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Article
Open AccessNiche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions
Microbiome engineering – the targeted manipulation of microbial communities – is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here...
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Article
Open AccessMarine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition
The Ocean microbiome has a crucial role in Earth’s biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity a...
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Article
Open AccessTop abundant deep ocean heterotrophic bacteria can be retrieved by cultivation
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a br...
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Article
Open AccessEcology of Endozoicomonadaceae in three coral genera across the Pacific Ocean
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their...
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Article
Open AccessDiversity of the Pacific Ocean coral reef microbiome
Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the exte...
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Article
Open AccessTelomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals
Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime i...
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Article
Open AccessBiosynthetic potential of the global ocean microbiome
Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnol...
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Article
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples,...
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Article
Open AccessDeep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58...
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Article
Open AccessMicrobiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cr...
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Article
Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions
Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara
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Article
Open AccessDiversity and distribution of marine heterotrophic bacteria from a large culture collection
Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean le...
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Article
Open AccessDisentangling the mechanisms sha** the surface ocean microbiota
The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we in...
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Article
Open AccessScaling of species distribution explains the vast potential marine prokaryote diversity
Global ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representi...
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Article
Open AccessMicrobial abundance, activity and population genomic profiling with mOTUs2
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, whic...
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Article
Open AccessLarge-scale ocean connectivity and planktonic body size
Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversit...
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Article
Open AccessCyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton
The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineage...
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Article
Why are there so many kinds of planktonic consumers? The answer lies in the allometric diet breadth
In an attempt to explain ‘Why are there so many kinds of animals?’ G.E. Hutchinson highlighted the food web context to suggest that diversity of primary producers should allow consumer richness to be maintained a...
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Chapter
Why are there so many kinds of planktonic consumers? The answer lies in the allometric diet breadth
In an attempt to explain ‘Why are there so many kinds of animals?’ G.E. Hutchinson highlighted the food web context to suggest that diversity of primary producers should allow consumer richness to be maintained a...
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Article
Factors controlling the colonial structure of Pediastrum tetras (Chlorophyceae)
Accounting for morphological plasticity in phytoplankton populations is relevant for taxonomy, systematic/evolutionary, and ecological studies. In this work, the green alga Pediastrum tetras (Ehrenberg) Ralfs was...
