Yucheng Wu

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes.

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested.

Bioremediation of polycyclic aromatic hydrocarbons contaminated soil with Monilinia sp.: degradation and microbial community analysis

Microcosms were set up with a PAHs-contaminated soil using biostimulation (addition of ground corn cob) and bioaugmentation (inoculated with Monilinia sp. W5-2). Degradation of polycyclic aromatic hydrocarbons and microbial community were examined at the end of incubation period. After 30xa0days, bioaugmented microcosms showed a 35xa0±xa00% decrease in total PAHs, while biostimulated and control microcosms showed 16xa0±xa09% and 3xa0±xa00% decrease in total PAHs, respectively. Bioaugmented microcosms also revealed 70xa0±xa08% and 72xa0±xa02% decreases in benzo[a]pyrene and anthracene, respectively, while the values for biostimulated and control microcosms were much lower. Detoxification of soils in bioaugmented microcosms was confirmed by genetic toxicity assay, suggesting important role of fungal remediation. Molecular fingerprint profiles and selective enumeration showed biostimulation with ground corn cob increased both number and abundance of indigenous aromatic hydrocarbons degraders and changed microbial community composition in soil, which is beneficial to natural attenuation of PAHs. At the same time, bioaugmentation with Monilinia strain W5-2 imposed negligible effect on indigenous microbial community. This study suggests that fungal remediation is promising in eliminating PAHs, especially the part of recalcitrant and highly toxic benzo[a]pyrene, in contaminated soil. It is also the first description of soil bioremediation with Monilinia sp.

Heterogeneity of archaeal and bacterial ammonia‐oxidizing communities in Lake Taihu, China

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities within the surface sediments of Lake Taihu, a large eutrophic freshwater lake in China, were investigated using molecular approaches targeting the ammonia monooxygenase subunit A (amoA) gene. Large intra-lake variability in the composition and the relative abundance of both groups of ammonia-oxidizing prokaryotes was observed. Archaeal amoA far outnumbered bacterial amoA at most sites except those located in the Eastern Taihu Bay. This bay, which is used for intensive pen aquaculture, harboured the most unique AOA communities but was dominated by AOB in terms of relative abundance. Accumulation of organic substances rather than presence of submersed macrophytes significantly influenced the relative abundance of AOA. In contrast, shifts in the abundance of AOB were not found to be significantly related to the investigated environmental parameters. Phylogenetic analysis showed that all archaeal amoA sequences fell within either the Crenarchaeotal Group (CG) I.1b or the CG I.1a subgroup, and all AOB clustered exclusively with the genus Nitrosomonas. These findings represent the first detailed survey of AOA in eutrophic freshwater lake sediments by demonstrating that AOA dominate the ammonia-oxidizing communities, and are negatively correlated with the accumulation of organic substances.

Degradation of Polycyclic Aromatic Hydrocarbons by Crude Extracts from Spent Mushroom Substrate and its Possible Mechanisms

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by pure laccase has been reported, but the high cost limited its application in environmental bioremediation. Here, we reported a study about PAHs degradation by crude extracts (CEs) containing laccase, which were obtained by extracting four spent mushroom (Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and Coprinus comatus) substrates. The results showed that anthracene, benzo[a]pyrene, and benzo[a]anthracene were top three degradable PAHs by CEs while naphthalene was most recalcitrant. The PAHs oxidation was enhanced in the presence of 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). Laccase included in CE might play a major role in PAHs degradation. The maximum degradation rate of anthracene and benzo[a]pyrene was observed by using crude extracts from P. eryngii while the highest laccase activities were found in crude extracts from A.xa0bisporus, moreover, crude extracts from P. eryngii, which contained less laccase activities, degraded more anthracene and benzo[a]pyrene than pure laccase with higher laccase activities. The lack of correlation between laccase activity and PAHs degradation rate indicated that other factors might also influence the PAHs degradation. Boiled CEs were added to determine the effect on PAHs degradation by laccase. The results showed that all four boiled CEs had improved the PAHs oxidation. The maximum improvement was observed by adding CEs from P. eryngii. It suggested that some mediators indeed existed in CEs and CEs from P. eryngii contained most. As a result, CEs from P. eryngii has the most application potential in PAHs bioremediation.

