ArticleThe ISME journal2013
Expression patterns reveal niche diversification in a marine microbial assemblage.
Article in The ISME journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
87 citing papers in PubMed.
- Functional dynamics of the gut microbiome in elderly people during probiotic consumption.mBio · 2015Trial
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- The impact of tropodithietic acid on microbial physiology under varying culture complexities.mSphere · 2025Article
- Article
- Microbial Community Metabolism of Coral Reef Exometabolomes Broadens the Chemodiversity of Labile Dissolved Organic Matter.Environmental microbiology · 2025Article
- Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning.The ISME journal · 2025Article
- Sexual reproduction during diatom bloom.ISME communications · 2025Article
- Article
- Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.Scientific data · 2024Article
- Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.Nature communications · 2024Article
- Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica.Journal of microbiology (Seoul, Korea) · 2023Article
- GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry.International journal of molecular sciences · 2023Article
- Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean.Microbiome · 2023Article
- A mutant fitness assay identifies bacterial interactions in a model ocean hot spot.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut.Applied and environmental microbiology · 2022Review
- Microbial metabolites in the marine carbon cycle.Nature microbiology · 2022Review
- Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom.The ISME journal · 2022Article
- Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf.Nature communications · 2022Article
- Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.Frontiers in microbiology · 2022Article
- Mechanism of interventional effect and targets of Zhuyu pill in regulating and suppressing colitis and cholestasis.Frontiers in pharmacology · 2022Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.