Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Acinas, Silvia G.; Sánchez, Pablo; Salazar, Guillem; Cornejo‐Castillo, Francisco M.; Sebastián, Marta; Logares, Ramiro; Royo-Llonch, Marta; Paoli, Lucas; Sunagawa, Shinichi; Hingamp, Pascal; Ogata, Hiroyuki; Lima‐Mendez, Gipsi; Roux, Simon; González, José M.; Arrieta, Jesús M.; Álam, Intikhab; Kamau, Allan; Bowler, Chris; Raes, Jeroen; Pesant, Stéphane; Bork, Peer; Agustı́, Susana; Gojobori, Takashi; Vaqué, Dolors; Sullivan, Matthew B.; Pedrós‐Alió, Carlos; Massana, Ramón; Duarte, Carlos M.; Gasol, Josep M.

doi:10.1038/s42003-021-02112-2

Cited by 132 publications

(182 citation statements)

References 131 publications

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“…The contigs > 1,000 bp were submitted to Metagenome Analysis Rapid Annotation using Subsystem Technology (MG-RAST; Keegan et al, 2016) for a similarity search using the SEED Subsystem (Overbeek et al, 2005) and the Kyoto Encyclopedia of Genes and Genomes (KEGG; Kanehisa and Goto, 2000) databases, using a cut-off E-value of 1e −5 , minimum identity of 60% and a minimum alignment length of 15 bp. SEED and KEGG annotations were normalized by the number of reads assigned to the prokaryotic single copy gene recA (Acinas et al, 2021) prior to calculating the relative abundances.…”

Section: Metagenomic Analysismentioning

confidence: 99%

Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

et al. 2021

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Sediment microbial communities play essential roles in marine ecosystem functioning. Their study is crucial to understand how environmental conditions affect microbial diversity and biogeochemical cycles. The Venice Lagoon, one of the largest Adriatic transitional systems, is subjected to different natural and anthropogenic stressors. In this study, surface sediments microbial communities were finely characterized using 16S rRNA gene amplicon sequencing and metagenomics. Samples were collected seasonally in 2019 and 2020 at different sites within Lagoon sub-basins. Our results indicated a stable spatial distribution of the sediment microbiome: salinity, grain size, and total organic carbon were found to be important drivers in shaping prokaryotic communities, while temperature had a minor role. We detected high microbial diversity at all stations, mainly due to low abundant taxa: bacteria represented the vast majority of the reads (∼96.1%), with Woeseia the most abundant genus (∼4.4%). The metagenomic analysis highlighted significant differences among sites in terms of biogeochemical processes (e.g., C, N, Fe, and S metabolism), and cell-cell interaction strategies (e.g., mobilome, regulations and cell signaling). Chioggia, a sandy site subjected to marine influence, presented the highest abundance of ammonia-oxidizing archaeon Candidatus Nitrosopumilus, in accordance with the highest amount of ammonia monooxygenase subunit genes. At the same site, sulfate-reducing bacteria (Desulfobacteria and Desulfobacterales) and sulfur-related genes were found in lower abundance. Marghera and Tresse, the most polluted sites, showed higher abundance of sewage-related bacteria and antibiotic and toxic compound resistance genes. Furthermore, these sites showed higher amount of genes related to cell-cell interaction, such as pathogenicity islands, transposable-elements, and biofilm formation. Our findings highlighted that sediment features and human-related activities have profound and long-term impacts on the surface sediment microbial communities of the Venice Lagoon.

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Section: Metagenomic Analysismentioning

confidence: 99%

Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

et al. 2021

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“…Competitive recruitment of the metagenomic reads from Tara Oceans ( 2 ), BioGEOTRACES ( 92 ), the Malaspina Global Expedition ( 93 ), the Southern California Bight near Los Angeles ( 32 ), and the northern Gulf of Mexico hypoxic zone ( 31 ) to the OM252 genomes was completed using the protocol available at http://merenlab.org/data/tara-oceans-mags/ . Reads were cleaned using illumina utils v2.6 ( 94 ) implementing the method described in reference 95 .…”

