دورية أكاديمية

Survival and rapid resuscitation permit limited productivity in desert microbial communities.

التفاصيل البيبلوغرافية
العنوان: Survival and rapid resuscitation permit limited productivity in desert microbial communities.
المؤلفون: Imminger S; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.; University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria., Meier DV; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.; Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany., Schintlmeister A; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.; Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria., Legin A; Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria., Schnecker J; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria., Richter A; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria., Gillor O; Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel., Eichorst SA; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria., Woebken D; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria. dagmar.woebken@univie.ac.at.
المصدر: Nature communications [Nat Commun] 2024 Apr 17; Vol. 15 (1), pp. 3056. Date of Electronic Publication: 2024 Apr 17.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Ecosystem* , Microbiota*, Desert Climate ; Soil Microbiology ; Rain ; Soil
مستخلص: Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2 H 2 O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
(© 2024. The Author(s).)
References: Reynolds, J. F. et al. Global desertification: building a science for dryland development. Science 316, 847–851 (2007). (PMID: 1749516310.1126/science.1131634)
Intergovernmental Panel on Climate Change. Desertification. Climate Change and Land: IPCC Special Report on Climate Change, Desertification, Land Degradation, Sustainable Land Management, Food Security, and Greenhouse Gas Fluxes in Terrestrial Ecosystems (Cambridge University Press, 2022).
Wang, L. et al. Dryland productivity under a changing climate. Nat. Clim. Change 12, 981–994 (2022). (PMID: 10.1038/s41558-022-01499-y)
Feng, S. & Fu, Q. Expansion of global drylands under a warming climate. Atmos. Chem. Phys. 13, 10081–10094 (2013). (PMID: 10.5194/acp-13-10081-2013)
Huang, J., Yu, H., Guan, X., Wang, G. & Guo, R. Accelerated dryland expansion under climate change. Nat. Clim. Change 6, 166–171 (2015). (PMID: 10.1038/nclimate2837)
Houston, J. Variability of precipitation in the Atacama desert: its causes and hydrological impact. Int. J. Climatol. 26, 2181–2198 (2006). (PMID: 10.1002/joc.1359)
Lehnert, L. W., Jung, P., Obermeier, W. A., Büdel, B. & Bendix, J. Estimating net photosynthesis of biological soil crusts in the Atacama using hyperspectral remote sensing. Remote Sens. 10, 891 (2018). (PMID: 10.3390/rs10060891)
Ben-Gai, T., Bitan, A., Manes, A., Alpert, P. & Rubin, S. Spatial and temporal changes in rainfall frequency distribution patterns in Israel. Theor. Appl. Clim. 61, 177–190 (1998). (PMID: 10.1007/s007040050062)
Shanan, L., Evenari, M. & Tadmor, N. H. Rainfall patterns in the Central Negev Desert. Isr. Explor. J. 17, 163–184 (1967).
Wang, L., Manzoni, S., Ravi, S., Riveros-Iregui, D. & Caylor, K. Dynamic interactions of ecohydrological and biogeochemical processes in water-limited systems. Ecosphere 6, 133 (2015). (PMID: 10.1890/ES15-00122.1)
Garcia-Pichel, F. The microbiology of biological soil crusts. Annu. Rev. Microbiol. 77, 149–171 (2023). (PMID: 3706877710.1146/annurev-micro-032521-015202)
Placella, S. A., Brodie, E. L. & Firestone, M. K. Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc. Natl Acad. Sci. USA 109, 10931–10936 (2012). (PMID: 22715291339086610.1073/pnas.1204306109)
Blazewicz, S. J. et al. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J. 14, 1520–1532 (2020). (PMID: 32203117724244210.1038/s41396-020-0617-3)
Barnard, R. L., Blazewicz, S. J. & Firestone, M. K. Rewetting of soil: revisiting the origin of soil CO 2 emissions. Soil Biol. Biochem. 147, 107819 (2020). (PMID: 10.1016/j.soilbio.2020.107819)
Jones, S. E. & Lennon, J. T. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl. Acad. Sci. USA 107, 5881–5886 (2010).
