Dormancy dynamics and dispersal contribute to soil microbiome resilience

In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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Dormancy dynamics and dispersal contribute to soil microbiome resilience

10.1101/730283 ◽

2019 ◽

Author(s):

Jackson W Sorensen ◽

Ashley Shade

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Resistance To Change ◽

Microbial Populations ◽

Soil Microbiome ◽

Community Resistance ◽

Soil Microbial ◽

The Press ◽

Community Transition ◽

Press Disturbance

AbstractIn disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities were sensitive within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment.

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Soil microbial community resistance to drought and links to C stabilization in an Australian grassland

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2016.08.024 ◽

2016 ◽

Vol 103 ◽

pp. 171-180 ◽

Cited By ~ 37

Author(s):

Alberto Canarini ◽

Yolima Carrillo ◽

Pierre Mariotte ◽

Lachlan Ingram ◽

Feike A. Dijkstra

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Community Resistance ◽

Soil Microbial

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Effect of Long-Term Zinc Pollution on Soil Microbial Community Resistance to Repeated Contamination

Bulletin of Environmental Contamination and Toxicology ◽

10.1007/s00128-012-0523-0 ◽

2012 ◽

Vol 88 (4) ◽

pp. 617-622 ◽

Cited By ~ 16

Author(s):

Beata Klimek

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Community Resistance ◽

Soil Microbial ◽

Zinc Pollution

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Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon

AMB Express ◽

10.1186/s13568-021-01225-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xu Zhang ◽

Chao Xue ◽

Dan Fang ◽

Xiaohui He ◽

Mengyu Wei ◽

...

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Disease Incidence ◽

Organic Fertilizer ◽

Microbial Community Composition ◽

Wilt Disease ◽

Soil Fumigation ◽

Soil Microbiome ◽

Soil Microbial Diversity ◽

Soil Microbial

AbstractFusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.

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Acetaminophen Concentrations Found in Recycled Wastewater alter Soil Microbial Community Structure and Functional Diversity

10.21203/rs.3.rs-221780/v1 ◽

2021 ◽

Author(s):

Nathan K. McLain ◽

Melissa Y. Gomez ◽

Emma W. Gachomo

Keyword(s):

Microbial Community ◽

Carboxylic Acids ◽

Soil Microbial Community ◽

Pharmaceutical Products ◽

Soil Microbiome ◽

Agricultural Field ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Greenhouse Study ◽

Biolog Ecoplate

Abstract The practice of using recycled wastewater (RWW) (aka reclaimed water) has been adopted to address the growing demand for clean water and has been largely successful. However, chemicals of emerging concern (CECs) including pharmaceutical products such as acetaminophen (APAP) remain in the water even after additional cleaning. When recycled waste water is used to irrigate crops or landscapes these chemicals can then enter these and adjacent environments. APAP is one such contaminant and has the potential to disrupt the soil microbiome associated with agricultural crops. We evaluated this possibility using a greenhouse study to mimic agricultural field conditions, and applied treatments of APAP concentrations found within the ranges observed for RWW effluents. Using Illumina sequencing based approaches we observed that APAP was able to cause shifts in the microbial community and positively select for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The biolog plates indicated that the metabolism of amino acids, carbohydrates, carboxylic acids, phenolics, and polymers was significantly higher in the presence of APAP. Together our observations indicate that the soil microbial community and functions were altered by APAP and demonstrates the need to change current RWW policies to address the presence of these chemicals.

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Unraveling negative biotic interactions determining soil microbial community assembly and functioning

The ISME Journal ◽

10.1038/s41396-021-01076-9 ◽

2021 ◽

Author(s):

Sana Romdhane ◽

Aymé Spor ◽

Julie Aubert ◽

David Bru ◽

Marie-Christine Breuil ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Soil Microbial Community ◽

Biotic Interactions ◽

Microbial Interactions ◽

Relative Fitness ◽

Soil Microbiome ◽

Soil Microbial ◽

Microbial Community Assembly

AbstractMicrobial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.

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