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Novel chemolithotrophic and anoxygenic phototrophic genomes extracted from ice-covered boreal lakes

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/grl.50152openalex-snapshot

High emission of carbon dioxide and methane during ice thaw in high latitude lakes

inferredcites →https://doi.org/10.1002/lno.10288openalex-snapshot

Methane oxidation at the water‐ice interface of an ice‐covered lake

inferredcites →https://doi.org/10.1007/s00248-012-0049-3openalex-snapshot

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

inferredcites →https://doi.org/10.1007/s10021-012-9585-4openalex-snapshot

Carbon Dioxide in Boreal Surface Waters: A Comparison of Lakes and Streams

inferredcites →https://doi.org/10.1007/s10021-015-9944-zopenalex-snapshot

Regional Variability and Drivers of Below Ice CO2 in Boreal and Subarctic Lakes

inferredcites →https://doi.org/10.1007/s10452-009-9278-zopenalex-snapshot

Perspectives in winter limnology: closing the annual cycle of freezing lakes

inferredcites →https://doi.org/10.1016/j.bbabio.2013.01.008openalex-snapshot

Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin

inferredcites →https://doi.org/10.1016/j.jmb.2004.05.028openalex-snapshot

Improved Prediction of Signal Peptides: SignalP 3.0

inferredcites →https://doi.org/10.1016/j.tim.2006.09.001openalex-snapshot

Prokaryotic photosynthesis and phototrophy illuminated

inferredcites →https://doi.org/10.1016/s0168-6496(98)00086-5openalex-snapshot

Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments

inferredcites →https://doi.org/10.1016/s0883-2927(99)00097-9openalex-snapshot

The ferrozine method revisited: Fe(II)/Fe(III) determination in natural waters

inferredcites →https://doi.org/10.1021/es010311popenalex-snapshot

Measurement of Methane Oxidation in Lakes: A Comparison of Methods

inferredcites →https://doi.org/10.1038/ismej.2011.184openalex-snapshot

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships

inferredcites →https://doi.org/10.1038/ismej.2012.21openalex-snapshot

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

inferredcites →https://doi.org/10.1038/ismej.2012.70openalex-snapshot

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

inferredcites →https://doi.org/10.1038/ismej.2012.86openalex-snapshot

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

inferredcites →https://doi.org/10.1038/ismej.2014.135openalex-snapshot

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

inferredcites →https://doi.org/10.1038/ismej.2015.241openalex-snapshot

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

inferredcites →https://doi.org/10.1038/ismej.2015.260openalex-snapshot

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

inferredcites →https://doi.org/10.1038/nature02340openalex-snapshot

Community structure and metabolism through reconstruction of microbial genomes from the environment

inferredcites →https://doi.org/10.1038/nature08551openalex-snapshot

Rationally tuning the reduction potential of a single cupredoxin beyond the natural range

inferredcites →https://doi.org/10.1038/nature08883openalex-snapshot

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

inferredcites →https://doi.org/10.1038/nature12352openalex-snapshot

Insights into the phylogeny and coding potential of microbial dark matter

inferredcites →https://doi.org/10.1038/ncomms3304openalex-snapshot

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

inferredcites →https://doi.org/10.1038/ngeo2578openalex-snapshot

Climate-sensitive northern lakes and ponds are critical components of methane release

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3103openalex-snapshot

Binning metagenomic contigs by coverage and composition

inferredcites →https://doi.org/10.1038/srep11841openalex-snapshot

Motion-induced blindness continues outside visual awareness and without attention

inferredcites →https://doi.org/10.1038/srep12102openalex-snapshot

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes

inferredcites →https://doi.org/10.1038/srep13803openalex-snapshot

Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin

inferredcites →https://doi.org/10.1046/j.1365-2427.2001.00687.xopenalex-snapshot

Sulphate reduction and sulphur cycling in lake sediments: a review

inferredcites →https://doi.org/10.1073/pnas.0801925105openalex-snapshot

Resistance, resilience, and redundancy in microbial communities

inferredcites →https://doi.org/10.1073/pnas.0805313105openalex-snapshot

Photoferrotrophs thrive in an Archean Ocean analogue

inferredcites →https://doi.org/10.1073/pnas.1419038112openalex-snapshot

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

inferredcites →https://doi.org/10.1093/bioinformatics/14.9.755openalex-snapshot

Profile hidden Markov models.

inferredcites →https://doi.org/10.1093/bioinformatics/bti057openalex-snapshot

PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/database/bap021openalex-snapshot