Lennon, J. T., den Hollander, F., Wilke-Berenguer, M. & Blath, J. Principles of seed banks and the emergence of complexity from dormancy. Nat. Commun. 12, 1–16 (2021). (PMID: 10.1038/s41467-021-24733-1)
Billi, D. & Potts, M. Life and death of dried prokaryotes. Res. Microbiol. 153, 7–12 (2002). (PMID: 1188190010.1016/S0923-2508(01)01279-7)
Lebre, P. H., Maayer, P. D. & Cowan, D. A. Xerotolerant bacteria: surviving through a dry spell. Nat. Rev. Microbiol. 15, 285–296 (2017). (PMID: 2831632910.1038/nrmicro.2017.16)
Beskrovnaya, P. et al. Structural, metabolic and evolutionary comparison of bacterial endospore and exospore formation. Front. Microbiol. 12, 630573 (2021). (PMID: 3376768010.3389/fmicb.2021.630573)
Meier, D. V., Imminger, S., Gillor, O. & Woebken, D. Distribution of mixotrophy and desiccation survival mechanisms across microbial genomes in an arid biological soil crust community. mSystems 6, e00786–20 (2021). (PMID: 33436509790147610.1128/mSystems.00786-20)
Garcia-Pichel, F., Johnson, S. L., Youngkin, D. & Belnap, J. Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado plateau. Microb. Ecol. 46, 312–321 (2003). (PMID: 1450241410.1007/s00248-003-1004-0)
Johnson, S. S. et al. Ancient bacteria show evidence of DNA repair. Proc. Natl Acad. Sci. USA 104, 14401–14405 (2007). (PMID: 17728401195881610.1073/pnas.0706787104)
Šťovíček, A., Kim, M., Or, D. & Gillor, O. Microbial community response to hydration-desiccation cycles in desert soil. Sci. Rep. 7, 45735 (2017). (PMID: 28383531538290910.1038/srep45735)
Armstrong, A. et al. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci. Rep. 6, 34434 (2016). (PMID: 27680878504108910.1038/srep34434)
Rajeev, L. et al. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J. 7, 2178–2191 (2013). (PMID: 23739051380626510.1038/ismej.2013.83)
Scherer, S., Ernst, A., Chen, T.-W. & Böger, P. Rewetting of drought-resistant blue-green algae: time course of water uptake and reappearance of respiration, photosynthesis, and nitrogen fixation. Oecologia 62, 418–423 (1984). (PMID: 2831089810.1007/BF00384277)
Rodriguez-Caballero, E. et al. Dryland photoautotrophic soil surface communities endangered by global change. Nat. Geosci. 11, 185–189 (2018). (PMID: 10.1038/s41561-018-0072-1)
Elbert, W. et al. Contribution of cryptogamic covers to the global cycles of carbon and nitrogen. Nat. Geosci. 5, 459–462 (2012). (PMID: 10.1038/ngeo1486)
Weber, B. et al. Biological soil crusts accelerate the nitrogen cycle through large NO and HONO emissions in drylands. Proc. Natl Acad. Sci. 112, 15384–15389 (2015). (PMID: 26621714468760010.1073/pnas.1515818112)
Chamizo, S., Belnap, J., Eldridge, D. J., Cantón, Y. & Issa, O. M. The role of biocrusts in arid land hydrology. In Biological Soil Crusts: An Organizing Principle in Drylands. (eds. Weber, B., Büdel, B., & Belnap, J.) Ch. 17 (Springer International Publishing, 2016).
