Publications

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    ABSTRACT: Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory (RMT)-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analyzed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140 to 269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbors. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations. This article is protected by copyright. All rights reserved.
    Environmental Microbiology 07/2015; DOI:10.1111/1462-2920.12981 · 6.24 Impact Factor
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    ABSTRACT: The soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downwards or upwards along an elevation gradient between 3200 and 3800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a two-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites, and more different from those in their "home" sites. Warming led to increases in the relative abundances of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria and decreases of Acidobacteria, Betaproteobacteria, and Deltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming/cooling. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 06/2015; DOI:10.1128/AEM.00557-15 · 3.95 Impact Factor
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    ABSTRACT: Over the past decade, the large-scale cultivation of seaweed Gracilaria has expanded rapidly in the Chinese coastal waters. The production of Gracilaria increased from 50,536 tons (t, dry weight) in 2003 to 114,722 t in 2010. The production of the seaweed ranks third only to kelps Saccharina (formerly referred to as Laminaria) and Undaria in China. Nan'ao located in Shantou City, Guangdong Province has been successfully developed as one of the major cultivation bases of Gracilaria lemaneiformis at an industrial scale in South China since 2000, and the farmed area increased by 11,538-fold from 0.13 ha in 2000 to 1500 ha in 2011. From lab-scale study to field industrial practice, it has been documented that Gracilaria cultivation is beneficial in environmental improvements such as mitigating eutrophication, controlling harmful algal blooms, maintaining healthy mariculture systems, and sequestrating CO2. Gracilaria may significantly remediate contaminants in mariculture ecosystems and improve the water environment, and its cultivation provides a new approach to coastal environmental improvement in China and the world.
    Algal Research 05/2015; 9. DOI:10.1016/j.algal.2015.03.017 · 4.10 Impact Factor
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    ABSTRACT: Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts. Copyright © 2015 Smith et al.
    mBio 05/2015; 6(3). DOI:10.1128/mBio.00326-15 · 6.88 Impact Factor
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    ABSTRACT: The CRISPR-Cas9 system is a powerful and revolutionary genome-editing tool for eukaryotic genomes but its use in bacterial genomes is very limited. Here we investigated the use of the Streptococcus pyogenes CRISPR-Cas9 system in editing the genome of Clostridium cellulolyticum, a model microorganism for bioenergy research. Wildtype Cas9-induced double-strand breaks were lethal to C. cellulolyticum due to the minimal expression of non-homologous end joining (NHEJ) components in this strain. To circumvent this lethality, Cas9 nickase was applied to develop a single nick-triggered homologous recombination strategy, which allows precise one-step editing at intended genomic loci by transforming a single vector. This strategy has a high editing efficiency (>95%) even using short homologous arms (0.2 kb), is able to markerlessly deliver foreign genes into the genome in a single step, enables precise editing even at two very similar target sites differing by two bases preceding the seed region, and has a very high target site density (median interval distance of 9 bp and 95.7% gene coverage in C. cellulolyticum). Together, these results establish a simple and robust methodology for genome editing in NHEJ-ineffective prokaryotes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 04/2015; 81(13). DOI:10.1128/AEM.00873-15 · 3.95 Impact Factor
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    ABSTRACT: A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for one year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities towards prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities, and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI) and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over nine months. Montel tests suggested that the dynamics in the abundance, composition and structure of these key functional genes/groups was significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI) and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 04/2015; 81(12). DOI:10.1128/AEM.00043-15 · 3.95 Impact Factor
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    ABSTRACT: To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.The ISME Journal advance online publication, 7 April 2015; doi:10.1038/ismej.2015.45.
    The ISME Journal 04/2015; DOI:10.1038/ismej.2015.45 · 9.27 Impact Factor
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    ABSTRACT: Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receiving nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography. Copyright © 2015 Liang et al.
    mBio 04/2015; 6(2). DOI:10.1128/mBio.00240-15 · 6.88 Impact Factor
  • PLoS ONE 04/2015; 10(4):e0123179. DOI:10.1371/journal.pone.0123179 · 3.53 Impact Factor
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    ABSTRACT: Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for >3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. In this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase for a long term in response to this slowly-degrading, complex substrate. To test these hypotheses, groundwater microbial communities were monitored after HRC amendment for >1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO3-, Cr(VI), Fe(II) and SO42-. Our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer towards long-term Cr(VI) reduction.