MicroScope: a platform for microbial genome annotation and comparative genomics

inferredcites →https://doi.org/10.1093/nar/gkg847openalex-snapshot

Enzyme-specific profiles for genome annotation: PRIAM

inferredcites →https://doi.org/10.1093/nar/gkp698openalex-snapshot

FIGfams: yet another set of protein families

inferredcites →https://doi.org/10.1093/nar/gks1194openalex-snapshot

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

inferredcites →https://doi.org/10.1093/nar/gkt1076openalex-snapshot

Data, information, knowledge and principle: back to metabolism in KEGG

inferredcites →https://doi.org/10.1093/nar/gkt1140openalex-snapshot

Activities at the Universal Protein Resource (UniProt)

inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot

Pfam: the protein families database

inferredcites →https://doi.org/10.1093/nar/gku1243openalex-snapshot

The InterPro protein families database: the classification resource after 15 years

inferredcites →https://doi.org/10.1099/ijs.0.63728-0openalex-snapshot

Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 N)

inferredcites →https://doi.org/10.1099/mic.0.082313-0openalex-snapshot

Reconstruction of bacteriochlorophyll biosynthesis pathways in the filamentous anoxygenic phototrophic bacterium Oscillochloris trichoides DG-6 and evolution of anoxygenic phototrophs of the order Chloroflexales

inferredcites →https://doi.org/10.1101/054478openalex-snapshot

Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry

inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

inferredcites →https://doi.org/10.1111/1462-2920.12301openalex-snapshot

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

inferredcites →https://doi.org/10.1111/j.1365-2486.2004.00848.xopenalex-snapshot

A large carbon pool and small sink in boreal Holocene lake sediments

inferredcites →https://doi.org/10.1111/j.1461-0248.2009.01388.xopenalex-snapshot

Biodiversity in a complex world: consolidation and progress in functional biodiversity research

inferredcites →https://doi.org/10.1111/j.1462-2920.2007.01527.xopenalex-snapshot

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

inferredcites →https://doi.org/10.1111/j.1472-4669.2006.00057.xopenalex-snapshot

Planktonic microbial community composition across steep physical/chemical gradients in permanently ice‐covered Lake Bonney, Antarctica

inferredcites →https://doi.org/10.1111/j.1758-2229.2009.00022.xopenalex-snapshot

Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia

inferredcites →https://doi.org/10.1111/mec.13319openalex-snapshot

Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

inferredcites →https://doi.org/10.1126/science.1224041openalex-snapshot

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

inferredcites →https://doi.org/10.1126/science.1243768openalex-snapshot

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

inferredcites →https://doi.org/10.1126/science.251.4991.298openalex-snapshot

Arctic Lakes and Streams as Gas Conduits to the Atmosphere: Implications for Tundra Carbon Budgets

inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

inferredcites →https://doi.org/10.1128/aem.03230-13openalex-snapshot

Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating, Iron-Oxidizing, Acidophilic Bacterium “Ferrovum myxofaciens”

inferredcites →https://doi.org/10.1128/jb.05380-11openalex-snapshot

Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96

inferredcites →https://doi.org/10.1130/0091-7613(1998)026<0535:masocb>2.3.co;2openalex-snapshot

Magnitude and significance of carbon burial in lakes, reservoirs, and peatlands

inferredcites →https://doi.org/10.1186/1471-2105-4-41openalex-snapshot

The COG database: an updated version includes eukaryotes

inferredcites →https://doi.org/10.1186/2042-5783-1-5openalex-snapshot

The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist

inferredcites →https://doi.org/10.1186/gb-2007-8-1-r10openalex-snapshot

Prediction of effective genome size in metagenomic samples

inferredcites →https://doi.org/10.1186/gb-2007-8-9-r183openalex-snapshot

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

inferredcites →https://doi.org/10.1186/gb-2012-13-12-r122openalex-snapshot

Ray Meta: scalable de novo metagenome assembly and profiling

inferredcites →https://doi.org/10.1371/journal.pone.0116955openalex-snapshot

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

inferredcites →https://doi.org/10.1890/0012-9658(2003)084[0969:maasoc]2.0.co;2openalex-snapshot

METHANE AS A SOURCE OF CARBON AND ENERGY FOR LAKE PELAGIC FOOD WEBS

inferredcites →https://doi.org/10.1890/100014openalex-snapshot

Riverine coupling of biogeochemical cycles between land, oceans, and atmosphere

inferredcites →https://doi.org/10.3389/fmicb.2012.00273openalex-snapshot

Bacterial oxygen production in the dark

inferredcites →https://doi.org/10.3389/fmicb.2014.00713openalex-snapshot

Phototrophic Fe(II)-oxidation in the chemocline of a ferruginous meromictic lake

inferredcites →https://doi.org/10.3389/fmicb.2015.00068openalex-snapshot

Cellular compartmentalization of secondary metabolism

inferredcites →https://doi.org/10.3389/fmicb.2015.01072openalex-snapshot

Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8

inferredcites →https://doi.org/10.4319/lo.1996.41.4.0783openalex-snapshot

Flow cytometric determination of bacterial abundance in lake plankton with the green nucleic acid stain SYTO 13

inferredcites →https://doi.org/10.4319/lo.2009.54.6_part_2.2298openalex-snapshot

Lakes and reservoirs as regulators of carbon cycling and climate

inferredcites →https://doi.org/10.4319/lo.2013.58.6.1998openalex-snapshot

The under‐ice microbiome of seasonally frozen lakes

inferredcites →https://doi.org/10.5194/bg-6-209-2009openalex-snapshot

Methane dynamics in different boreal lake types

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41586-024-07180-yopenalex-snapshot

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre

inferred← citeshttps://doi.org/10.1101/2020.07.07.190934openalex-snapshot

Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center

inferred← citeshttps://doi.org/10.1111/1462-2920.14285openalex-snapshot

Bloom of a denitrifying methanotroph, ‘ Candidatus Methylomirabilis limnetica’, in a deep stratified lake

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