RTK: efficient rarefaction analysis of large datasets

Saary, Paul; Forslund, Kristoffer; Bork, Peer; Hildebrand, Falk

doi:10.1093/bioinformatics/btx206

Cited by 96 publications

(91 citation statements)

References 11 publications

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“…Furthermore, using minimap2 67 to find genes at 95% similarity threshold, we compared the soil gene catalogue with the Tara Oceans gene catalogue 13 , human gut gene catalogue 12 and the proGenomes prokaryotic database 26 . The gene catalogue nucleotide and amino acid sequences and abundance matrix estimates from rtk 68 have been deposited at http://vm-lux. embl.de/~hildebra/Soil_gene_cat/.…”

Section: Methodsmentioning

confidence: 99%

Structure and function of the global topsoil microbiome

Bahram

Hildebrand

Forslund

et al. 2018

Nature

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1,571

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Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

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Section: Methodsmentioning

confidence: 99%

Structure and function of the global topsoil microbiome

Bahram

Hildebrand

Forslund

et al. 2018

Nature

Self Cite

1,571

1,134

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“…After discarding singletons [33], each cluster was designated as an operational taxonomic unit (OTU). Rarefaction curves were calculated using RTK [34] with default settings. Non-metric multidimensional scaling (NMDS) analysis was conducted using Bray-Curtis dissimilarities, and multi-response permutation procedures (MRPP) test was conducted with 999 permutations and same dissimilarity indices.…”

Section: Methodsmentioning

confidence: 99%

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hiraoka

Hirai

Matsui

et al. 2019

Preprint

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32Hadal trench bottom (>6,000 m below sea level) sediments harbor higher microbial cell abundance 33 compared to adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic 34 matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different 35 trench systems has not been explored yet. Here, we carried out small subunit ribosomal RNA gene tag 36 sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three 37 trench regions in the northwest Pacific Ocean: the Japan, and Mariana Trenches. 38 Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and 39 nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic 40 locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic 41 consortiums that covaried across regions. Our results further support that the endogenous OM cycle is driven 42 by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition 43 to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra-and inter-trench 44 distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel 45 insights into ultra-deep-sea microbial ecology, one of the last frontiers on our planet. 46 48The abyssal plain extends from the continental slope to the rim of deep trenches (3,000-6,000 m 49 below sea level [mbsl]) and covers 85% of the global seafloor area, while the hadal zone (>6,000 mbsl) 50 comprises 1-2% of it [1, 2]. In general, abyssal water and sediments are usually oligotrophic, and physical and 51 chemical conditions (e.g., salinity, temperature, dissolved oxygen, and nutrient concentrations) in hadal water 52 are similar to the overlying abyssal water despite the higher hydrostatic pressure [1-3]. However, cell 53 abundance and microbial carbon turnover rates are significantly higher at hadal compared to abyssal seafloors, 54 especially below the sediment surface, while microbial abundance in surface sediments are sometimes 55 comparable between hadal and abyssal sites [4]. This could be attributed to factors apart from differences in 56 the vertical downward flux of sinking organic matter (OM) from the ocean surface and hydrostatic pressure. 57Hadal zones are generally located in oceanic trenches that are formed along plate boundaries by 58 movement of oceanic plates, and thus experience episodic and/or regular landslides [5, 6]. These landslides 59 cause downward transportation of surface sediments along with relatively fresh OM via the funnel effect of 60 trench geomorphology [7][8][9][10][11]. Moreover, higher sedimentation rates and concentrations of subseafloor 61 organic compounds in trench bottom sediments compared to neighboring abyssal sediments have been 62 reported in multiple trench regions under oligotrophic and eutroph...

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“…After discarding singletons [37], each cluster was designated as an operational taxonomic unit (OTU). Collector's curve was calculated using RTK [38] with default settings. Nonmetric multidimensional scaling (NMDS) analysis was conducted using Bray-Curtis dissimilarities, and multiresponse permutation procedures (MRPP) test was conducted with 999 permutations and same dissimilarity indices.…”

Section: Bioinformaticsmentioning

confidence: 99%

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hiraoka

Hirai

Matsui

et al. 2019

ISME J

113

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Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra-and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.

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RTK: efficient rarefaction analysis of large datasets

Cited by 96 publications

References 11 publications

Structure and function of the global topsoil microbiome

Structure and function of the global topsoil microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

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