    Environmental Science & Technology 04/2015; DOI:10.1021/acs.est.5b00024 · 5.48 Impact Factor
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    ABSTRACT: Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.
    Scientific Reports 03/2015; 5:9316. DOI:10.1038/srep09316 · 5.58 Impact Factor
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    ABSTRACT: The expanding use of single-walled carbon nanotubes (SWCNTs) raises environmental concerns. Wastewater treatment systems are potential recipients of SWCNTs containing influent, yet the impacts of SWCNTs on these systems are poorly documented. In this study, the microbial responses to SWCNTs in simulated phenol wastewater treatment systems were investigated. The phenol removal rates were improved in all SWCNTs-treated sequencing batch reactors during the first 20 days, but when facing higher phenol concentration (1000 mg/L) after 60 days, reactors with the highest concentration (3.5 g/L) of SWCNTs exhibited a notably decreased phenol removal capacity. Cell viability tests, scanning electron microscopy analysis and DNA leakage data suggested that SWCNTs protected microbes from inactivation possibly by producing more bound extracellular polymeric substances (EPS), which could create a protective barrier for the microbes. Illumina sequencing of 16S rRNA gene amplicons revealed that the bacterial diversity did not change significantly except for a minor reduction after the immediate addition of SWCNTs. Bacterial community structure significantly shifted after SWCNTs addition and did not recover afterwards. Zoogloea increased significantly upon SWCNTs shocking. At final stage, Rudaea and Mobilicoccus increased, while Burkholderia, Singulisphaera, Labrys and Mucilaginibacter decreased notably. The shifts of these dominant genera may be associated with altered sludge settling, aromatic degradation and EPS production. This study suggested that SWCNTs exerted protective rather than cytotoxic effects on sludge microbes of phenol wastewater treatment systems and they affected the bacterial community structure and diversity at test concentrations. These findings provide new insights into our understanding of the potential effects of SWCNTs on wastewater treatment processes.
    Environmental Science & Technology 03/2015; DOI:10.1021/es5053045 · 5.48 Impact Factor
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    ABSTRACT: The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.
    Scientific Reports 02/2015; 5:8605. DOI:10.1038/srep08605 · 5.58 Impact Factor
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    ABSTRACT: Warming has been shown to cause soil carbon (C) loss in northern grasslands owing to accelerated microbial decomposition that offsets increased grass productivity. Yet, a multi-decadal survey indicated that the surface soil C stock in Tibetan alpine grasslands remained relatively stable. To investigate this inconsistency, we analyzed the feedback responses of soil microbial communities to simulated warming by soil transplant in Tibetan grasslands. Whereas microbial functional diversity decreased in response to warming, microbial community structure did not correlate with changes in temperature. The relative abundance of catabolic genes associated with nitrogen (N) and C cycling decreased with warming, most notably in genes encoding enzymes associated with more recalcitrant C substrates. By contrast, genes associated with C fixation increased in relative abundance. The relative abundance of genes associated with urease, glutamate dehydrogenase and ammonia monoxygenase (ureC, gdh and amoA) were significantly correlated with N2O efflux. These results suggest that unlike arid/semiarid grasslands, Tibetan grasslands maintain negative feedback mechanisms that preserve terrestrial C and N pools. To examine whether these trends were applicable to the whole plateau, we included these measurements in a model and verified that topsoil C stocks remained relatively stable. Thus, by establishing linkages between microbial metabolic potential and soil biogeochemical processes, we conclude that long-term C loss in Tibetan grasslands is ameliorated by a reduction in microbial decomposition of recalcitrant C substrates.
