Scaling plant nitrogen use and uptake efficiencies in response to nutrient addition in peatlands.

Nitrogen (N) is the primary growth-limiting nutrient in many terrestrial ecosystems, and therefore plant production per unit N taken up (i.e., N use efficiency, NUE) is a fundamentally important component of ecosystem function. Nitrogen use efficiency comprises two components: N productivity (A(N), plant production per peak biomass N content) and the mean residence time of N in plant biomass (MRT(N)). We utilized a five-year fertilization experiment to examine the manner in which increases in N and phosphorus (P) availability affected plant NUE at multiple biological scales (i.e., from leaf to community level). We fertilized a natural gradient of nutrient-limited peatland ecosystems in the Upper Peninsula of Michigan, USA, with 6 g N x m(-2) x yr(-1), 2 g P x m(-2) x yr(-1), or a combination of N and P. Our objectives were to determine how changes in carbon and N allocation within a plant to leaf and woody tissue and changes in species composition within a community, both above- and belowground, would affect (1) NUE; (2) the adaptive trade-off between the components of NUE; (3) the efficiency with which plants acquired N from the soil (N uptake efficiency); and (4) plant community production per unit soil N availability (N response efficiency, NRE). As expected, N and P addition generally increased aboveground production and N uptake. In particular, P availability strongly affected the way in which plants took up and used N. Nitrogen use efficiency response to nutrient addition was not straightforward. Nitrogen use efficiency differed between leaf and woody tissue, among species, and across the ombrotrophic-minerotrophic gradient because plants and communities were adapted to maximize either A(N) or MRT(N), but not both concurrently. Increased N availability strongly decreased plant and community N uptake efficiency, while increased P availability increased N uptake efficiency, particularly in a nitrogen-fixing shrub. Nitrogen uptake efficiency was more important in controlling overall plant community response to soil N availability than was NUE, and above- and belowground community N uptake efficiencies responded to nutrient addition in a similar manner. Our results demonstrate that plants respond to nutrient availability at multiple biological scales, and we suggest that N uptake efficiency may be a more representative measurement of plant responses to nutrient availability gradients than plant NUE.

Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2.

Understanding the responses of biological communities to elevated CO2 (eCO2) is a central issue in ecology, but little is known about the influence of eCO2 on the structure and functioning (and consequent feedbacks to plant productivity) of the belowground microbial community. Here, using metagenomic technologies, we showed that 10 years of field exposure of a grassland ecosystem to eCO2 dramatically altered the structure and functional potential of soil microbial communities. Total microbial and bacterial biomass were significantly increased at eCO2, but fungal biomass was unaffected. The structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 as indicated by detrended correspondence analysis (DCA) of gene-based pyrosequencing data and functional gene array data. While the abundance of genes involved in decomposing recalcitrant C remained unchanged, those involved in labile C degradation and C and N fixation were significantly increased under eCO2. Changes in microbial structure were significantly correlated with soil C and N contents and plant productivity. This study provides insights into potential activity of microbial community and associated feedback responses of terrestrial ecosystems to eCO2.

Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico.

Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing approximately 2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO(4)(3-), NH(4)(+), Mn(II), porosity, and Si(OH)(4) might play major roles in shaping the microbial community structure in the marine sediments.

Molecular diversity of 16S rRNA and gyrB genes in copper mines.

The molecular diversities of the microbial communities from four sites impacted by acid mine drainage (AMD) at Dexing Copper Mine in Jiangxi province of China were studied using 16S rRNA sequences and gyrB sequences. Of the four sampled sites, each habitat exhibited distinct geochemical characteristics and the sites were linked geographically allowing us to correlate microbial community structure to geochemical characteristics. In the present study, we examined the molecular diversity of 16S rRNA and gyrB genes from water at these sites using a PCR-based cloning approach. We found that the microbial community appears to be composed primarily of Proteobacteria, Acidobacteria, Actinobacteria, Nitrospira, Firmicutes, Chlorella and unknown phylotypes. Of clones affiliated with Nitrospira, Leptospirillum ferrooxidans, Leptospirillum ferriphilum and Leptospirillum group III were all detected. Principal-component analysis (PCA) revealed that the distribution of the microbial communities was influenced greatly by geochemical characteristics. The overall PCA profiles showed that the sites with similar geochemical characteristics had more similar microbial community structures. Moreover, our results also indicated that gyrB sequence analysis may be very useful for differentiating very closely related species in the study of microbial communities.

Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems.

To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11). Based on the results of microarray hybridizations, specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. The detection limit was 5 ng of genomic DNA in the absence of background DNA. Strong linear relationships between the signal intensity and the target DNA were observed (r(2) approximately 0.98). Application of this type of the microarray to analyze the acidic environments and bioleaching systems demonstrated that the developed microarray appeared to be useful for profiling differences in microbial community structures of acidic environments and bioleaching systems. Our results indicate that this technology has potential as a specific, sensitive, and quantitative tool in revealing a comprehensive picture of the compositions of genes related with acidophilic microorganism and the microbial community in acidic environments and bioleaching systems, although more work is needed to improve.