Dataset Information

Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil.

ABSTRACT: Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ?4% of metabolic genes changed in expression with N addition, while three times as many (?12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.

SUBMITTER: Albright MBN

PROVIDER: S-EPMC6052259 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil.

Albright Michaeline B N MBN Johansen Renee R Lopez Deanna D Gallegos-Graves La Verne V Steven Blaire B Kuske Cheryl R CR Dunbar John J

Applied and environmental microbiology 20180717 15

Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial comm ...[more]

PMID: 29802185

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Project description:Soil extracellular enzymes play a significant role in the N mineralization process. However, few studies have documented the linkage between enzyme activity and the microbial community that performs the function. This study examined the effects of inorganic and organic N fertilization on soil microbial communities and their N mineralization functions over 4 years. Soils were collected from silage corn field plots with four contrasting N treatments: control (no additional N), ammonium sulfate (AS; 100 and 200 kg of N ha-1), and compost (200 kg of N ha-1). Illumina amplicon sequencing was used to comprehensively assess the overall bacterial community (16S rRNA genes), bacterial ureolytic community (ureC), and bacterial chitinolytic community (chiA). Selected genes involved in N mineralization were also examined using quantitative real-time PCR and metagenomics. Enzymes (and marker genes) included protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF). Compost significantly increased diversity of overall bacterial communities even after one application, while ammonium fertilizers had no influence on the overall bacterial communities over four seasons. Bacterial ureolytic and chitinolytic communities were significantly changed by N fertilization. Compost treatment strongly elevated soil enzyme activities after 4 years of repeated application. Functional gene abundances were not significantly affected by N treatments, and they were not correlated with corresponding enzyme activities. N mineralization genes were recovered from soil metagenomes based on a gene-targeted assembly. Understanding how the structure and function of soil microbial communities involved with N mineralization change in response to fertilization practices may indicate suitable agricultural management practices that improve ecosystem services while reducing negative environmental consequences.IMPORTANCE Agricultural N management practices influence the enzymatic activities involved in N mineralization. However, specific enzyme activities do not identify the microbial species directly involved in the measured process, leaving the link between the composition of the microbial community and the production of key enzymes poorly understood. In this study, the application of high-throughput sequencing, real-time PCR, and metagenomics shed light on how the abundance and diversity of microorganisms involved in N mineralization respond to N management. We suggest that N fertilization has significantly changed bacterial ureolytic and chitinolytic communities.

Project description:Soil salinization due to seawater intrusion along coastal areas is an increasing threat to rice cultivation worldwide. While the detrimental impact on rice growth and yield has been thoroughly studied, little is known about how severe salinity affects structure and function of paddy soil microbial communities. Here, we examined their short-term responses to half- and full-strength seawater salinity in controlled laboratory experiments. Slurry microcosms were incubated under anoxic conditions, with rice straw added as carbon source. Stress exposure time was for 2 days after a pre-incubation period of 7 days. Relative to the control, moderate (300 mM NaCl) and high (600 mM NaCl) salt stress suppressed both net consumption of acetate and methane production by 50% and 70%, respectively. Correspondingly, community-wide mRNA expression decreased by 50-65%, with significant changes in relative transcript abundance of family-level groups. mRNA turnover was clearly more responsive to salt stress than rRNA dynamics. Among bacteria, Clostridiaceae were most abundant and the only group whose transcriptional activity was strongly stimulated at 600 mM NaCl. In particular, clostridial mRNA involved in transcription/translation, fermentation, uptake and biosynthesis of compatible solutes, and flagellar motility was significantly enriched in response salt stress. None of the other bacterial groups were able to compete at 600 mM NaCl. Their responses to 300 mM NaCl were more diverse. Lachnospiraceae increased, Ruminococcaceae maintained, and Peptococcaceae, Veillonellaceae, and Syntrophomonadaceae decreased in relative mRNA abundance. Among methanogens, Methanosarcinaceae were most dominant. Relative to other family-level groups, salt stress induced a significant enrichment of transcripts related to the CO dehydrogenase/acetyl-coenzyme A synthase complex, methanogenesis, heat shock, ammonium uptake, and thermosomes, but the absolute abundance of methanosarcinal mRNA decreased. Most strikingly, the transcriptional activity of the Methanocellaceae was completely suppressed already at 300 mM NaCl. Apparently, the key taxonomic groups involved in the methanogenic breakdown of plant polymers significantly differ in their ability to cope with severe salt stress. Presumably, this different ability is directly linked to differences in their genetic potential and metabolic flexibility to reassign available energy resources for cellular adaptation to salt stress.

Project description:The continuous use of nitrogen (N) fertilizers to increase soil fertility and crop productivity often results in unexpected environmental effects and N losses through biological processes, such as nitrification and denitrification. In this study, multidisciplinary approaches were employed to assess the effects of N fertilization in a long-term (~20 years) field experiment in which a fertilizer gradient (0, 200, 400, and 600 kg N ha-1 yr-1) was applied in a winter wheat-summer maize rotation cropping system in the North China Plain, one of the most intensive agricultural regions in China. The potential nitrification/denitrification rates, bacterial community structure, and abundances of functional microbial communities involved in key processes of the N cycle were assessed during both the summer maize (SM) and winter wheat (WW) seasons. Long-term N fertilization resulted in a decrease in soil pH and an increase in soil organic matter (OM), total N and total carbon concentrations. Potential nitrification/denitrification and the abundances of corresponding functional N cycling genes were positively correlated with the fertilization intensity. High-throughput sequencing of the 16S rRNA gene revealed that the increased fertilization intensity caused a significant decrease of bacterial diversity in SM season, while changed the microbial community composition such as increasing the Bacteroidetes abundance and decreasing Acidobacteria abundance in both SM and WW seasons. The alteration of soil properties markedly correlated with the variation in microbial structure, as soil pH and OM were the most predominant factors affecting the microbial structure in the SM and WW seasons, respectively. Furthermore, consistently with the results of functional gene quantification, functional prediction of microbial communities based on 16S rRNA sequence data also revealed that the abundances of the key nitrificaiton/denitrification groups were elevated by long-term N inputs. Taken together, our results suggested that soil microbial community shifted consistently in both SM and WW seasons toward a higher proportion of N-cycle microbes and exhibited higher N turnover activities in response to long-term elevated N fertilizer. These findings provided new insights into the molecular mechanisms responsible for N loss in intensively N fertilized agricultural ecosystems.

Dataset Information

Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil.

Publications

Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil.

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