Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology 17, 569–586 (2019).
Google Scholar
Azam, F. et al. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series 10, 257–263 (1983).
Google Scholar
Jiao, N. et al. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nature Reviews Microbiology 8, 593–599 (2010).
Google Scholar
Zhang, C. et al. Evolving paradigms in biological carbon cycling in the ocean. National Science Review 5, 481–499 (2018).
Google Scholar
Mestre, M. et al. Sinking particles promote vertical connectivity in the ocean microbiome. Proceedings of the National Academy of Sciences 115, E6799–E6807 (2018).
Google Scholar
Baumas, C. M. J. et al. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions. The ISME Journal 15, 1695–1708 (2021).
Google Scholar
Ortega-Retuerta, E., Joux, F., Jeffrey, W. H. & Ghiglione, J. F. Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the beaufort sea (canadian arctic). Biogeosciences 10, 2747–2759 (2013). BG.
Google Scholar
Ganesh, S., Parris, D. J., DeLong, E. F. & Stewart, F. J. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME Journal 8, 187–211 (2014).
Google Scholar
Chen, S. et al. Interactions between marine group ii archaea and phytoplankton revealed by population correlations in the northern coast of south china sea. Frontiers in Microbiology 12 (2022).
Eloe, E. A. et al. Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environmental Microbiology Reports 3, 449–458 (2011).
Google Scholar
Salazar, G. et al. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol 24, 5692–706 (2015).
Google Scholar
Karner, M. & Herndl, G. J. Extracellular enzymatic activity and secondary production in free-living and marine-snow-associated bacteria. Marine Biology 113, 341–347 (1992).
Google Scholar
Grossart, H.-P., Tang, K. W., Kiørboe, T. & Ploug, H. Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages. FEMS Microbiology Letters 266, 194–200 (2007).
Google Scholar
Fierer, N. et al. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal 6, 1007–1017 (2012).
Google Scholar
Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proceedings of the National Academy of Sciences 112, 10967–10972 (2015).
Google Scholar
Chen, Y. et al. Large amounts of easily decomposable carbon stored in subtropical forest subsoil are associated with r-strategy-dominated soil microbes. Soil Biology and Biochemistry 95, 233–242 (2016).
Google Scholar
Hou, S. et al. Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. The ISME Journal 12, 981–996 (2018).
Google Scholar
Cleveland, C. C., Nemergut, D. R., Schmidt, S. K. & Townsend, A. R. Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition. Biogeochemistry 82, 229–240 (2007).
Google Scholar
Ho, A., Di Lonardo, D. P. & Bodelier, P. L. E. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiology Ecology 93 (2017).
Xing, J. et al. Fluxes, seasonal patterns and sources of various nutrient species (nitrogen, phosphorus and silicon) in atmospheric wet deposition and their ecological effects on Jiaozhou Bay, North China. Sci Total Environ 576, 617–627 (2017).
Google Scholar
Zhang, L., Xiong, L., Li, J. & Huang, X. Long-term changes of nutrients and biocenoses indicating the anthropogenic influences on ecosystem in Jiaozhou Bay and Daya Bay, China. Mar Pollut Bull 168, 112406 (2021).
Google Scholar
Zhang, X. et al. Effects of organic nitrogen components from terrestrial input on the phytoplankton community in Jiaozhou Bay. Marine Pollution Bulletin 174, 113316 (2022).
Google Scholar
Sharp, J. et al. Final dissolved organic carbon broad community intercalibration and preliminary use of DOC reference materials. Marine Chemistry 77 (2002).
Walters, W. et al. Improved bacterial 16S rrna gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1 (2016).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37, 852–857 (2019).
Google Scholar
Li, D. et al. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102, 3–11 (2016).
Google Scholar
Mikheenko, A., Saveliev, V. & Gurevich, A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32, 1088–90 (2016).
Google Scholar
Yu, K. et al. Recovery of high-qualitied genomes from a deep-inland salt lake using BASALT. bioRxiv https://doi.org/10.1101/2021.03.05.434042 (2021).
Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Google Scholar
Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–7 (2016).
Google Scholar
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat Methods 11, 1144–6 (2014).
Google Scholar
Nayfach, S. et al. New insights from uncultivated genomes of the global human gut microbiome. Nature 568 (2019).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–55 (2015).
Google Scholar
Olm, M. R, Brown, C. T. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. The ISME Journal 5 (2017).
Albanese, D. & Donati, C. Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality. F1000Research 10 (2021).
Bowers, R. M. et al. Minimum information about a single amplified genome (misag) and a metagenome-assembled genome (mimag) of bacteria and archaea. Nature Biotechnology 35, 725–731 (2017).
Google Scholar
Parks, D. H. et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol 38, 1079–1086 (2020).
Google Scholar
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics (2019).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–7 (2004).
Google Scholar
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–3 (2009).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PloS one 25, e9490–e9490 (2010).
Google Scholar
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP367774 (2022).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP367809 (2022).
Tao, J. Jiaozhou bay 16S rDNA & metagenome dataset. figshare https://doi.org/10.6084/m9.figshare.19690459.v6 (2022).
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