Section: Methodsmentioning

confidence: 99%

“…OM252 community diversity was assessed using the skbio.diversity algorithmic suite v0.5.6 ( http://scikit-bio.org/docs/latest/diversity.html ). Recruited OM252 reads from 588 metagenomic samples including TARA ( 2 ), BioGEOTRACES ( 92 ), and Malaspina Global Expedition ( 93 ) were normalized to transcripts per million (TPM) values and used analogously for count dissimilarities. TPM calculations were performed using ( https://github.com/thrash-lab/counts_to_tpm ).…”

Section: Methodsmentioning

confidence: 99%

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )

et al. 2021

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“…Some deep ecotypes could be opportunistic taxa within the bathypelagic assemblages, conferring them a broader capability of substrate utilization (Sebastián et al, 2021). Alternatively, mixotrophy., i.e., carrying out chemolithoautotrophic inorganic carbon fixation and heterotrophy (Sorokin, 2003;Alonso-Sáez et al, 2010) has been recently suggested to represent an ecologically relevant trait for prokaryotes to survive across the global dark ocean (Acinas et al, 2021).…”

Section: Hydrography and Dom Quality Indicators Driving Niche Partitioningmentioning

confidence: 99%

Vertical Niche Partitioning of Archaea and Bacteria Linked to Shifts in Dissolved Organic Matter Quality and Hydrography in North Atlantic Waters

Rodríguez‐Ramos

Nieto‐Cid

Auladell³

et al. 2021

Front. Mar. Sci.

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Understanding the factors that modulate prokaryotic assemblages and their niche partitioning in marine environments is a longstanding challenge in marine microbial ecology. This study analyzes amplicon sequence variant (ASV) diversity and co-occurrence of prokaryotic (Archaea and Bacteria) communities through coastal-oceanic gradients in the NW Iberian upwelling system and adjacent open-ocean (Atlantic Ocean). Biogeographic patterns were investigated in relation with environmental conditions, mainly focusing on the optical signature of the dissolved organic matter (DOM). Alpha- and beta-diversity were horizontally homogeneous [with the only exception of Archaea (∼1700 m depth), attributed to the influence of Mediterranean water, MW], while beta-diversity was significantly vertically stratified. Prokaryotic communities were structured in four clusters (upper subsurface, lower subsurface, intermediate, and deep clusters). Deep (>2000 m) archaeal and bacterial assemblages, and intermediate (500-2000 m) Bacteria (mainly SAR202 and SAR406), were significantly related to humic-like DOM (FDOM-M), while intermediate Archaea were additionally related to biogeochemical attributes of the high-salinity signature of MW. Lower subsurface (100-500 m) Archaea (particularly one ASV belonging to the genus Candidatus Nitrosopelagicus) were mainly related to the imprint of high-salinity MW, while upper subsurface (≤100 m) archaeal assemblages (particularly some ASVs belonging to Marine Group II) were linked to protein-like DOM (aCDOM254). Conversely, both upper and lower subsurface bacterial assemblages were mainly linked to aCDOM254 (particularly ASVs belonging to Rhodobacteraceae, Cyanobacteria, and Flavobacteriaceae) and nitrite concentration (mainly members of Planctomycetes). Most importantly, our analysis unveiled depth-ecotypes, such as the ASVs MarG.II_1 belonging to the archaeal deep cluster (linked to FDOM-M) and MarG.II_2 belonging to the upper subsurface cluster (related to FDOM-T and aCDOM254). This result strongly suggests DOM-mediated vertical niche differentiation, with further implications for ecosystem functioning. Similarly, positive and negative co-occurrence relationships also suggested niche partitioning (e.g., between the closely related ASVs Thaum._Nit._Nit._Nit._1 and _2) and competitive exclusion (e.g., between Thaum._Nit._Nit._Nit._4 and _5), supporting the finding of non-randomly, vertically structured prokaryotic communities. Overall, differences between Archaea and Bacteria and among closely related ASVs were revealed in their preferential relationship with compositional changes in the DOM pool and environmental forcing. Our results provide new insights on the ecological processes shaping prokaryotic assembly and biogeography.

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Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Cited by 132 publications

References 131 publications

Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )

Vertical Niche Partitioning of Archaea and Bacteria Linked to Shifts in Dissolved Organic Matter Quality and Hydrography in North Atlantic Waters

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