Xiangui Lin

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau.

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4–1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r = 0.443, P = 0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.

The effects of mineral fertilizer and organic manure on soil microbial community and diversity

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H′), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.

Autotrophic growth of nitrifying community in an agricultural soil

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13CO2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the 13C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that 13CO2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.

Community Structure of Ammonia-Oxidizing Bacteria under Long-Term Application of Mineral Fertilizer and Organic Manure in a Sandy Loam Soil

ABSTRACT The effects of mineral fertilizer (NPK) and organic manure on the community structure of soil ammonia-oxidizing bacteria (AOB) was investigated in a long-term (16-year) fertilizer experiment. The experiment included seven treatments: organic manure, half organic manure N plus half fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). N fertilization greatly increased soil nitrification potential, and mineral N fertilizer had a greater impact than organic manure, while N deficiency treatment (PK) had no significant effect. AOB community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the amoA gene, which encodes the α subunit of ammonia monooxygenase. DGGE profiles showed that the AOB community was more diverse in N-fertilized treatments than in the PK-fertilized treatment or the control, while one dominant band observed in the control could not be detected in any of the fertilized treatments. Phylogenetic analysis showed that the DGGE bands derived from N-fertilized treatments belonged to Nitrosospira cluster 3, indicating that N fertilization resulted in the dominance of Nitrosospira cluster 3 in soil. These results demonstrate that long-term application of N fertilizers could result in increased soil nitrification potential and the AOB community shifts in soil. Our results also showed the different effects of mineral fertilizer N versus organic manure N; the effects of P and K on the soil AOB community; and the importance of balanced fertilization with N, P, and K in promoting nitrification functions in arable soils.

Long-Term Balanced Fertilization Decreases Arbuscular Mycorrhizal Fungal Diversity in an Arable Soil in North China Revealed by 454 Pyrosequencing

A balanced fertilization can increase crop yields partly due to stimulated microbial activities and growths. In this study, we investigated arbuscular mycorrhizal fungi (AMF) in arable soils to determine the optimal practices for an effective fertilization. We used pyrosequencing-based approach to study AMF diversity, as well as their responses to different long-term (>20 years) fertilizations, including OM (organic manure) and mix chemical fertilizers of NP (nitrogen-phosphorus), NK (nitrogen-potassium), and NPK (nitrogen-phosphorus-potassium). Results revealed that 124,998 of 18S rRNA gene fragments were dominated by Glomeromycota with 59,611 sequences, generating 70 operational taxonomic units (OTUs), of which the three largest families were Glomeraceae, Gigasporaceae and Acaulosporaceae. In Control and NK plots, AMF diversity and richness significantly decreased under long-term P fertilizations, such as NP, NPK, and OM. Concomitantly, the AMF community structure shifted. Supported by canonical correspondence analysis, we hereby propose that long-term balanced fertilization, especially P fertilizer with additional N fertilizer, helps the build-up of soil nutrients. Consequently, some AMF community constituents are sacrificed, propelled by the self-regulation of plant-AMF-microbes system, resulting in an agro-ecosystem with a better sustainability. This knowledge would be valuable toward better understandings of AMF community in agro-ecosystem, and long-term ecosystem benefits of the balanced fertilization.

Bioaccessibility, dietary exposure and human risk assessment of heavy metals from market vegetables in Hong Kong revealed with an in vitro gastrointestinal model.

A systematic survey of heavy metal (HM) concentrations and bioaccessibilities in market vegetables in Hong Kong were carried out for assessing potential health risk to local inhabitants. The average concentrations of Cd, Pb, Cr, Ni, Cu, and Zn in nine major groups of fresh vegetable varied within 0.007-0.053, 0.05-0.17, 0.05-0.24, 0.26-1.1, 0.62-3.0, and 0.96-4.3 mg kg(-1), respectively, and their average bioaccessibilities varied within 21-96%, 20-68%, 24-62%, 29-64%, 30-77%, and 69-94%, respectively. The bioaccessible estimated daily intakes (BEDIs) of Cd, Pb, Cr, Ni, Cu, and Zn from vegetables were far below the tolerable limits. The total bioaccessible target hazard quotient (TBTHQ) of the six HMs was 0.18 and 0.64 for average and high consumers, respectively, with Cd and leafy vegetable being the major risk contributors. Risk assessment of HMs from foods should be modified by taking bioaccessibility into account.

