Air pollution below WHO levels decreases by 40 % the links of terrestrial microbial networks

Karimi, Battle; Meyer, Caroline; Gilbert, Daniel; Bernard, Nadine

doi:10.1007/s10311-016-0589-8

Cited by 32 publications

(24 citation statements)

References 30 publications

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“…Overall, perturbed systems show lower connections (edges) than no-perturbed systems. For example, urban air (polluted) showed 40% fewer connections than rural air (no polluted) (Karimi et al, 2016). This pattern has also been observed in soil systems by different land uses, where crop soils have shown lower connections than natural forest soils (Lupatini et al, 2014).…”

Section: Discussionmentioning

confidence: 62%

Soil Bacterial Community Associated With High Potato Production and Minimal Water Use

Gumiere

Matteau

Constant

et al. 2019

Front. Environ. Sci.

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In agriculture, water consumption for crop production represents 69% of all water use. Precision irrigation systems based on available soil water have been developed to improve crop production, reducing water use. Besides the improvements in irrigation management, a better resolution of the optimal water level is required, and revealing the impact of soil matric potential on the soil microbial community may help. Here, the effect of four soil matric potential treatments (−15 kPa, −25 kPa, −30 kPa, and −45 kPa) was evaluated on the soil microbial community across three potato cultivars and two soil types (silt and sand). The results confirmed the soil matric potential with −25 kPa as the optimal irrigation level, which promoted high potato production using the minimal water use. The irrigation levels affected the composition, predicted functionality, and the ecological network of soil bacterial community. Water excess (−15 kPa) and deficit (−30 and −45 kPa) promoted an increase in microbial interaction and alpha-diversity. The results suggested higher Positive/Negative ratio for phyla Proteobacteria, Actinobacteria, and Acidobacteria in optimal irrigation level (−25 kPa) than other irrigation levels. Also, correlation analyses revealed an interesting association between the irrigation levels, potato production, and bacterial functionality, especially in the carbon cycle (fixation and emission). Therefore, this study proposed important associations between the soil bacterial community and water management, focusing on high potato production and minimal water use. The advancement of this knowledge may lead to a more comprehensive assessment of the optimal irrigation levels of others crop production systems. Furthermore, the inclusion of biological mechanisms, especially microbial interactions, in agriculture studies has the potential to contribute to the development of water management practices conducive to both increasing crop yield and maintaining a sustainable soil environment.

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Section: Discussionmentioning

confidence: 62%

Soil Bacterial Community Associated With High Potato Production and Minimal Water Use

Gumiere

Matteau

Constant

et al. 2019

Front. Environ. Sci.

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“…Instead of biodiversity, non-random patterns in microbial species co-occurrence and associated metrics are being integrated to amplify the differences that subtle perturbation make [20,51], e.g. a temperature increase of 1 °C for 5 years [19], soil contamination with mercury for several decades [16], and annual litter decomposition [17]. Our analysis provides a framework for studying microbial communities, co-occurrence, and networks under mild anthropogenic perturbation by adding S. acidaminiphila.…”

Section: Discussionmentioning

confidence: 99%

“…This whole new way of artificially disturbing a microbial ecosystem at a small scale provides a chance for researchers to observe and investigate changes in microbial communities in response to gradual and subtle perturbation. In addition, the generalization of such laboratory-scale experimental findings to real environmental changes might help monitor and sound the alarm about mild changes from chronic atmospheric pollution [19], agricultural practices [17], and metallic contaminants in the soil [16] at an early stage, which can then be countered with ecosystem management strategies.…”

Section: Discussionmentioning

confidence: 99%

“…Competitive microbes may compete with one another, leading to a negative correlation trend [14,15]. Studies of co-occurrence networks in microbial communities have confirmed the connection between network structure and chronic (and weak) environmental changes due to soil anthropization [16], litter quality [17], and air pollution [18,19], in which microbial biodiversity-e.g. Shannon and inverse Simpson index-might therefore lead to the conclusion that the ecosystem remains unaltered if the perturbation is of moderate intensity.…”

Section: Introductionmentioning

confidence: 95%

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A Network-Based Approach to Deciphering A Dynamic Microbiome’s Response to A Subtle Perturbation

Shaw

Liu

Weng

et al. 2020

Preprint

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Background: Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Declines in biodiversity lead to more than just species loss. The exponentially growing human population and its exploitation of natural resources affect the environment from local to global scales via climate change, global warming, and other human-driven environmental problems. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to moderate or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations.Results: Recent studies have proven that co-occurrence patterns are effective for measuring responses to subtle perturbations. In this study, we mimicked dynamic microbial ecosystems under pressure from subtle perturbations by adding a key microbial species and comparing network topologies. The present study is a comprehensive investigation of how a network-oriented method can be used to track microbiome dynamics after a key species, S. acidaminiphila, is added into anaerobic digestion reactors of swine manure. Microbial networks before and after bioaugmentation with S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes.Conclusions: This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

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“…Another set of community-wide metrics can be computed from the structure of biotic interactions within ecological networks (reviewed in Vacher et al, 2016;Layeghifard et al, 2017). Based on empirical evidence of the variation in network structure under environmental disturbance (Tylianakis et al, 2007;Zhou et al, 2011;Karimi et al, 2016;Ma et al, 2018), their properties have been suggested as potential indicators of ecosystem functioning and integrity (Gray et al, 2014;Karimi et al, 2017;Bohan et al, 2011Bohan et al, , 2017Lau et al, 2017;Tylianakis et al, 2017;Pellissier et al, 2018;Delmas et al, 2019). In recent years, a growing interest in these approaches has led to a series of studies employing EG to infer ecological networks from microbial communities data (Zhou et al, 2011;Lupatini et al, 2014;Zappelini et al, 2015;Pérez-Valera et al, 2017;Pauvert et al, 2019) and from macroinvertebrates (Compson et al, 2019) to explore the links between network properties (e.g.…”

Section: The Environmental Genomics Revolution For Biodiversity Reseamentioning

confidence: 99%

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

Cordier¹,

Sáez²,

Apothéloz-Perret-Gentil³

et al. 2020

Preprint

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A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

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Air pollution below WHO levels decreases by 40 % the links of terrestrial microbial networks

Abstract: International audienc

Cited by 32 publications

References 30 publications

Soil Bacterial Community Associated With High Potato Production and Minimal Water Use

Soil Bacterial Community Associated With High Potato Production and Minimal Water Use

A Network-Based Approach to Deciphering A Dynamic Microbiome’s Response to A Subtle Perturbation

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

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