The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

Jurburg, Stephanie D.; Konzack, Maximilian; Eisenhauer, Nico; Heintz‐Buschart, Anna

doi:10.1101/2020.04.28.063271

Cited by 2 publications

(2 citation statements)

References 38 publications

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“…In contrast, EWAS requires no prior knowledge, given the capacity to obtain information for any organism with a phylogenetic gene marker present in sequencing databases [45][46][47][48]. An EWAS approach is primarily limited by the poor quality of metadata reported for most sequencing projects [49] and a historical lack of standardization in sequencing workflows. These drawbacks are partially compensated for by the sheer volume of available sequencing projects and renewed efforts to systematize data publishing will improve the efficacy of EWAS over time [50].…”

Section: Introductionmentioning

confidence: 99%

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Wilhelm

Amsili

Kurtz

et al. 2023

ISME Communications

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Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

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Section: Introductionmentioning

confidence: 99%

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Wilhelm

Amsili

Kurtz

et al. 2023

ISME Communications

View full text Add to dashboard Cite

show abstract

“…In contrast, EWAS requires no prior knowledge, with information gained for any organism represented in sequencing databases [45][46][47][48]. An EWAS approach is primarily limited by the poor quality of metadata reported for most sequencing projects [49] and a historical lack of standardization in sequencing workflows. These drawbacks are partially compensated for by the sheer volume of available sequencing projects.…”

Section: Introductionmentioning

confidence: 99%

Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils

Wilhelm

Amsili

Kurtz

et al. 2022

Preprint

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Soil health assessment may be enhanced by monitoring changes in bacterial populations that are indicators of various biological, physical, and chemical properties of soil. However, the lack of ecological information for many abundant bacteria in agricultural soils limits our understanding of indicator responses and, thus, their utility for guiding management. We identified bacterial indicators of twelve conventional measures of soil health, and tillage intensity, from a 16S rRNA gene-based survey of farmland across North America. We then analyzed trends according to bacterial life-history frameworks and an environment-wide association survey (EWAS) to gain ecological insights. Life-history traits were assessed using genomic traits inferred from taxonomic classifications and included: genome size, rrn copy number, and coding density. An EWAS was conducted using 89 studies of agricultural land management. Most bacterial indicators were positively correlated with biological measures and negatively correlated with physical and chemical measures of soil health, revealing broad differences in the way management shapes bacterial associations with soil health. High soil health ratings corresponded with life-history traits associated with metabolic dependency (smaller genome and lower coding density), while lower health scores corresponded with traits selected for by environmental instability and disturbance (larger genome and multiple rrn). Trade-offs in community-weighted genome size explained most variation in overall health score. EWAS confirmed the importance of disturbance-adapted bacterial indicators, underscoring the impacts of tillage on soil bacterial communities. These findings provide insights into the ecological relationships between bacterial indicators and soil health and illustrate new approaches for interpreting patterns in microbiome data.

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The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

Cited by 2 publications

References 38 publications

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils

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