Publications

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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). · 2.21 Impact Factor
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    ABSTRACT: Serious nitrogen (N) deposition in terrestrial ecosystems causes soil acidification and changes the structure and function of the microbial community. However, it is unclear how these changes are dependent on N deposition rates, other factors induced by N (e.g., pH), and their interactions. In this study, we investigated the responses of soil prokaryotic community structure and stability after a 13-year N addition in the semi-arid Leymus chinensis steppe in Inner Mongolia, China. Our results demonstrated that the prokaryotic community structure changed at the low N addition rate of 1.75 g N m−2 yr−1; however, dramatic changes in microbial abundance, respiratory quotient, and prokaryotic diversity occurred at N addition rates of more than 5.25 g N m−2 yr−1 when the soil pH dropped below 6.0. The two patterns indicated the difference in driving forces for different microbial properties. The N-driven and pH-driven processes are likely the most important mechanisms determining the responses of bacterial community to N. Some copiotrophic/oligotrophic bacteria, e.g., Proteobacteria and Acidobacteria, changed their relative abundances with the N addition continuously even at a low rate, indicating that they were more sensitive to N directly. Some bacterial groups significantly changed their relative abundance at a high N addition rate when pH dropped below 6.0, e.g., Verrucomicrobia and Armatimonadetes, indicating that they were more sensitive to pH below 6.0. N addition altered the prokaryotic community structure through enrichment of copiotrophic bacteria (species adjustment) at low N addition rates and through enrichment of nitrophilous taxa and significant loss of diversity at high N rates. The results also demonstrated that a high N addition diminished the stability of the prokaryotic community structure and activity through reduction in species diversity and bacterial interaction. Overall, this study supported the hypothesis that the responses of prokaryota to N were dependent on deposition rates, and N-driven and pH-driven processes were the important mechanisms to control the shift of the prokaryotic community.
    Soil Biology and Biochemistry 12/2014; 79:81–90. · 4.41 Impact Factor
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    ABSTRACT: Microbe plays an important role in driving biogeochemical cycles, thus it is of great interest to understand microbial responses and feedbacks to global changes. We have recently analyzed functional potentials of soil microbial community via a high-throughput, microarray-based metagenomic tool named GeoChip 3.0 to illustrate microbial responses to global changes simulated by soil transplant and/or maize cropping. Here we describe detailed experimental design, data collection and pre-processing to support our published studies by Liu et al. [5] and Zhao et al. [14].
    Genomics Data. 12/2014;
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    ABSTRACT: To examine microbial responses to climate change, we used a microarray-based metagenomics tool named GeoChip 4.0 to profile soil microbial functional genes along four sites/elevations of a Tibetan mountainous grassland. We found that microbial communities differed among four elevations. Soil pH, temperature, NH4+–N and vegetation diversity were four major attributes affecting soil microbial communities. Here we describe in details the experiment design, the data normalization process, soil and vegetation analyses associated with the study published on ISME Journal in 2014 [1], whose raw data have been uploaded to Gene Expression Omnibus (accession number GSM1185243).
    Genomics Data. 12/2014;
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    ABSTRACT: Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involv
    PLoS ONE 11/2014; 9(11):e112609. · 3.53 Impact Factor
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    ABSTRACT: Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased toward deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, likely due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons, and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.This article is protected by copyright. All rights reserved.
    Molecular Ecology 11/2014; · 5.84 Impact Factor
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    ABSTRACT: Characteristics of a microbial community are important as they indicate the status of aquatic ecosystems. In the present study, the metabolic and phylogenetic profile of the bacterioplankton community in Guishan coastal water (Pearl River Estuary), South China Sea, at 12 sites (S1-S12) were explored by community-level physiological profiling (CLPP) with BIOLOG Eco-plate and denaturing gradient gel electrophoresis (DGGE). Our results showed that the core mariculture area (S6, S7 and S8) and the sites associating with human activity and sewage discharge (S11 and S12) had higher microbial metabolic capability and bacterial community diversity than others (S1-5, S9-10). Especially, the diversity index of S11 and S12 calculated from both CLPP and DGGE data (H>3.2) was higher than that of others as sewage discharge may increase water nitrogen and phosphorus nutrient. The bacterial community structure of S6, S8, S11 and S12 was greatly influenced by total phosphorous, salinity and total nitrogen. Based on DGGE fingerprinting, proteobacteria, especially γ- and α-proteobacteria, were found dominant at all sites. In conclusion, the aquaculture area and wharf had high microbial metabolic capability. The structure and composition of bacterial community were closely related to the level of phosphorus, salinity and nitrogen.
