Reference health
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
1 of 78 checkable references need attention · checked 2026-07-23
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
2 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1093/femsec/fiy072/4983120
The 77 checked references that resolve
resolves10.1080/10408390802067514
Biogenic Amines in Fish: Roles in Intoxication, Spoilage, and Nitrosamine Formation—A Review
resolves10.1038/ncomms13219
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
resolves10.1128/AEM.66.12.5259-5266.2000
Molecular Characterization of Methanotrophic Isolates from Freshwater Lake Sediment
resolves10.1038/ismej.2015.241
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
resolves10.1371/journal.pone.0125353
Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes
resolves10.1371/journal.pone.0056103
The Role of Nitrogen Fixation in Cyanobacterial Bloom Toxicity in a Temperate, Eutrophic Lake
resolves10.1099/ijsem.0.001927
Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales
resolves10.1038/nbt.3893
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
resolves10.1126/science.1249213
Global rates of marine sulfate reduction and implications for sub–sea-floor metabolic activities
resolves10.1073/pnas.1512651112
Aquatic carbon cycling in the conterminous United States and implications for terrestrial carbon accounting
resolves10.1128/AEM.02132-17
Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal
resolves10.1038/ismej.2012.8
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
resolves10.1128/JB.185.10.2980-2987.2003
Methylotrophy in
<i>Methylobacterium extorquens</i>
AM1 from a Genomic Point of View
resolves10.1007/s10021-006-9013-8
Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget
resolves10.1128/AEM.03006-05
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
resolves10.1111/j.1462-2920.2004.00657.x
Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes
resolves10.1128/AEM.69.7.3701-3709.2003
Heterotrophic Bacterial Growth Efficiency and Community Structure at Different Natural Organic Carbon Concentrations
resolves10.1038/ismej.2015.260
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria
resolves10.1038/ismej.2009.153
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
resolves10.1038/ismej.2014.135
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
resolves10.1093/plankt/fbi043
Polymeric and free sugars released by three phytoplanktonic species from a freshwater tropical eutrophic reservoir
resolves10.4319/lo.2011.56.2.0734
Reconstructing the various facets of dissolved organic carbon bioavailability in freshwater ecosystems
resolves10.1371/journal.pone.0032772
The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population
resolves10.7717/peerj.3812
Ananke: temporal clustering reveals ecological dynamics of microbial communities
resolves10.1128/mSystems.00091-17
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
resolves10.1073/pnas.081610398
A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from
<i>Chlorobium tepidum</i>
that is involved with sulfur metabolism and the response to oxidative stress
resolves10.1128/mSphere.00277-17
Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
resolves10.1016/S0959-440X(97)80072-3
Structural and sequence-based classification of glycoside hydrolases
resolves10.1099/mic.0.044669-0
Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system
resolves10.1186/1471-2105-11-119
Prodigal: prokaryotic gene recognition and translation initiation site identification
resolves10.4319/lo.2001.46.7.1691
Whole‐lake mineralization of allochthonous and autochthonous organic carbon in a large humic lake (örträsket, N. Sweden)
resolves10.1099/ijs.0.029165-0
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
resolves10.1046/j.1432-1327.2002.02849.x
Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle
resolves10.1128/JB.01259-06
Whole-Genome Analysis of the Methyl
<i>tert</i>
-Butyl Ether-Degrading Beta-Proteobacterium
<i>Methylibium petroleiphilum</i>
PM1
resolves10.7717/peerj.1165
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
resolves10.3354/ame01620
Green sulphur bacteria as a component of the photosynthetic plankton community in small dimictic humic lakes with an anoxic hypolimnion
resolves10.4319/lo.2004.49.2.0588
Autochthonous versus allochthonous carbon sources of bacteria: Results from whole‐lake <sup>13</sup>C addition experiments
resolves10.1093/bioinformatics/btp698
Fast and accurate long-read alignment with Burrows–Wheeler transform
resolves10.1101/127035
Bacterial community composition and dynamics spanning five years in freshwater bog lakes
resolves10.1186/2047-217X-1-18
SOAPdenovo2: an empirically improved memory-efficient short-read
<i>de novo</i>
assembler
resolves10.1093/bioinformatics/btr507
FLASH: fast length adjustment of short reads to improve genome assemblies
resolves10.1093/nar/gkr1044
IMG: the integrated microbial genomes database and comparative analysis system
resolves10.1371/journal.pone.0035314
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
resolves10.1038/ismej.2011.84
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
resolves10.1111/j.1758-2229.2011.00289.x
Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton
resolves10.1101/gr.186072.114
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
resolves10.1007/s00248-010-9722-6
Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes
resolves10.1016/j.bbamcr.2014.11.021
[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation
resolves10.1038/ismej.2012.21
Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
resolves10.1038/srep12102
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
resolves10.1371/journal.pone.0009490
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
resolves10.1093/femsec/fiv105
Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems
resolves10.1016/j.biotechadv.2015.12.003
Algae–bacteria interactions: Evolution, ecology and emerging applications
resolves10.1038/nature12352
Insights into the phylogeny and coding potential of microbial dark matter
resolves10.1128/mSphere.00327-18
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
resolves10.1038/s41467-017-01086-2
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
resolves10.1038/ismej.2015.55
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
resolves10.1038/ismej.2012.162
<i>In situ</i> substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake
resolves10.1128/AEM.01541-09
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
resolves10.1890/1051-0761(2006)016[2064:DALAWA]2.0.CO;2
DENITRIFICATION ACROSS LANDSCAPES AND WATERSCAPES: A SYNTHESIS
resolves10.4319/lo.2007.52.2.0487
Interannual dynamics and phenology of bacterial communities in a eutrophic lake
resolves10.1065/espr2002.12.142
Eutrophication of freshwater and coastal marine ecosystems a global problem
resolves10.1890/070140
Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes
The 2 references without a DOI — listed, not checked
no DOI — not checkedR: a language and environment for statistical computing
no DOI — not checkedcowplot: streamlined plot theme and plot annotations for “ggplot2”
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work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
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