Eldridge, D. J. & Leys, J. F. Exploring some relationships between biological soil crusts, soil aggregation and wind erosion. J. Arid Environ. 53, 457–466 (2003). (PMID: 10.1006/jare.2002.1068)
Chaudhary, V. B. et al. Untangling the biological contributions to soil stability in semiarid shrublands. Ecol. Appl. 19, 110–122 (2009). (PMID: 1932317610.1890/07-2076.1)
Belnap, J. The world at your feet: desert biological soil crusts. Front. Ecol. Environ. 1, 181–189 (2003). (PMID: 10.1890/1540-9295(2003)001[0181:TWAYFD]2.0.CO;2)
Bay, S. K. et al. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. ISME J. 15, 3339–3356 (2021). (PMID: 34035443852892110.1038/s41396-021-01001-0)
Meyer, N. R., Fortney, J. L. & Dekas, A. E. NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single‐cell rates of microbial activity. Environ. Microbiol. 23, 81–98 (2021). (PMID: 3300052810.1111/1462-2920.15264)
Kopf, S. H. et al. Heavy water and 15 N labeling with NanoSIMS analysis reveals growth-rate dependent metabolic heterogeneity in chemostats. Environ. Microbiol. 17, 2542–2556 (2015). (PMID: 25655651458789610.1111/1462-2920.12752)
Musat, N. et al. The effect of FISH and CARD-FISH on the isotopic composition of 13 C- and 15 N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst. Appl. Microbiol. 37, 267–276 (2014). (PMID: 2470290510.1016/j.syapm.2014.02.002)
Woebken, D. et al. Revisiting N 2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 9, 485–496 (2015). (PMID: 2530371210.1038/ismej.2014.144)
Zhang, X., Gillespie, A. L. & Sessions, A. L. Large D/H variations in bacterial lipids reflect central metabolic pathways. Proc. Natl Acad. Sci. USA 106, 12580–12586 (2009). (PMID: 19617564272235110.1073/pnas.0903030106)
Slade, D. & Radman, M. Oxidative stress resistance in Deinococcus radiodurans. Microbiol. Mol. Biol. Rev. 75, 133–191 (2011). (PMID: 21372322306335610.1128/MMBR.00015-10)
Bay, S. K. et al. Trace gas oxidizers are widespread and active members of soil microbial communities. Nat. Microbiol. 6, 246–256 (2021). (PMID: 3339809610.1038/s41564-020-00811-w)
Giguere, A. T. et al. Acidobacteria are active and abundant members of diverse atmospheric H 2 -oxidizing communities detected in temperate soils. ISME J. 15, 363–376 (2021). (PMID: 3302429110.1038/s41396-020-00750-8)
Daly, M. J. et al. Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306, 1025–1028 (2004). (PMID: 1545934510.1126/science.1103185)
Andrews, S. C. The Ferritin-like superfamily: evolution of the biological iron storeman from a rubrerythrin-like ancestor. Biochim. Biophys. Acta 1800, 691–705 (2010). (PMID: 2055381210.1016/j.bbagen.2010.05.010)
Iturriaga, G., Suárez, R. & Nova-Franco, B. Trehalose metabolism: from osmoprotection to signaling. Int. J. Mol. Sci. 10, 3793–3810 (2009). (PMID: 19865519276916010.3390/ijms10093793)
Man, L. P. et al. Energetic basis of microbial growth and persistence in desert ecosystems. mSystems 5, e00495–19 (2022).
Govorunova, E. G., Sineshchekov, O. A., Li, H. & Spudich, J. L. Microbial rhodopsins: diversity, mechanisms, and optogenetic applications. Annu. Rev. Biochem. 86, 1–28 (2014).
