Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe

We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning.

1. Biodiversity is declining worldwide with detrimental effects on ecosystems. However, we lack a quantitative understanding of the shape of the relationship between microbial biodiversity and ecosystem function (BEF). This limits our understanding of how microbial diversity depletion can impact key functions for human well-being, including pollutant detoxification. 2. Three independent microcosm experiments were conducted to evaluate the direction (i.e. positive, negative or null) and the shape of the relationships between bacterial diversity and both broad (i.e. microbial respiration) and specialized (i.e. toxin degradation) functions in five Australian and two UK freshwater ecosystems using next-generation sequencing platforms. 3. Reduced bacterial diversity, even after accounting for biomass, caused a decrease in broad (i.e. cumulative microbial respiration) and specialized (biodegradation of two important toxins) functions in all cases. Unlike the positive but decelerating BEF relationship observed most frequently in plants and animals, most evaluated functional measurements were related to bacterial diversity in a non-redundant fashion (e.g. exponentially and/or linearly). 4. Synthesis. Our results suggest that there is a lack of functional redundancy in the relationship between bacterial diversity and ecosystem functioning; thus the consequences of declining microbial diversity on ecosystem functioning and human welfare have likely been considerably underestimated

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1-3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.Peer reviewe

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Corrected by: Erratum: Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database [GigaScience. 5, 1, (2016) (1-11)] DOI: 10.1186/s13742-016-0126-5. In GigaScience 6(5):1, the authorship list should have included Leon Court, who was responsible for sample collection and preparation, sampling design and sequencing method design. The authors regret this omission.BACKGROUND Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. FINDINGS BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’. CONCLUSIONS Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.Andrew Bissett, Anna Fitzgerald, Thys Meintjes, Pauline M. Mele, Frank Reith, Paul G. Dennis, Martin F. Breed, Belinda Brown, Mark V. Brown, Joel Brugger, Margaret Byrne, Stefan Caddy-Retalic, Bernie Carmody, David J. Coates, Carolina Correa, Belinda C. Ferrari, Vadakattu V. S. R. Gupta, Kelly Hamonts, Asha Haslem, Philip Hugenholtz, Mirko Karan, Jason Koval, Andrew J. Lowe, Stuart Macdonald, Leanne McGrath, David Martin, Matt Morgan, Kristin I. North, Chanyarat Paungfoo-Lonhienne, Elise Pendall, Lori Phillips, Rebecca Pirzl, Jeff R. Powell, Mark A. Ragan, Susanne Schmidt, Nicole Seymour, Ian Snape, John R. Stephen, Matthew Stevens, Matt Tinning, Kristen Williams, Yun Kit Yeoh, Carla M. Zammit, and Andrew Youn

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Background: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. Findings: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Conclusions: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services

Structuur en polluent-afbraakactiviteit van de microbiële gemeenschap in eutroof riviersediment beïnvloed door opwellend grondwater gepollueerd met gechloreerde alifatische koolwaterstoffen

