetotrophic and hydrogenotrophic methanogenesis.

CONCLUSIONS

The identification of new bacterial genera and species involved in biogas production provides insights into novel designs of solid-state fermentation under mesophilic or low-temperature conditions.

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in the central Sahara (Mauritania). Three of the four gueltas (Ilij, Molomhar and Hamdoun) are located at the source of three different wadis belonging to the same hydrologic basin, whereas the fourth (El Berbera) belongs to a different basin. Overall, sequences belonging to tailed bacteriophages were the most abundant in all four metagenomes although electron microscopy and sequencing confirmed the presence of other viral groups, such as large DNA viruses. We observed a decrease in the local viral biodiversity in El Berbera, a guelta with sustained human activities, compared with the pristine Ilij and Molomhar, and sequences related to viruses infecting crop pests were also detected as a probable consequence of the agricultural use of the soil. However, the structure of the El Berbera viral community shared the common global characteristics of the pristine gueltas, that is, it was dominated by Myoviridae and, more particularly, by virulent phages infecting photosynthetic cyanobacteria, such as Prochlorococcus and Synechococcus spp. In contrast, the Hamdoun viral community was characterized by a larger proportion of phages with the potential for a temperate lifestyle and by dominant species related to phages infecting heterotrophic bacteria commonly found in terrestrial environments. We hypothesized that the differences observed in the structural and functional composition of the Hamdoun viral community resulted from the critically low water level experienced by the guelta.

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.