Flores‐Uribe, J. et al. Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: some thoughts and possible implications for activity. Environ. Microbiol. Rep. 11, 419–424 (2019). (PMID: 3061806610.1111/1758-2229.12730)
Meredith, L. K. et al. Consumption of atmospheric hydrogen during the life cycle of soil‐dwelling actinobacteria. Environ. Microbiol. Rep. 6, 226–238 (2014). (PMID: 2498352710.1111/1758-2229.12116)
Greening, C., Grinter, R. & Chiri, E. Uncovering the metabolic strategies of the dormant microbial majority: towards integrative approaches. mSystems 4, e00107–e00119 (2019). (PMID: 31120024652954210.1128/mSystems.00107-19)
Islam, Z. F. et al. Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide. ISME J. 13, 1801–1813 (2019). (PMID: 30872805677605210.1038/s41396-019-0393-0)
Greening, C., Berney, M., Hards, K., Cook, G. M. & Conrad, R. A soil actinobacterium scavenges atmospheric H 2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. Proc. Natl Acad. Sci. USA 111, 4257–4261 (2014). (PMID: 24591586396404510.1073/pnas.1320586111)
Constant, P., Chowdhury, S. P., Pratscher, J. & Conrad, R. Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high‐affinity [NiFe]‐hydrogenase. Environ. Microbiol. 12, 821–829 (2010). (PMID: 2005087610.1111/j.1462-2920.2009.02130.x)
Berney, M. & Cook, G. M. Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS ONE 5, e8614–11 (2010). (PMID: 20062806279952110.1371/journal.pone.0008614)
Jordaan, K. et al. Hydrogen-oxidizing bacteria are abundant in desert soils and strongly stimulated by hydration. mSystems 5, e01131–20 (2020). (PMID: 33203691767700310.1128/mSystems.01131-20)
Steven, B., Belnap, J. & Kuske, C. R. Chronic physical disturbance substantially alters the response of biological soil crusts to a wetting pulse, as characterized by metatranscriptomic sequencing. Front. Microbiol. 9, 2382 (2018). (PMID: 30349515618681510.3389/fmicb.2018.02382)
León-Sobrino, C., Ramond, J.-B., Maggs-Kölling, G. & Cowan, D. A. Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a hyper-arid Namib Desert soil. Front. Microbiol. 10, 1054 (2019). (PMID: 31139170652777110.3389/fmicb.2019.01054)
Maier, S. et al. Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions. ISME J. 16, 1012–1024 (2022). (PMID: 3476445410.1038/s41396-021-01127-1)
Barnard, R. L., Osborne, C. A. & Firestone, M. K. Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate. ISME J. 9, 946–957 (2015). (PMID: 2531431910.1038/ismej.2014.192)
Adessi, A., de Carvalho, R. C., Philippis, R. D., Branquinho, C. & da Silva, J. M. Microbial extracellular polymeric substances improve water retention in dryland biological soil crusts. Soil Biol. Biochem. 116, 67–69 (2018). (PMID: 10.1016/j.soilbio.2017.10.002)
Felde, V. J. M. N. L. et al. Soil microstructure as an under-explored feature of biological soil crust hydrological properties: case study from the NW Negev Desert. Biodivers. Conserv. 23, 1687–1708 (2014). (PMID: 10.1007/s10531-014-0693-7)
Ram, A. & Aaron, Y. Negative and positive effects of topsoil biological crusts on water availability along a rainfall gradient in a sandy arid area. CATENA 70, 437–442 (2007). (PMID: 10.1016/j.catena.2006.11.012)
Miller, D. E. & Gardner, W. H. Water infiltration into stratified soil. Soil Sci. Soc. Am. J. 26, 115–119 (1962). (PMID: 10.2136/sssaj1962.03615995002600020007x)
Boyle, M., Frankenberger, W. T. & Stolzy, L. H. The influence of organic matter on soil aggregation and water infiltration. J. Prod. Agric. 2, 290–299 (1989). (PMID: 10.2134/jpa1989.0290)
Katuwal, S. et al. Linking air and water transport in intact soils to macropore characteristics inferred from X-ray computed tomography. Geoderma 237, 9–20 (2015). (PMID: 10.1016/j.geoderma.2014.08.006)
Yu, J., Glazer, N. & Steinberger, Y. Carbon utilization, microbial biomass, and respiration in biological soil crusts in the Negev Desert. Biol. Fertil. Soils 50, 285–293 (2014). (PMID: 10.1007/s00374-013-0856-9)
Bertrand, R. L. Lag phase is a dynamic, organized, adaptive, and evolvable period that prepares bacteria for cell division. J. Bacteriol. 201, e00697–18 (2019). (PMID: 30642990641691410.1128/JB.00697-18)
McCool, G. J., Fernandez, T., Li, N. & Cannon, M. C. Polyhydroxyalkanoate inclusion‐body growth and proliferation in Bacillus megaterium. FEMS Microbiol. Lett. 138, 41–48 (1996). (PMID: 10.1111/j.1574-6968.1996.tb08132.x)
Swenson, T. L., Karaoz, U., Swenson, J. M., Bowen, B. P. & Northen, T. R. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nat. Commun. 9, 19 (2018). (PMID: 29296020575022810.1038/s41467-017-02356-9)
Baran, R. et al. Exometabolite niche partitioning among sympatric soil bacteria. Nat. Commun. 6, 8289 (2015). (PMID: 2639210710.1038/ncomms9289)
Blagodatskaya, E. & Kuzyakov, Y. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol. Biochem. 67, 192–211 (2013). (PMID: 10.1016/j.soilbio.2013.08.024)
Couradeau, E. et al. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat. Commun. 10, 2770 (2019). (PMID: 31235780659123010.1038/s41467-019-10542-0)
Caro, T. A., McFarlin, J., Jech, S., Fierer, N. & Kopf, S. Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil. Proc. Natl Acad. Sci. USA 120, e2211625120 (2023). (PMID: 370369801012008010.1073/pnas.2211625120)
Lange, O. L. Twenty-three years of growth measurements on the crustose lichen Caloplaca aurantia in the central Negev Desert. Isr. J. Bot. 39, 383–394 (1990).
