Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Diamond, Spencer; Andeer, Peter F.; Zhou, Li; Crits-Christoph, Alexander; Burstein, David; Anantharaman, Karthik; Lane, Katherine R.; Thomas, Brian C.; Pan, Chongle; Northen, Trent; Banfield, Jillian F.

doi:10.1038/s41564-019-0449-y

Cited by 163 publications

(209 citation statements)

References 86 publications

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“…These MAG binning methods have been used in unveiling previously uncharacterised genomic diversity [27,28,29], but metagenomic assembly and binning results in the loss of some information. This compounded data loss means as little as 24.2-36.4% of reads [30,31] and ~23% of genomes [31] are successfully assembled and binned in some metagenomic analyses. The Critical Assessment of Metagenome Interpretation (CAMI) challenge's (https://data.camichallenge.org/) Assessment of Metagenome BinnERs (AMBER) [32] benchmarks di erent MAG recovery methods in terms of global completeness and bin purity.…”

Section: Mainmentioning

confidence: 99%

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Maguire

Jia²,

Gray³

et al. 2020

Preprint

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MotivationMetagenomic methods have emerged as a key tool in public-health microbiology for surveillance of virulence factor (VF) and antimicrobial resistance (AMR) genes. However, metagenomic data, even when assembled, typically results in complex, mixed sets DNA sequence fragments rather than fully resolved individual genomes. Recently, metagenome-assembled genomes (MAGs) have emerged as a promising approach that groups sequences into bins that are likely derived from the same underlying genome. However, MAGs have not been well assessed for their ability to identify some of the key sequences of interest for infectious disease surveillance purposes: AMR and VFs associated with mobile genetic elements (MGEs) such as plasmids and genomic islands (GIs). We hypothesized that due to the di erent copy number and sequence composition of plasmids and GIs compared to core genome sequence, such sequences will be under-represented in MAG-based approaches. ResultsTo evaluate the impact of MAG recovery methods on recovery of AMR genes and MGEs, we generated a simulated metagenomic dataset comprised of 30 genomes with up to 16.65% of the chromosomal DNA consisting of GIs and 65 associated plasmids. MAGs were then recovered from this data using 12 di erent MAG pipelines and evaluated for recovery accuracies. Across all pipelines, 81.9-94.3% of chromosomes were recovered and binned. However, only 37.8-44.1% of GIs and 1.5-29.2% of plasmids were recovered and correctly binned at >50% coverage. In terms of AMR and VF genes associated with MGEs, 0-45% of GI-associated AMR genes and 0-16% of GI-associated VF genes were correctly assigned. More strikingly, 0% of plasmid-borne VF or AMR genes were recovered. This work shows that regardless of the MAG recovery approach used, plasmid and GI dominated sequences will disproportionately be left unbinned or incorrectly binned. From a public-health perspective, this means MAG approaches are less suited for analysis of mobile genes, especially key groups such as AMR and VF genes. This underlines the utility of read-based and long-read approaches to thoroughly evaluate the resistome in metagenomic data.

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Section: Mainmentioning

confidence: 99%

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Maguire

Jia²,

Gray³

et al. 2020

Preprint

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“…4) All genomes must be publically available for download, not just the de-replicated genome set. Many potential metagenomic studies were disqualified based on criteria (3) and (4), leading to the ultimate selection of three genome sets for follow up analysis (Diamond et al, 2019;Olm et al, 2019;Tully et al, 2018). Recent studies involving large-scale genome binning (Parks et al, 2017;Pasolli et al, 2019) could not be included because their pre-de-replication sets included replicate genomes from the same time series', leading to artificial genome clusters.…”

Section: Preparation Of Genome Setsmentioning

confidence: 99%

“…The second set contains 1,166 genomes from the ocean, including Bacteria and Archaea (Tully et al, 2018). The third set contains 1,859 genomes from a meadow soil ecosystem (Diamond et al, 2019) that spans a large number of diverse phylogenetic groups. We also included 4,800 genomes from NCBI RefSeq, accessed February 2018, where we randomly selected 10 genomes from each of the 480 bacterial species with at least 10 genomes.…”

Section: Preparation Of Genome Setsmentioning

confidence: 99%

“…Sets of microbial genomes without the selection biases introduced by isolation were generated from metagenomic studies of three environments: infant fecal samples (Olm et al, 2019), the ocean (Tully et al, 2018), and a meadow soil ecosystem (Diamond et al, 2019)). A taxonomically balanced set of genomes from Refseq was generated by randomly choosing 10 genomes from each of the 480 species in RefSeq with at least 10 genomes ( Supplemental Table S1 ).…”

Section: Discrete Sequence Groups Exist In All Analyzed Genome Setsmentioning

confidence: 99%

“…For example, only 24.2% of the reads could be assembled and binned in a rent study of permafrost metagenomes (Woodcroft et al, 2018). More recently, only 36.4% of reads were assembled into binned contigs, and genomes were reconstructed for only~23% of the detected bacteria in complex soil metagenomes (Diamond et al, 2019). Absent dramatic improvements in sequencing technologies, complex communities can be more fully characterized through analysis of assembled and unbinned single copy marker genes, for example the 16S rRNA gene, ribosomal genes, or tRNA-ligase genes (Brown et al, 2015;Emerson et al, 2016;Hamilton et al, 2016;Probst et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Consistent metagenome-derived metrics verify and define bacterial species boundaries

Olm

Crits-Christoph

Diamond

et al. 2019

Preprint

Self Cite

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Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. We compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity, and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of non-synonymous and synonymous nucleotide differences ( dN / dS ) decrease until ANI values approach 98%, estimates for homologous recombination approached zero at~95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full length 16S rRNA genes were least useful because they were under-recovered from metagenomes, but many ribosomal proteins displayed both high metagenomic recoverability and species-discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.

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Microbial controls on net production of nitrous oxide in a denitrifying woodchip bioreactor

et al. 2021

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Denitrifying woodchip bioreactors are potential low‐cost technologies for the removal of nitrate (NO3−) in water through denitrification. However, if environmental conditions do not support microbial communities performing complete denitrification, other N transformation processes will occur, resulting in the export of nitrite (NO2−), nitrous oxide (N2O), or ammonium (NH4+). To identify the factors controlling the relative accumulation of NO2−, N2O, and/or NH4+ in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO3− from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N2O reduction, and dissimilatory NO3− reduction to NH4+ were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly correlated with increases in porewater N2O concentrations and indicated the preferential selection of incomplete denitrifying pathways ending with N2O. Temperature and the total organic carbon/NO3− ratio were strongly correlated with NH4+ concentrations and inversely correlated with the ratio between denitrification genes and the genes indicative of ammonification (Σnir/nrfA), suggesting an environmental control on NO3− transformations. Overall, our results for a denitrifying woodchip bioreactor operated at hydraulic residence times of 1.0–2.6 d demonstrate the temporal development in the microbial community and indicate an increased potential for N2O emissions with time from the denitrifying woodchip bioreactor.

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Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Cited by 163 publications

References 86 publications

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Consistent metagenome-derived metrics verify and define bacterial species boundaries

Microbial controls on net production of nitrous oxide in a denitrifying woodchip bioreactor

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