Alin SR, Johnson TC. Carbon cycling in large lakes of the world: a synthesis of production, burial, and lake-atmosphere exchange estimates. Glob Biogeochemical Cycles. 2007;21:GB3002.
Durisch-Kaiser E, Schmid M, Peeters F, Kipfer R, Dinkel C, Diem T, et al. What prevents outgassing of methane to the atmosphere in Lake Tanganyika? J Geophys Res. 2011;116:G02022.
Takahashi T, Koblmüller S. The adaptive radiation of Cichlid fish in Lake Tanganyika: a morphological perspective. Int J Evolut Biol. 2011;2011:1–14.
Salzburger W. Understanding explosive diversification through Cichlid fish genomics. Nat Rev Genet. 2018;19:705–17.
Corman JR, McIntyre PB, Kuboja B, Mbemba W, Fink D, Wheeler CW, et al. Upwelling couples chemical and biological dynamics across the littoral and pelagic zones of Lake Tanganyika, East Africa. Limnol Oceanogr. 2010;55:214–24.
Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, et al. Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal. Appl Environ Microbiol. 2017;84:e02132–17.
Cabello‐Yeves PJ, Zemskaya TI, Zakharenko AS, Sakirko MV, Ivanov VG, Ghai R, et al. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat. Limnol Oceanogr. 2019;65:1471–88.
De Wever A. Spatio-temporal dynamics in the microbial food web in Lake Tanganyika. University of Gent; 2006. p. 1–169.
Pirlot S, Unrein F, Descy J-P, Servais P. Fate of heterotrophic bacteria in Lake Tanganyika (East Africa): fate of bacteria in Lake Tanganyika. FEMS Microbiol Ecol. 2007;62:354–64.
Schubert CJ, Durisch-Kaiser E, Wehrli B, Thamdrup B, Lam P, Kuypers MMM. Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika). Environ Microbiol. 2006;8:1857–63.
Shade A, Kent AD, Jones SE, Newton RJ, Triplett EW, McMahon KD. Interannual dynamics and phenology of bacterial communities in a eutrophic lake. Limnol Oceanogr. 2007;52:487–94.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–68.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
The Genome Standards Consortium, Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Bushnell B. BBMAP. https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/. 2014.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:13219.
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195.
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:1–6.
Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis. Genome Biol Evol. 2015;7:2727–46.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Miller MA, Pfeiffer W, Schwartz Terri. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop. New Orleans, LA; 2010. p. 1–8.
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev. 2011;1:14.
Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD. TaxAss: leveraging a custom freshwater database achieves fine-scale taxonomic resolution. mSphere. 2018;3:e00327–18.
Soo RM, Hemp J, Parks DH, Fischer WW, Hugenholtz P. On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science. 2017;355:1436–40.
Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, et al. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ. 2018;6:e6075.
Bendall ML, Stevens SL, Chan L-K, Malfatti S, Schwientek P, Tremblay J, et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 2016;10:1589–601.
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.
Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, et al. An expanded genomic representation of the phylum cyanobacteria. Genome Biol Evolution. 2014;6:1031–45.
Zhou Z, Tran P, Liu Y, Kieft K, Anantharaman K. METABOLIC: a scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes. bioRxiv. 2019;761643.
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–W101.
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, et al. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res. 2019;47:D649–59.
Edmond JM, Stallard RF, Craig H, Craig V, Weiss RF, Coulter GW. Nutrient chemistry of the water column of Lake Tanganyika. Limnol Oceanogr. 1993;38:725–38.
Verburga P, Hecky RE. The physics of the warming of Lake Tanganyika by climate change. Limnol Oceanogr. 2009;54:2418–30.
Järvinen M, Salonen K, Sarvala J, Vuorio K, Virtanen A. The stoichiometry of particulate nutrients in Lake Tanganyika—implications for nutrient limitation of phytoplankton. Hydrobiologia. 1999;407:81–8.
Ehrenfels B, Bartosiewicz M, Mbonde AS, Baumann KBL, Dinkel C, Junker J, et al. Thermocline depth and euphotic zone thickness regulate the abundance of diazotrophic cyanobacteria in Lake Tanganyika. Preprint at https://doi.org/10.5194/bg-2020-214 (2020).
Tran P, Ramachandran A, Khawasik O, Beisner BE, Rautio M, Huot Y, et al. Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered Lakes. Environ Microbiol. 2018;20:2568–84.
Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, et al. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia. PLoS ONE. 2012;7:1–11.
Damrow R, Maldener I, Zilliges Y. The multiple functions of common microbial carbon polymers, glycogen and PHB, during stress responses in the non-diazotrophic Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol. 2016;7:966.
Paerl HW, Otten TG. Duelling ‘CyanoHABs’: unravelling the environmental drivers controlling dominance and succession among diazotrophic and non-N2-fixing harmful cyanobacteria. Environ Microbiol. 2016;18:316–24.
Raymond J, Siefert JL, Staples CR, Blankenship RE. The natural history of nitrogen fixation. Mol Biol Evol. 2004;21:541–54.
Berman-Frank I, Lundgren P, Falkowski P. Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res Microbiol. 2003;154:157–64.
Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-valera F. Reconstruction of diverse verrucomicrobial genomes from metagenome datasets of freshwater reservoirs. Front Microbiol. 2017;8:2131.
Hansel CM, Fendorf S, Jardine PM, Francis CA. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microbiol. 2008;74:1620–33.
Edlund A, Hårdeman F, Jansson JK, Sjöling S. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environ Microbiol. 2008;10:2051–63.
Beman JM, Carolan MT. Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone. Nat Commun. 2013;4:2705.
Schoell M, Tietze K, Schoberth SM. Origin of methane in Lake Kivu (East-Central Africa). Chem Geol. 1988;71:257–65.
Bogard MJ, del Giorgio PA, Boutet L, Chaves MCG, Prairie YT, Merante A, et al. Oxic water column methanogenesis as a major component of aquatic CH4 fluxes. Nat Commun. 2014;5:5350.
Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, et al. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol. 2016;1:16170.
Gao Q, Chen S, Kimirei IA, Zhang L, Mgana H, Mziray P, et al. Wet deposition of atmospheric nitrogen contributes to nitrogen loading in the surface waters of Lake Tanganyika, East Africa: a case study of the Kigoma region. Environ Sci Pollut Res. 2018;25:11646–60.
Chale FMM. Inorganic nutrient concentrations and chlorophyll in the euphotic zone of Lake Tanganyika. Hydrobiologia. 2004;523:189–97.
Higgins SN, Hecky RE, Taylor WD. Epilithic nitrogen fixation in the rocky littoral zones of Lake Malawi, Africa. Limnol Oceanogr. 2001;46:976–82.
Brion N, Nzeyimana E, Goeyens L, Nahimana D, Tungaraza C, Baeyens W. Inorganic nitrogen uptake and river inputs in northern Lake Tanganyika. J Gt Lakes Res. 2006;32:553–64.
Norici A, Hell R, Giordano M. Sulfur and primary production in aquatic environments: an ecological perspective. Photosynth Res. 2005;86:409–17.
Botz RW, Stoffers P. Light hydrocarbon gases in Lake Tanganyika hydrothermal fluids (East-Central Africa). Chem Geol. 1993;104:217–24.
Tiercelin J-J, Pflumio C, Castrec M, Boulégue J, Gente P, Rolet J, et al. Hydrothermal vents in Lake Tanganyika, East African, Rift system. Geology. 1993;21:499–502.
Elsgaard L, Prieur D. Hydrothermal vents in Lake Tanganyika harbor spore-forming thermophiles with extremely rapid growth. J Gt Lakes Res. 2011;37:203–6.
Preisler A, de Beer D, Lichtschlag A, Lavik G, Boetius A, Jørgensen BB. Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. ISME J. 2007;1:341–53.
McAllister SM, Moore RM, Gartman A, Luther GW, Emerson D, Chan CS. The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives. FEMS Microbiol Ecol. 2019;95:fiz015.
Carpenter SR. Phosphorus control is critical to mitigating eutrophication. Proc Natl Acad Sci. 2008;105:11039–40.
Lewis WM, Jr. Causes for the high frequency of nitrogen limitation in tropical lakes. SIL Proceedings. vol. 28. 2002; p. 210–3.
De Keyzer ELR, Masilya Mulungula P, Alunga Lufungula G, Amisi Manala C, Andema Muniali A, Bashengezi Cibuhira P, et al. Local perceptions on the state of the pelagic fisheries and fisheries management in Uvira, Lake Tanganyika, DR Congo. J Great Lakes Res. 2020;46:1740–53.
Mölsä, H. Management of fisheries on Lake Tanganyika challenges for research and the community. University of Kuopio; 2008.
Foley B, Jones ID, Maberly SC, Rippey B. Long-term changes in oxygen depletion in a small temperate lake: effects of climate change and eutrophication. Freshw Biol. 2012;57:278–89.
Source: Ecology - nature.com