    The ISME Journal 02/2015; DOI:10.1038/ismej.2015.19 · 9.27 Impact Factor
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    ABSTRACT: Although phytoplankton are the major source of marine dissolved organic matter (DOM), their blooms are a global problem that can greatly affect marine ecological systems, especially free-living bacteria, which are the primary DOM degraders. In this study, we analyzed free-living bacterial communities from Xiamen sea during an Akashiwo sanguine bloom using Illumina MiSeq sequencing of 16S rRNA gene amplicons. The bloom was probably stimulated by low salinity and ended after abatement of eutrophication pollution. A total of 658,446 sequence reads and 11,807 OTUs were obtained in both bloom and control samples with Alpha-proteobacteria and Gamma-proteobacteria being the predominant classes detected. The bloom decreased bacterial diversity, increased species evenness, and significantly changed the bacterial community structure. Bacterial communities within the bloom were more homogeneous than those within the control area. The bacteria stimulated by this bloom included the SAR86 and SAR116 clades and the AEGEAN-169 marine group, but a few were suppressed. In addition, many bacteria known to be associated with phytoplankton were detected only in the bloom samples. This study revealed the great influence of an A. sanguinea bloom on free-living bacterial communities, and provided new insights into the relationship between bacteria and A. sanguinea in marine ecosystems.
    Scientific Reports 02/2015; 5(5):8476. DOI:10.1038/srep08476 · 5.58 Impact Factor
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    ABSTRACT: Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions. Copyright © 2015 Zhou et al.
    mBio 01/2015; 6(1). DOI:10.1128/mBio.02288-14 · 6.88 Impact Factor
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    ABSTRACT: Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2 (eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2 for 12 years. Long-term eCO2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. Relative abundances of 119 OTUs (∼ 27% of the total captured sequences) were changed significantly. Significantly changed OTUs under eCO2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4 (+)availability. This study provided novel insights into how eCO2 shapes soil fungal communities in grassland ecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 01/2015; 81(7). DOI:10.1128/AEM.04040-14 · 3.95 Impact Factor
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    ABSTRACT: Networks of engineered waterways are critical in meeting growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. Based on PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, it was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters studied spatially, only three metals, namely potassium, copper and aluminum significantly explained between 7-11 % of the variation in taxa and functions, based on Distance-based Linear Models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.
    Environmental Science and Technology 01/2015; 49(3). DOI:10.1021/es504531s · 5.48 Impact Factor
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    ABSTRACT: Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
    FEMS Microbiology Ecology 01/2015; 91(1). DOI:10.1093/femsec/fiu003 · 3.88 Impact Factor
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    ABSTRACT: Microbial-driven biogeochemical cycles in wetlands impacted by global warming pose a potential downstream eutrophication risk. However, the consequences of ongoing warming on the functional and metabolic potential of sediment microbial communities are largely unknown. We incubated sediment samples under both ambient temperature conditions (control) and simulated warming conditions of 5°C above ambient temperature (warmed) using a novel field microcosm system. In warmed samples, we observed in situ a decreased thickness of the oxidized sediment layer and associated lower sediment redox potential. GeoChip 4.0, a comprehensive functional gene microarray, demonstrated that many functional genes that are involved in oxidation–reduction reactions and in phosphorus (P) degradation were preferentially enriched under warming conditions. The enriched genes included those genes encoding carbon monoxide dehydrogenase, acetyl-CoA carboxylase biotin carboxylase (ppc), and ribulose-1,5-bisphosphate carboxylase (Rubisco) for carbon fixation; nitrate reductases (narG) and nitrous oxide reductases (nosZ) for denitrification; cytochrome c for metal reduction; and exopolyphosphatase (ppx) for polyphosphate degradation. The redox potential was one of the most significant parameters linked to microbial functional gene structure. These results demonstrate that the enhanced hypoxia and anaerobic metabolic pathways accelerated sediment P mobilization in freshwater wetland subject to warming, raising the potential of water eutrophication.
    Hydrobiologia 01/2015; 743(1). DOI:10.1007/s10750-014-2039-6 · 2.21 Impact Factor

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