scholarly journals Historical Nitrogen Deposition and Straw Addition Facilitate the Resistance of Soil Multifunctionality to Drying-Wetting Cycles

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Gongwen Luo ◽  
Tingting Wang ◽  
Kaisong Li ◽  
Ling Li ◽  
Junwei Zhang ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Functional Capacity ◽  
Ecosystem Functioning ◽  
Cellulose Degradation ◽  
Soil Microbial Communities ◽  
Equation Modeling ◽  
Organic C ◽  
Soil Microbial ◽  
Positive Effects

ABSTRACT Climate change is predicted to alter precipitation and drought patterns, which has become a global concern as evidence accumulates that it will affect ecosystem services. Disentangling the ability of soil multifunctionality to withstand this stress (multifunctionality resistance) is a crucial topic for assessing the stability and adaptability of agroecosystems. In this study, we explored the effects of nutrient addition on multifunctionality resistance to drying-wetting cycles and evaluated the importance of microbial functional capacity (characterized by the abundances of genes involved in carbon, nitrogen and phosphorus cycles) for this resistance. The multifunctionality of soils treated with nitrogen (N) and straw showed a higher resistance to drying-wetting cycles than did nonamended soils. Microbial functional capacity displayed a positive linear relationship with multifunctionality resistance. Random forest analysis showed that the abundances of the archeal amoA (associated with nitrification) and nosZ and narG (denitrification) genes were major predictors of multifunctionality resistance in soils without straw addition. In contrast, major predictors of multifunctionality resistance in straw amended soils were the abundances of the GH51 (xylan degradation) and fungcbhIF (cellulose degradation) genes. Structural equation modeling further demonstrated the large direct contribution of carbon (C) and N cycling-related gene abundances to multifunctionality resistance. The modeling further elucidated the positive effects of microbial functional capacity on this resistance, which was mediated potentially by a high soil fungus/bacterium ratio, dissolved organic C content, and low pH. The present work suggests that nutrient management of agroecosystems can buffer negative impacts on ecosystem functioning caused by a climate change-associated increase in drying-wetting cycles via enriching functional capacity of microbial communities. IMPORTANCE Current climate trends indicate an increasing frequency of drying-wetting cycles. Such cycles are severe environmental perturbations and have received an enormous amount of attention. Prediction of ecosystem’s stability and adaptability requires a better mechanistic understanding of the responses of microbially mediated C and nutrient cycling processes to external disturbance. Assessment of this stability and adaptability further need to disentangle the relationships between functional capacity of soil microbial communities and the resistance of multifunctionality. Study of the physiological responses and community reorganization of soil microbes in response to stresses requires large investments of resources that vary with the management history of the system. Our study provides evidence that nutrient managements on agroecosystems can be expected to buffer the impacts of progressive climate change on ecosystem functioning by enhancing the functional capacity of soil microbial communities, which can serve as a basis for field studies.

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

2013 ◽  
Vol 80 (5) ◽  
pp. 1777-1786 ◽  
Author(s):  
Chengwei Luo ◽  
Luis M. Rodriguez-R ◽  
Eric R. Johnston ◽  
Liyou Wu ◽  
Lei Cheng ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Cellulose Degradation ◽  
Global Climate ◽  
Soil Microbial Communities ◽  
Predictive Ability ◽  
Metagenomic Data ◽  
Data Sets ◽  
Soil Microbial

ABSTRACTSoil 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 (∼13%) and CO2production (∼10%), and to nitrogen cycling, including denitrification (∼12%), 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.

scholarly journals Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

mBio ◽  
2011 ◽  
Vol 2 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Ye Deng ◽  
Feng Luo ◽  
Zhili He ◽  
Yunfeng Yang
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput ◽  
Network Topology ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Microbial Populations ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Soil Microbial

ABSTRACT Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO2, is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO2 enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO2 levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. IMPORTANCE The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO2 level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.

scholarly journals Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

2016 ◽  
Vol 82 (22) ◽  
pp. 6518-6530 ◽  
Author(s):  
Grace Pold ◽  
Andrew F. Billings ◽  
Jeff L. Blanchard ◽  
Daniel B. Burkhardt ◽  
Serita D. Frey ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Carbon ◽  
Carbon Cycling ◽  
Temperate Forest ◽  
Mineral Soil ◽  
Soil Microbial Communities ◽  
Organic Horizon ◽  
Soil Microbial ◽  
Carbohydrate Degradation

ABSTRACTAs Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated withActinobacteriain all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.IMPORTANCEThe massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.

scholarly journals Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities

2020 ◽  
Vol 110 (5) ◽  
pp. 1049-1055
Author(s):  
Emily W. Lankau ◽  
Dianne Xue ◽  
Rachel Christensen ◽  
Amanda J. Gevens ◽  
Richard A. Lankau
Keyword(s):  
Microbial Communities ◽  
Indirect Effects ◽  
Common Scab ◽  
Soil Microbial Communities ◽  
Farm Management ◽  
Equation Modeling ◽  
Soil Conditions ◽  
Potato Market ◽  
Soil Microbial ◽  
Soil Bacterial

Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.

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