Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems

1. Micobial community (diversity and functional traits) underpin the sustainability of 11 agroecosystems. Assembly processes influence microbial community composition 12 and in turn determine their functional traits. However we have a poor 13 understanding of how assembly processes that govern microbial community 14 interact through time to maintain soil fertility. 15 2. Flooded rice fields are one kind of agroecosystems with high level of 16 sustainability. Ancient rice paddies have a history of cultivation spanning 17 hundreds or thousands of years and thus provide an ideal opportunity to explore 18 relationships between community assembly processes and agroecosystem 19 sustainability. In this study, we used statistical null models to evaluate temporal 20 patterns of bacterial community assembly processes along rice cultivation years 21 and their associations with increases in soil fertility in paddy agroecosystems. 22 3. We found that stochasticity was a persistent force structuring paddy soil microbial 23 communities, putatively due to frequent flooding that facilities dispersal. However, 24 determinism gradually increased over centuries of agriculture and corresponded to 25 increases in soil fertility. Accordingly, multifunctionality, calculated using 26 enzymes catalyzing key soil functions in carbon, nitrogen, phosphorous and sulfur 27 cycling significantly increased along rice cultivation years. We therefore propose 28 that balanced assembly processes preserve a diverse array of traits that can dominate under various circumstanceswhile allowing for traits relevant to soil fertility to be selected for by soil fertility, thus supporting multifunctionality that underpins agroecosystem sustainability. 4. In total, our results highlight that knowledge on temporal microbial assembly processes, community composition, and ecological function in context of soil fertility is key to understanding ecological mechanisms maintaining agroecosystem sustainability.

• Publication year

  2020

• Venue

  Functional Ecology

• Publication date

  2020-03-24

• Fields of study

  Agricultural and Food Sciences, Biology, Environmental Science

• Identifiers
  DOI 10.1111/1365-2435.13550
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Soil Health

  2020cited by this paper
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  2019cited by this paper
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• Multiple, Compounding Disturbances in a Forest Ecosystem: Fire Increases Susceptibility of Soil Edaphic Properties, Bacterial Community Structure, and Function to Change with Extreme Precipitation Event

  2019cited by this paper
• Factors influencing aquatic and terrestrial bacterial community assembly.

  2019cited by this paper
• Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions

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  2017cited by this paper
• Balanced Fertilization Decreases Environmental Filtering on Soil Bacterial Community Assemblage in North China

  2017influential reference
• Stochastic Community Assembly: Does It Matter in Microbial Ecology?

  2017cited by this paper
• Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields

  2017cited by this paper
• Shifts in microbial communities with increasing soil fertility across a chronosequence of paddy cultivation in subtropical China

  2017influential reference
• Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes

  2016cited by this paper
• Soil abiotic and biotic controls on plant performance during primary succession in a glacial landscape

  2016cited by this paper
• A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

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• Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

  2016influential reference
• Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

  2016influential reference
• Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

  2015cited by this paper
• Bacillus asahii comes to the fore in organic manure fertilized alkaline soils

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• Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities

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• Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

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• Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession

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• Soil biodiversity and human health

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• Aggregate dynamics and associated soil organic matter in topsoils of two 2,000-year paddy soil chronosequences

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• Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories

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  2014cited by this paper
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• Black carbon accrual during 2000 years of paddy‐rice and non‐paddy cropping in the Yangtze River Delta, China

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• Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

  2014cited by this paper
• Patterns and Processes of Microbial Community Assembly

  2013cited by this paper
• Soil bacterial community succession during long‐term ecosystem development

  2013cited by this paper
• Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction.

  2013cited by this paper
• Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

  2013cited by this paper
• Changes in assembly processes in soil bacterial communities following a wildfire disturbance

  2013cited by this paper
• Quantifying community assembly processes and identifying features that impose them

  2013influential reference
• Stochastic and deterministic assembly processes in subsurface microbial communities

  2012cited by this paper
• Plant Species Richness and Ecosystem Multifunctionality in Global Drylands

  2012cited by this paper
• Soil characteristic response times and pedogenic thresholds during the 1000-year evolution of a paddy soil chronosequence

  2011cited by this paper
• Organic carbon accumulation in a 2000-year chronosequence of paddy soil evolution

  2011cited by this paper
• Disentangling the importance of ecological niches from stochastic processes across scales

  2011cited by this paper
• Global food demand and the sustainable intensification of agriculture

  2011cited by this paper
• Persistence of soil organic matter as an ecosystem property

  2011cited by this paper
• Four opportunities for studies of ecological succession.

  2011cited by this paper
• Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments

  2010cited by this paper
• Hidden patterns of phylogenetic non-stationarity overwhelm comparative analyses of niche conservatism and divergence

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• Picante: R tools for integrating phylogenies and ecology

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  2009cited by this paper
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  2008cited by this paper
• The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems.

  2008cited by this paper
• Toward an ecological classification of soil bacteria.

  2007cited by this paper
• Phylogenetic clustering and overdispersion in bacterial communities.

  2006cited by this paper
• Changes in Soil C and N Contents and Mineralization across a Cultivation Chronosequence of Paddy Fields in Subtropical China

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• Pedogenic evolution of paddy soils in different soil landscapes

  2003cited by this paper
• Phylogenies and Community Ecology

  2002cited by this paper
• Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees

  2000cited by this paper
• Microbiology of flooded rice paddies.

  2000cited by this paper
• Soil health and sustainability: managing the biotic component of soil quality

  2000cited by this paper

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