    Journal of Ocean University of China 10/2014; 13(5). · 0.38 Impact Factor
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    ABSTRACT: We have begun investigations on microbial communities from Alaskan tundra permafrost (AK) and Oklahoma temperate grassland (OK) soils, both of which have been experimentally warmed in-situ 2 °C above ambient temperature for one year. Our analyses of well-replicated 16S rRNA gene amplicon, meta-transcriptomic, and whole-community shotgun metagenomic datasets from these soils showed small but significant shifts in community composition, gene expression, and functional metabolic potential compared to control (un-warmed) adjacent communities. Greater taxonomic compositional differences were observed at the OK site relative to AK, presumably resulting from longer generation times due to the less optimal conditions for growth at permafrost soils. The most pronounced bacterial taxon shifts observed at OK site, which were somewhat also observed at the AK site, were an increase in abundance of Actinobacteria and decrease in Acidobacteria and Planctomycetes, all representing major phyla in soils, particularly in regards to C-cycling. While shifts in gene pathways due to warming were mild over the 1-year period, our findings show that each site responds differently to warming. OK communities of warmed plots were enriched in genes involved in heat shock response and cellular surface structures, particularly, trans-membrane transporters for glucosides and ferrous iron, whereas their AK counterparts were enriched in metabolic pathways related to labile carbon mobilization and oxidation. By implementing a new contig binning strategy, we recovered large genomic fragments (>500kbp continuous; 2-3Mbp non-continuous) representing several abundant populations (0.2-2% of the total community). These populations appeared to be highly conserved across spatial and environmental gradients at the AK site. Population abundances across samples correspond highly to measured soil characteristics (pH, moisture, SOM, etc.). Our study offers new insights on how soil microbial communities mediate feedback responses of the soil ecosystem to climate change and also addresses basic ecological questions regarding microbial population heterogeneity and biogeography in soils.
    Argonne Soil Metagenomics Meeting, St. Charles, Illinois; 10/2014
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    ABSTRACT: Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.
    BMC Genomics 09/2014; 15(1):753. · 4.04 Impact Factor
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    ABSTRACT: Background/Question/Methods Understanding the responses and the underlying mechanisms of ecological communities to environmental changes is a central issue in ecology. Mean temperature rising on Earth surface represents a pervasive environmental change that is predicted to alter global biodiversity, yet our understanding of the emergent biodiversity impacts is very limited, particularly on taxa-area relationships (TARs) (or spatial scaling of biodiversity), which is one of the few fundamental laws in ecology. Although TARs have been intensively examined, how temperature affects TARs remain elusive remains elusive, particularly in microbial communities. Our main objectives of this study are to understand: (i) Are TARs universally applicable to soil microbial communities at a continental scale? (ii) What are the typical spatial turnover rates for in soil microbial communities? (iii) Whether and how do spatial turnover rates of microbial communities change with temperature as well as plants? To address these questions, we used high throughput sequencing technology to analyze 126 soil samples from six LTER (long-term ecological research) forest locations of different latitudes in North America, whose temperature ranges from -4 to 27°C. Results/Conclusions Our results revealed that the microbial communities in forest soils of six locations across North America exhibited flatter taxa-area relationships (Pearson correlation coefficient r = 0.999) and the slopes (z values) were from 0.068 to 0.085 across six different sites. Although z values from microbial community were relative smaller than the corresponding aboveground plant communities (z = 0.10-0.31), a strong positive correlation was observed between microbial and plant z values (r = 0.782, p = 0.033). Furthermore, both microbial and plant z values significantly increase with the mean annual temperatures across six sampling sites (r = 0.928 for plant community, r = 0.783 for microbial community), indicating that the z values are not constant and the spatial scaling of both plant and microbial communities is temperature dependent. Elucidating temperature-dependent spatial scaling of microbial biodiversity is fundamental to biodiversity preservation, ecosystem restoration and environmental management.