Chlorinated aliphatic hydrocarbons (CAHs), which are among the most prev alent groundwater contaminants in the industrialized world, have a large potential to discharge into rivers as contaminated baseflow. This cause s diffuse contamination of the surface water and imposes environmental r isks. However, the fate of the infiltrating groundwater pollutants is in fluenced by the sediment zone in eutrophic rivers where biodegradation o f CAHs may reduce the discharge. The strong reducing conditions that may prevail in such river sediments, the abundance of organic material and the presence of CAHs could provide an ideal environment for halorespirin g bacteria, which yield energy for growth from the reductive dechlorinat ion of CAHs. By transforming the CAHs into their nontoxic end products d uring passage of the groundwater, the river sediment would act as a natu ral biobarrier, protecting the surface water from CAH pollution. This study explored the potential of eutrophic river sediments to attenu ate the infiltration of CAH-polluted groundwater discharging into the ri ver Zenne near Brussels, Belgium. Active biotic reductive dechlorination of CAHs in the sediment was suggested by a high dechlorination activity in batch- and column biodegradation tests performed with sediment sampl es, and by the detection of dechlorination products in sediment pore wat er. Monitoring of CAH concentrations and stable isotope ratios of the CA Hs (d13C) and the water (d2H and d18O), allowed to identify different bi otic and abiotic CAH attenuation processes and to delineate their spatia l distribution in the riverbed. In a 45 by 15 m long stretch of the rive r Zenne, pore water samples were repeatedly collected at 25 locations an d three depths in the riverbed. Microbial reductive dechlorination of th e CAHs was observed at 30 to 40% of the investigated locations and there fore appeared the most widespread CAH attenuation process in the Zenne r iverbed, followed by dilution by surface water-mixing and unpolluted gro undwater discharge. The distribution of those processes proved to be spa tially and temporally heterogeneous. Analysis of pore water samples from stationary sampling devices, installed at three locations in the Zenne riverbed, revealed that the extent of biodegradation from 120 to 20 cm d epth in the riverbed, measured by the increase in d13C of the CAHs, rema ined rather constant over time. At those locations, the observed decreas e in the pore water CAH concentrations during vertical discharge of the CAH-polluted groundwater from 120 to 20 cm depth in the sediments, was c aused by a combination of biodegradation and dilution by infiltrating su rface water. The relative contribution of those two processes to the obs erved CAH attenuation varied both spatially and temporally in the Zenne riverbed. Since dilution by surface-water mixing, which is criticized as a natural attenuation process, occasionally contributed to the observed concentration decrease to a larger extent than biodegradation, this cou ld affect acceptance of the Zenne as a natural biobarrier. Bacteria from the genus Dehalococcoides, known for their CAH dechlorinat ion capacity, were detected in Zenne sediments from all investigated riv erbed locations and depths within the test area. Since these species wer e enriched in river sediment columns that actively degraded the CAHs, th ese bacteria were probably associated with the reductive dechlorination activity in the Zenne sediments. The detection of genes related to bvcA and vcrA, encoding the vinyl chloride reductive dehalogenase enzymes in Dehalococcoides, strengthened this hypothesis. Their detection implies t hat energy for growth is recovered from the degradation of the main grou ndwater pollutants discharging into the Zenne, i.e. cis-dichloroethene ( cis-DCE) and vinyl chloride (VC), to nontoxic ethene. By using DGGE-fing erprint analysis of relevant nucleic acid markers, it was shown that the Zenne river sediments were inhabited by a metabolically diverse bacteri al community. A large diversity of sulfate-reducing bacteria, Geobactera ceae and methanogens, which potentially compete with halorespiring bacte ria for electron resources, was identified. The high organic carbon leve l in the top of the riverbed, originating from organic matter deposition from the eutrophic surface water, resulted in a homogeneous microbial c ommunity structure that differed from the microbial community structure of the sediment underneath this layer. Continuous tests performed with Zenne sediments or aquifer collected wit hin the CAH plume adjacent to the river demonstrated that the Zenne sedi ments have a higher CAH reductive dechlorination potential than the poll uted aquifer. While reductive dechlorination of the CAHs to their non-to xic end products continuously occurred in all columns containing river s ediments, biodegradation of CAHs was never observed in the aquifer colum ns. Furthermore, results of the column tests indicated that CAH biodegra dation in the riverbed is affected by the groundwater residence time and the presence of co-contaminants. Whereas 21 µM VC, 3 µM cis-D CE and 0.37 µM 1,1-dichloroethane (1,1-DCA) were totally removed fr om the groundwater at a pore water velocity of 2.7 and 5.4 cm/day, those CAHs reached the top of the approximately 1 m long sediment layer in th e columns at a pore water velocity of 9.2 cm/day. Biodegradation of 1,1- DCA was inhibited by the presence of cis-DCE and VC and therefore only o ccurred at heights in the river sediment columns where cis-DCE and VC we re partially reduced. Although CAHs were never detected in the surface water, 26 to 28% of the investigated locations in the riverbed did not show CAH attenuation. Mo reover, CAHs were not completely removed from the discharging groundwate r at 20 cm depth in the riverbed in 67 to 70% of the remaining riverbed locations. Although attenuation processes in the top 20 cm of the riverb ed could further remove residual CAH, our data suggest that CAHs reached the surface water at certain locations in the studied riverbed section. Therefore, it was concluded that an increase in the extent of biodegrad ation in the riverbed is needed for acceptance of the Zenne biobarrier a s a viable remedial option for attenuation of discharging CAH-polluted g roundwater. Since the moderate extent of biodegradation of the CAHs in t he riverbed, despite the presence and activity of halorespiring bacteria and apparently ideal conditions for reductive dechlorination, was possi bly due to a low residence time of the CAHs in the Zenne sediments, an i ncrease in the groundwater residence time in the riverbed could improve the Zenne biobarrier efficiency.status: publishe

Influence of copper on expression of nirS, noRrB and nosZ and the transcription and activity of NIR, NOR and N₂O in the denitrifying soil bacteria Pseudomonas stutzeri

Reduction of the potent greenhouse gas nitrous oxide (N₂O) occurs in soil environments by the action of denitrifying bacteria possessing nitrous oxide reductase (N₂OR), a dimeric copper (Cu)-dependent enzyme producing environmentally benign dinitrogen (N₂). We examined the effects of increasing Cu concentrations on the transcription and activity of nitrite reductase (NIR), nitric oxide reductase (NOR) and N₂OR in Pseudomonas stutzeri grown anaerobically in solution over a 10-day period. Gas samples were taken on a daily basis and after 6 days, bacterial RNA was recovered to determine the expression of nirS, norB and nosZ encoding NIR, NOR and N₂OR respectively. Results revealed that 0.05 mM Cu caused maximum conversion of N₂O to N₂ via bacterial reduction of N₂O. As soluble Cu generally makes up less than 0.001% of total soil Cu, extrapolation of 0.05 mg l-l soluble Cu would require soils to have a total concentration of Cu in the range of, 150-200 μg g-1 to maximize the proportion of N₂O reduced to N₂. Given that many intensively farmed agricultural soils are deficient in Cu in terms of plant nutrition, providing a sufficient concentration of biologically accessible Cu could provide a potentially useful microbial-based strategy of reducing agricultural N₂O emissions

TaxaSE : exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both \textitin-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects