Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon

Sul, Woo Jun; Asuming-Brempong, Samuel; Wang, Qiong; Tourlousse, Dieter M.; Penton, C. Ryan; Deng, Ye; Rodrigues, Jorge L. M.; Adiku, S.G.K.; Jones, James W.; Zhou, Jizhong; Cole, James R.; Tiedje, James M.

doi:10.1016/j.soilbio.2013.05.007

Cited by 208 publications

(111 citation statements)

References 31 publications

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“…This was further supported by the diversity indices H= and J=, which differed significantly between continuous-corn soils (G1) and soils also currently under corn but with a different crop in preceding years (G4). Land use change alters not only free-living nitrogen-fixing microorganisms (29) but also soil ammonia oxidizer communities in agricultural systems (30), as well as the overall bacterial (31,32) and other functional gene diversity (33).…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Zhang

Penton

Xue

et al. 2015

Appl Environ Microbiol

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cThe sequencing chips and kits of the Ion Torrent Personal Genome Machine (PGM), which employs semiconductor technology to measure pH changes in polymerization events, have recently been upgraded. The quality of PGM sequences has not been reassessed, and results have not been compared in the context of a gene-targeted microbial ecology study. To address this, we compared sequence profiles across available PGM chips and chemistries and with 454 pyrosequencing data by determining error types and rates and diazotrophic community structures. The PGM was then used to assess differences in nifH-harboring bacterial community structure among four corn-based cropping systems. Using our suggested filters from mock community analyses, the overall error rates were 0.62, 0.36, and 0.39% per base for chips 318 and 314 with the 400-bp kit and chip 318 with the Hi-Q chemistry, respectively. Compared with the 400-bp kit, the Hi-Q kit reduced indel rates by 28 to 59% and produced one to seven times more reads acceptable for downstream analyses. The PGM produced higher frameshift rates than pyrosequencing that were corrected by the RDP FrameBot tool. Significant differences among platforms were identified, although the diversity indices and overall site-based conclusions remained similar. For the cropping system analyses, a total of 6,182 unique NifH operational taxonomic units at 5% amino acid dissimilarity were obtained. The current crop type, as well as the crop rotation history, significantly influenced the composition of the soil diazotrophic community detected.

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Section: Discussionmentioning

confidence: 99%

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Zhang

Penton

Xue

et al. 2015

Appl Environ Microbiol

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“…Therefore, it requires complex operation, long cycles and high costs. High-throughput sequencing technology requires no cloning construction and presents high throughput, in which the 454 sequencing technique presents the longest sequence reads, opening the door to the comprehensive and efficient understanding of the information of microflora in fermented food (Navarro-Noya et al, 2013;Poulsen et al, 2013;Sul et al, 2013;Yu et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Microbiota in Naturally Fermented Cabbage of Northeastern Part of China by High-throughput Sequencing of the V3-V4 Regions of the 16S rRNA Gene

Li¹,

Yue²

2016

IJAB

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To cite this paper: Li, X. and X. Yue, 2016. Analysis of the microbiota in naturally fermented cabbage of northeastern part of China by high-throughput sequencing of the V3-V4 regions of the 16S rRNA gene. AbstractIn order to explore the microbiota in naturally fermented cabbage of northeastern part of China, the sequencing of the V3-V4 regions of the 16S rRNA gene of the microbiota in naturally fermented cabbage of northeastern part of China was made in this experiment by using the 454 FLX+ platform. A total of 302,327 valid sequences of 16 samples were obtained by 454 pyrosequencing. Evaluation of the richness of microflora of the samples by calculating Chao1 index showed that the microbiota of the samples from Daqing presented a higher richness. Beta diversity analysis showed species overlap with a very low content in the samples from Heilongjiang, Jilin and Liaoning. Heat-map showed significant differences among the dominant bacteria of different provinces. The results of sample analysis based on microbiota showed that the Lactobacilli content of the samples from Daqing, Heihe and Songyuan was more than 50%, and that from Heihe was up to 69.6%. In addition, Wohlfahrtiimonas was found for the first time in fermented food in this experiment, revealing the security risks of traditional methods.

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“…Several studies have recently attempted to quantify the impacts of elevated temperatures (11) and CO 2 levels (12, 13), input of exogenous organic matter of varied degrees of recalcitrance (14,15), a substantial reduction in soil organic matter (16), and different regimes of nitrogen fertilization (17) on soil microbial communities. Most of these studies analyzed small subunit rRNA (16S rRNA) gene sequences recovered from the indigenous communities and revealed important differences in community composition in response to the perturbations.…”

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confidence: 99%

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Luo

Rodriguez-R

Johnston

et al. 2014

Appl Environ Microbiol

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135

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Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (ϳ13%) and CO 2 production (ϳ10%), and to nitrogen cycling, including denitrification (ϳ12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G؉C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.

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Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon

Abstract: 2016-12-23T18:49:38

Cited by 208 publications

References 31 publications

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Analysis of the Microbiota in Naturally Fermented Cabbage of Northeastern Part of China by High-throughput Sequencing of the V3-V4 Regions of the 16S rRNA Gene

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

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