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods Although the latitudinal of biodiversity pattern is well-documented and intensively studied in plant and animal ecology, it is not clear whether microbes also exhibit similar latitudinal diversity gradients. Due to their small size, extreme abundance, high dispersal capabilities, and low extinction rates, some have hypothesized that unicellular organisms should exhibit little or no latitudinal diversity patterns. To determine whether soil microbes exhibit latitudinal diversity gradients and whether such patterns are closely and mechanistically related temperature as predicted by metabolic theory of ecology (MTE), we surveyed the diversity of microbes in 126 soil samples from six forest sites in North America. These sites provide variation in ecosystem type from boreal to tropical forest, in average annual temperature from -4 to 27°C, and a rough gradient of latitude from 9-40oN, and in other abiotic and biotic environmental variables such as soil pH, moisture and plant diversity. High-throughput sequencing technology has been implemented on 16S rRNA genes for bacteria, on internal transcribed spacers (ITS) for fungi, and on nifH for nitrogen fixing bacteria. Results/Conclusions The microbes in the soil at our forest sites exhibited strong correlations with latitude and environmental temperature. Taxon richness and taxonomic diversity measured by the Shannon index decreased significantly with the increasing latitude in all three assays: for bacteria, fungi, and N-fixers. As predicted by MTE, the numbers of microbial taxa based on all three genes increased exponentially with environmental temperature (R2=0.26-0.92). However, the turnover rates between sites in taxon richness was 2-5 times smaller than for coexisting tree species, suggesting that the methods of estimating biodiversity for microbes and plants are not comparable, and/or the two groups of organisms respond very different to environmental variation in climate and related variables. To our knowledge, this is the first time that diversity of soils microbes has been shown to be associated with environmental temperature and latitude. Elucidating such diversity patterns and the underlying mechanisms is important for understanding the complex ecology of forest soils and for assessing the effects of human-caused changes in climate, land use, and other factors.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods Environmental contamination by radionuclides such as uranium, plutonium, and cesium can have severe impacts on aquatic (e.g., groundwater, sediment) microbiological communities. However, very little work has been done to look at how this type of contamination affects microeukaryotes (fungi and protists) and their viral pathogens in the subsurface. These organisms are important links between trophic levels within microbial communities: Fungi, the breakdown of organic matter through decay and disease, and the transport of nutrients by mycorrhizal members; protists the movement of nutrients upward in the food chain by grazing on bacteria and other organisms; and the release of nutrients by viruses as infected hosts die. Groundwater samples were collected and filtered from 15 monitoring wells at the Oak Ridge Integrated Field Research Center site representing a range of uranium contamination levels (0.001 to 55.286 mg/L). DNA from the samples was labeled and analyzed on a functional gene microarray (GeoChip 5.0) containing 11,416 probes, covering ~26,000 sequences of both functional (involved in biogeochemical cycling) and phylogenetic genes from fungi and protists and 1051 probes, covering ~1800 sequences from viral families known to infect these organisms. Results/Conclusions Between 1479 and 3532 probes from microeukaryotes and their viruses were detected per sample. Detected viral probes included proteins involved with viral structural (capsid), host recognition, and replication. Eukaryotic sequences included functional genes such as chitinases, laccases, and zinc transporters as well as phylogenetic markers (e.g., actin, heat shock protein 90 (hsp90)). The Mantel analysis showed uranium concentration and pH were found to be important environmental factors for microeukaryotes (rM = 0.722, p = 0.002), while dissolved organic carbon (DOC) and sulfide were found to be important environmental factors for viruses that infect these microorganisms (rM = 0.551, p = 0.001). It was also found that, when probes were available, sequences for either the host or other closely related organisms of the fungal and protistian viruses detected were also found to be present. This study demonstrates the ability of functional gene arrays to study both microeukaryotes and their viruses in contaminated environments.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods It is well documented that plant roots can substantially alter rates of litter decomposition in soil. However, the mechanisms underlying “priming” are poorly understood. Identifying the mechanisms by which roots alter the microbial mediation of decomposition is essential to predicting the impacts of changing environments on soil decomposition processes. We examined effects of Avena fatua roots on 13C-labeled root litter decomposition in a California grassland soil over two simulated growing-seasons, with focus on microbial community function and composition. The abundance, composition and functional potential of soil microbial communities were analyzed by qPCR, Illumina MiSeq sequencing of 16S and ITS amplicons and GeoChip 4. Results/Conclusions The presence of the annual grass roots consistently suppressed rates of labeled litter decomposition. Presence of plants significantly altered the abundance, composition and functional potential of microbial communities. Significantly higher signal intensities of genes capable of degrading low molecular weight organic compounds (e.g., glucose, formate and malate) were observed in microbial communities from planted soils, while microorganisms in unplanted soils had higher relative abundances of genes involved in degradation of some macromolecules (e.g., hemicellulose and lignin). Additionally, microbial communities from planted soils showed molecular characteristics of water stress (higher signal intensities of proV and proW, genes involved in osmotic stress response). The results from functional gene analyses suggest two possible mechanisms for the reduced rates of litter decomposition: 1) microbial preferential utilization of simple substrates from plant root exudates and 2) reduction in microbial activity due to soil drying from evapotranspiration. We propose a conceptual model of the mechanisms by which plants modulate microbial mediation of decomposition.