Seasonal variation and controlling factors of anaerobic ammonium oxidation in freshwater river sediments in the Taihu Lake region of China

Anaerobic ammonium oxidation (anammox) has been recently recognized as an important pathway for the removal of fixed nitrogen (N) from aquatic systems. However, the functions of anammox in freshwater river systems remain uncertain. In this study, we evaluated the occurrence of anammox activity in two rivers in the Taihu Lake region in China during a seasonal survey. Homogenized sediments were incubated with (15)N-labeled NO3(-) and NH4(+) amendments to determine the potential importance of the anammox process relative to canonical denitrification. Production of (29)N2 and (30)N2 in slurries was determined using membrane inlet mass spectrometry. Potential anammox rates in the two river sediments ranged from 0.11±0.07 to 6.79±1.28 μmol N m(-2) h(-1) and the remove of N by anammox accounted for 0.8±0.00% to 10.7±0.03% of total N2 production. Potential anammox rates varied spatially and temporally in the two rivers, with the highest and lowest mean anammox rates appearing during summer and early autumn and during winter, respectively. The variation of the percentage of anammox to total N2 production displayed the same trend with potential anammox rates. Water temperature and NO3(-) content in sediments were the main factors affecting anammox activity. Anammox bacteria were detected in sediment samples using barcode pyrosequencing. The 16S rRNA anammox gene sequences in the river sediments were affiliated with Candidatus Kuenenia, Candidatus Jettenia, and Candidatus Scalindua, among which C. Kuenenia dominated the anammox bacterial communities. Our results confirmed the presence of anammox bacteria but their role is relatively small in removing fixed N from freshwater river systems.

Autotrophic Growth of Bacterial and Archaeal Ammonia Oxidizers in Freshwater Sediment Microcosms Incubated at Different Temperatures

ABSTRACT Both bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [13C]bicarbonate labeling of bacterial amoA genes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms. Nitrosomonas sp. strain Is79A3 and Nitrosomonas communis lineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The 13C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant 13C labeling of Nitrososphaera-like archaea and changes in the abundance and composition of archaeal amoA genes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions.

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.

Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils

PurposeAcidic red soils account for 21% of land area in China and contain low ammonia concentration due to ionization to ammonium. The unusual high affinity for ammonia of marine Nitrosopumilus maritimus and acidophilic soil Nitrosotalea devanaterra has suggested that ammonia-oxidizing archaea (AOA) may have greater selective advantage over ammonia-oxidizing bacteria (AOB) in ammonia-limited environment because ammonia rather than ammonium is thought to be the actual substrate for oxidation. The aim of this study was to assess whether nitrification activity can be attributed to AOA and/or AOB by relating community structures of AOA and AOB to nitrification activity in acidic red soils in southern China.Materials and methodsIn this study, the composition and abundance of AOA community were investigated in acidic red soils of coniferous Pinus forest, broad-leaf Cinnamomum forest, bush forest (BF), and a 30-year agricultural field converted from bush forest (BFA). The composition of AOA based on archaeal amoA genes were analyzed by denaturant gradient gel electrophoresis, and the abundances of AOA communities were determined by real-time quantitative polymerase chain reaction, while soil nitrification activity was measured using 15N pool enrichment technique.Results and discussion15N pool enrichment technique indicated nitrification activity in acidic red soils, but AOB were not detected. The absence of AOB in acidic red soils could be well explained by the low ammonia concentration ranging from 17.8 to 34.3xa0nM, which is far below the known threshold values required to support the growth of AOB in culture. Nitrification activity change coupled well with abundance and composition changes of archaeal amoA genes, particularly for acidic BF and BFA soils. Phylogenetic analysis demonstrated that the putatively active AOA were related to amoA transcripts in a hot spring within the soil Crenarchaeota group 1.1b lineage.ConclusionsThese results suggest that AOA play important roles in ammonia oxidation in acidic red soils tested in this study.

Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotA with high laccase activity and copper independence

Bacterial laccase CueO from Escherichia coli can oxidize polycyclic aromatic hydrocarbons (PAHs); however, its application in the remediation of PAH-contaminated soil mainly suffers from a low oxidation rate and copper dependence. It was reported that a laccase with a higher redox potential tended to have a higher oxidation rate; thus, the present study investigated the oxidation of PAHs using another bacterial laccase CotA from Bacillus subtilis with a higher redox potential (525xa0mV) than CueO (440xa0mV). Recombinant CotA was overexpressed in E.xa0coli and partially purified, exhibiting a higher laccase-specific activity than CueO over a broad pH and temperature range. CotA exhibited moderate thermostability at high temperatures. CotA oxidized PAHs in the absence of exogenous copper. Thereby, secondary heavy metal pollution can be avoided, another advantage of CotA over CueO. Moreover, this study also evaluated some unexplained phenomena in our previous study. It was observed that the oxidation of PAHs with bacterial laccases can be promoted by copper. The partially purified bacterial laccase oxidized only two of the 15 tested PAHs, i.e., anthracene and benzo[a]pyrene, indicating the presence of natural redox mediators in crude cell extracts. Overall, the recombinant CotA oxidizes PAHs with high laccase activity and copper independence, indicating that CotA is a better candidate for the remediation of PAHs than CueO. Besides, the findings here provide a better understanding of the oxidation of PAHs using bacterial laccases.