Quantifying human impact on Earth's microbiome

Pointing, Stephen B.; Fierer, Noah; Smith, Gavin J.D.; Steinberg, Peter D.; Wiedmann, Martin

doi:10.1038/nmicrobiol.2016.145

Cited by 21 publications

(16 citation statements)

References 15 publications

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“…Nevertheless, the potential mechanisms for the relationships between soil pH and bacterial diversity need more investigation in spite of having attracted wide attention (de Carvalho et al, ; Fierer & Jackson, ; Kuramae et al, ; Stegen et al, ). Taken together, the effects of forest degradation on microbial community composition and diversity should be taken into account in forest management practices given the fact that soil microbial communities represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions (Pointing et al, ; Rodrigues et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Soil microbial abundance, community composition, activity and ecophysiological adaptation to environmental changes at the community level can shift the C, energy and nutrient flows at the ecosystem level (Schimel, Balser, & Wallenstein, ). Therefore, better understanding of how microbial communities respond to land‐use changes and feedback to soil biogeochemical cycling beyond the microhabitat scale is crucially needed in both microbial ecology and ecosystem modelling communities (Pointing, Fierer, Smith, Steinberg, & Wiedmann, ).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, better understanding of how microbial communities respond to land-use changes and feedback to soil biogeochemical cycling beyond the microhabitat scale is crucially needed in both microbial ecology and ecosystem modelling communities (Pointing, Fierer, Smith, Steinberg, & Wiedmann, 2016).…”

mentioning

confidence: 99%

“…Such changes can significantly affect soil microbial attributes. For example, global pattern studies showed that soil microbial abundance was correlated with soil and climate factors (Pointing et al, 2016;Serna-Chavez, Fierer, & van Bodegom, 2013;Xu, Thornton, & Post, 2013). Fierer and Jackson (2006) reported that soil pH explained the variances of diversity and richness of soil bacterial communities by 70 and 58%, respectively.…”

mentioning

confidence: 99%

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Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

Zhou

Wang

Luo

2017

Global Ecol Biogeogr

139

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

Zhou

Wang

Luo

2017

Global Ecol Biogeogr

139

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“…Additionally, these tools and approaches, while developed for bacteria and archaea, could be expanded to all domains of life 43 . To achieve greater utility for the EMP and similar projects, we must continually improve metadata collection and curation, ontologies, support for multi-omics data, and access to computational resources.…”

Section: A More Precise and Scalable Cataloguementioning

confidence: 99%

A communal catalogue reveals Earth’s multiscale microbial diversity

Thompson¹,

Sanders²,

McDonald³

et al. 2017

Nature

Self Cite

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1,758

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A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

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Understanding the Anthropocene through the lens of landfill microbiomes

Achmon

Dowdy

et al. 2018

Frontiers in Ecol & Environ

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Rapid increases in human population and per‐capita waste production have resulted in accelerated growth in the size and number of landfills. We propose that microbiota within landfills can contribute to a better understanding of the Anthropocene thus far. Because landfills are characterized by conditions that are uncommon in natural, non‐anthropogenic environments, they present a novel, rapidly growing, and essentially unstudied ecological system. Anthropogenic impacts may lead to unique adaptations in resident microbial communities, resulting in novel assemblages, activities, and features that differ from those in natural environments. Modern tools like molecular and bioinformatic techniques allow scientists to characterize these communities in unprecedented detail. A nuanced understanding of the adaptations, such as novel degradation abilities, that arise from such unusual selection pressures could facilitate improvements in bioremediation. Furthermore, similarities between landfill formation and geological deposition processes suggest that landfills will be preserved in future geological records and, consequently, may be suitable for dating anthropogenic influences at the local scale. Studying landfill microbiomes could therefore help to define the Anthropocene and reveal its consequences.

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Quantifying human impact on Earth's microbiome

Cited by 21 publications

References 15 publications

Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

A communal catalogue reveals Earth’s multiscale microbial diversity

Understanding the Anthropocene through the lens of landfill microbiomes

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