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.

The Role of Metal Nanoparticles in Influencing Arbuscular Mycorrhizal Fungi Effects on Plant Growth

A knowledge gap still remains concerning the in situ influences of nanoparticles on plant systems, partly due to the absence of soil microorganisms. Arbuscular mycorrhizal fungi (AMF) can form a mutualistic symbiosis with the roots of over 90% of land plants. This investigation sought to reveal the responses of mycorrhizal clover (Trifolium repens) to silver nanoparticles (AgNPs) and iron oxide nanoparticles (FeONPs) along a concentration gradient of each. FeONPs at 3.2 mg/kg significantly reduced mycorrhizal clover biomass by 34% by significantly reducing the glomalin content and root nutrient acquisition of AMF. In contrast, no negative effects of AgNPs at concentrations over 0.1 mg/kg were observed; however, AgNPs at 0.01 mg/kg inhibited mycorrhizal clover growth. In response to the elevated AgNPs content, the ability of AMF to alleviate AgNPs stress (via increased growth and ecological behaviors) was enhanced, which decreased Ag content and the activities of antioxidant enzymes in plants. These results were further supported by X-ray microcomputed tomography. Our findings suggest that in soil ecosystem, the influence of nanometals on plant systems would be more complicated than expected, and more attention should be focused on plant responses in combination with those of soil microorganisms.

Isolation of polycyclic aromatic hydrocarbons (PAHs)-degrading Mycobacterium spp. and the degradation in soil

The goal of this study was to isolate PAHs degraders that can utilize PAHs associated with soil particulates and investigate the biodegradation of PAHs on agar plate, in liquid culture and soil. Two Mycobacterium strains (NJS-1 and NJS-P) were isolated from PAHs-contaminated farmland soil using enrichment based on soil slurry. The isolates could degrade five test PAHs including pyrene, phenanthrene, fluoranthene, anthracene and benzo[a]pyrene on plate, but showed different effects in liquid culture, especially for fluoranthene. Isolate NJS-1 was capable of utilizing benzo[a]pyrene as a sole carbon and energy source, and an enhanced degradation was observed when pyrene was supplied as cometabolic substrate. Reintroduction of the isolates into sterile contaminated soil resulted in a significant removal of aged pyrene and fluoranthene (over 40%) in 2-months incubation. In pyrene-spiked soil, the degradation of pyrene and fluoranthene increased to 90% and 50%, respectively. Comparing PAHs degradation on plate, in liquid culture and soil, we can conclude that there was corresponding degradation in different test systems. In addition, the degradation of aged PAHs in soil suggested the potential application of two isolates in further bioremediation.

Contrasting elevational diversity patterns between eukaryotic soil microbes and plants

The diversity of eukaryotic macroorganisms such as animals and plants usually declines with increasing elevation and latitude. By contrast, the community structure of prokaryotes such as soil bacteria does not generally correlate with elevation or latitude, suggesting that differences in fundamental cell biology and/or body size strongly influence diversity patterns. To distinguish the influences of these two factors, soil eukaryotic microorganism community structure was investigated in six representative vegetation sites along an elevational gradient from forest to alpine tundra on Changbai Mountain in Northeast China, and compared with our previous determination of soil bacterial community structure along the same gradient. Using bar-coded pyrosequencing, we found strong site differences in eukaryotic microbial community composition. However, diversity of the total eukaryotic microorganism community (or just the fungi or protists alone) did not correlate with elevation. Instead, the patterns of diversity and composition in the total eukaryotic microbial community (and in the protist community alone) were closely correlated with soil pH, suggesting that just as for bacteria, acidity is a particularly important determinant of eukaryotic microbial distributions. By contrast, as expected, plant diversity at the same sites declined along our elevational gradient. These results together suggest that elevational diversity patterns exhibited by eukaryotic microorganisms are fundamentally different from those of plants.