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients such as competitive exclusion, neutral dynamics, and environmental filtering make predictions for how functional diversity should vary at different spatial scales and across broad diversity gradients. In an effort to assess the generality of latitude and temperature and to assess several prominent theories generating diversity patterns, we examined soil microbial and plant taxonomic and functional diversity along a latitudinal gradient. Comparisons of patterns of diversity across such disparate groups of organisms are rare. Both Plants and Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of plants, but especially microbial communities, are still difficult. This is due to the importance of pairing reliable local surveys with taxon abundance and within site trait measures and functional measures from extremely diverse and often uncultivable nature of most micro-organisms. We test predictions by quantifying differing measures of diversity via functional traits. Measures of functional diversity were based on plant and microbial functional traits that representing major axes of plant strategy variation as well as microbial resource use and functioning. We utilized high throughput sequencing and functional gene array, to analyze microbial functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. We assessed functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling and energy metabolism. We ask, are shifts in taxonomic diversity best explained by trait shifts and patterns of functional trait diversity. We assess both soil and tree assemblages within sites that span temperate and tropical New World. Results/Conclusions Our results enable one of the first comparison of functional diversity within and across microbial and plant species communities across latitude. In contrast to recent studies that have shown that climate only has a relative weak signal in patterns of single trait shifts across climate gradients, we show that when differences in species abundances are taken into account that multivariate shifts in trait composition is largely explained by climate (~ 80 – 98%). We find that soil temperature, in particular, appears to have the strongest effect in shifts in community trait diversity. Overall, our results show that shifts in taxonomic diversity are best explained and viewed by shifts in community trait composition. While we highlight several challenges that remain in fully comparing patterns of diversity across differing taxonomic groups, nevertheless, our findings have important implications for assessing biodiversity theory and for the main drivers that structure diversity gradients.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods Grassland fire is an influential ecosystem disturbance that may change and reallocate plant biomass, alter nutrient cycling, and potentially influence soil microbial communities. The frequency and intensity of grassland fire is likely to increase under regional and global climate change. However, so far, it is still unclear how soil microbial communities are influenced by the interactions of fire and other climate change factors. Here, we examined fire effects on soil microbial communities by a functional gene based microarray technique, GeoChip 4.6, under different combinations of global change conditions (CO2, C; temperature, T; precipitation, P; and nitrogen, N) after one growing season following a single, low-severity burning treatment at the Jasper Ridge Global Change Experiment. Results/Conclusions Results show that the microbial functional genes significantly shifted when the fire co-occurred with certain combinations of other treatments (split-plot multivariate permutation ANOVA, p < 0.05 under elevated N, PN, CP, CTP and TPN, p < 0.1 under elevated T, P, CT, CN and TN), indicating strong interactive effect of fire and other global change factors on soil microbial functional communities. Specifically, 34 % of the genes involved in carbon, nitrogen, phosphorous and sulfur cycling had increased abundance (paired t-test, p < 0.05, the same for other mentioned gene abundance tests) by fire when extra precipitation was added during the growing season following the fire, but 24 % of these genes decreased in abundance by fire under elevated temperature, which possibly contributed to observed lowered soil moisture in burn plots. In contrast, only less than 0.03 % genes showed abundance change by the single treatment of fire, although fire was likely to increase soil ammonia content. This could be due to carbon, phosphorous and other substrate limitations and/or the decrease in soil moisture caused by fire. Consistently, fire effect on microbial functional genes was trivial under nitrogen deposition. These results indicates the importance of soil moisture in constraining fire effects on soil microbial communities and potentially nutrient cycling bioprocesses in this Mediterranean climate mediated California grassland.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods Climate is thought to drive variation in plant growth rates via direct effects on the kinetics of photosynthesis and respiration. However, recent studies have shown that plant growth rates converge across climate gradients to a common scaling relationship with plant functional traits and plant biomass, suggesting that climatic variation in growth rates does not reflect a direct kinetic control of climate but instead an indirect control via constraints on maximum plant size and growing season length. We evaluated these hypotheses by: (1) extending metabolic scaling theory to include hypothesized relationships between climate variables (temperature, precipitation, evapotranspiration, and growing season length) and key plant functional traits (net carbon assimilation rates, specific leaf area, carbon use efficiency, tree carbon mass fraction, and leaf mass allocation) to predict mass growth rates of individual plants, and (2) assessing these relationships for 1580 woody plant species using functional trait and allometry data compiled from the literature with climate and stem diameter growth data collected from over 15,000 individual trees at 35 sites spanning broad gradients in latitude and elevation. Results/Conclusions Our results show that comparing normalized rates of biomass growth per individual plant reveals a remarkable overlap across sites. Almost none of the variation in plant growth rates was explained by climate variables; instead, most of the variation was explained by variation in plant functional traits and total plant biomass. These results suggest that woody plants across broad climate gradients converge to a similar normalized growth rates as a result of directional shifts in functional traits across climate gradients. This extension of metabolic scaling theory suggests that climatic variation in growth rates reflects not a direct kinetic control of growth physiology, but instead an indirect control on maximum plant size and/or growing season length.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Background/Question/Methods Nitrous oxide (N2O) is emitted by bacteria in soils and oceans as a major greenhouse gas. It also regulates stratospheric ozone in Earth's atmosphere. Microorganisms harboring the nosZ gene encoding N2O reductase can reduce N2O to N2, thus removing N2O from the atmosphere. However, little is known about the distribution, diversity, composition and structure of nosZ communities and their contributions to the global N2O balance. Here we analyzed N2O-reducing soil microbial communities using Illumina MiSeq sequencing of nosZ amplicons. We collected 21 samples with a nested design from six forests: five long-term ecological research (LTER) sites, including Niwot, Harvard Forest, Coweeta, HJ Andrews, and Luquillo, and Barro Colorado Island, Panama. The six forests are found along a temperature/latitude gradient (with annual mean temperature from -4 to 27oC) in North America. Results/Conclusions A total of 2,372,939 high quality sequences were generated using a cutoff of nucleic acid sequence identity of 95%. They were clustered into 3,976 operational taxonomic units (OTUs) across all six sites (Niwot: 1,443; Harvard Forest: 1,704; HJ Andrews: 1,233; Coweeta: 1,747; Luquillo: 1,052; Barro Colorado Island: 988). Permutational multivariate analysis of variance (PERMANOVA) and detrended correspondence analysis (DCA) showed that the composition and structure of N2O-reducing communities varied significantly (p < 0.01) across six forests. Latitude, total soil carbon and nitrogen, soil pH, precipitation, and plant richness were the major factors shaping the N2O-reducing community structure. No significant correlations were found between nosZ richness and temperature. This study provides new insights into our understanding of the distribution and diversity of N2O-reducing microbial communities in forest soils.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
    PLoS ONE 08/2014; 9(8):e104427. · 3.53 Impact Factor
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    ABSTRACT: Deciphering microbial communities and their role in Earth’s biosphere is crucial for addressing challenges in human health, agriculture, bioremediation and other natural processes. While next-generation sequencing platforms are still under development to improve accuracy, read length and sequencing depth, microarray-based methods have become an attractive alternative for 16S rRNA gene microbial community comparisons. The hybridization method is well-established in the laboratory. Thus main areas of improvement lie with the development of improved bioinformatics and statistical procedures for microarray data, rather than with improvements to the platform itself. In this communication we applied recently-developed bioinformatics tools to re-analyze G3 PhyloChip™ DNA microarray data acquired from deep ocean samples collected during the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. We show that data collected with the G3 PhyloChip™ assay can be analyzed at various stages of resolution, from individual probes to pairs of probes to quartets of probes and finally at the commonly used probe-set level where each probe-set is associated with one operational taxonomic unit (OTU). Our analysis methods comprised topological data analysis to facilitate the detection of outlier bio-specimens and the reconstruction of empirical OTUs (eOTUs) in an unsupervised manner, without the need of pre-defined reference OTUs (rOTUs). We observed that the quartet level provided sufficient resolution for identifying a subtle outlier sample with TDA while the eOTU reconstruction was useful for annotation of the taxa associated with significant population changes in the elevated hydrocarbon waters. The presented methods will improve the deduction of important biological processes from G3 PhyloChip experiments.
    Edited by Zhili He, 08/2014; Caister Academic Press.
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    ABSTRACT: Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation.
    BMC Microbiology 07/2014; 14(1):179. · 2.98 Impact Factor

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