Pointing, S. B. & Belnap, J. Microbial colonization and controls in dryland systems. Nat. Rev. Microbiol. 10, 551–562 (2012). (PMID: 2277290310.1038/nrmicro2831)
Daly, M. J. et al. Protein oxidation implicated as the primary determinant of bacterial radioresistance. PLoS Biol. 5, e92 (2007). (PMID: 17373858182814510.1371/journal.pbio.0050092)
Santos, S. P. et al. The interplay between Mn and Fe in Deinococcus radiodurans triggers cellular protection during paraquat-induced oxidative stress. Sci. Rep. 9, 17217 (2019). (PMID: 31748604686820010.1038/s41598-019-53140-2)
Warren, C. R. Pools and fluxes of osmolytes in moist soil and dry soil that has been re-wet. Soil Biol. Biochem. 150, 108012 (2020). (PMID: 10.1016/j.soilbio.2020.108012)
Empadinhas, N. et al. Organic solutes in Rubrobacter xylanophilus: the first example of di-myo-inositol-phosphate in a thermophile. Extremophiles 11, 667–673 (2007). (PMID: 1751073510.1007/s00792-007-0084-z)
Angel, R., Soares, M. I. M., Ungar, E. D. & Gillor, O. Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J. 4, 553–563 (2010). (PMID: 2003307010.1038/ismej.2009.136)
Bachar, A. et al. Soil microbial abundance and diversity along a low precipitation gradient. Microb. Ecol. 60, 453–461 (2010). (PMID: 2068358810.1007/s00248-010-9727-1)
Ben‐David, E. A., Zaady, E., Sher, Y. & Nejidat, A. Assessment of the spatial distribution of soil microbial communities in patchy arid and semi‐arid landscapes of the Negev Desert using combined PLFA and DGGE analyses. FEMS Microbiol. Ecol. 76, 492–503 (2011). (PMID: 2140169310.1111/j.1574-6941.2011.01075.x)
Angel, R. & Conrad, R. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environ. Microbiol. 11, 2598–2610 (2009). (PMID: 1960195710.1111/j.1462-2920.2009.01984.x)
Eichorst, S. A. et al. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol. Ecol. 91, fiv106 (2015). (PMID: 26324854462987310.1093/femsec/fiv106)
Polerecky, L. et al. Calculation and interpretation of substrate assimilation rates in microbial cells based on isotopic composition data obtained by nanoSIMS. Front. Microbiol. 12, 621634 (2021). (PMID: 34917040867060010.3389/fmicb.2021.621634)
Kopf, S. H. et al. Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum. Proc. Natl Acad. Sci. USA 113, E110–E116 (2016). (PMID: 2671574110.1073/pnas.1512057112)
Griffiths, R. I., Whiteley, A. S., O’Donnell, A. G. & Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 5488–5491 (2000). (PMID: 110979349248810.1128/AEM.66.12.5488-5491.2000)
Paulin, M. M. et al. Improving Griffith’s protocol for co-extraction of microbial DNA and RNA in adsorptive soils. Soil Biol. Biochem. 63, 37–49 (2013). (PMID: 10.1016/j.soilbio.2013.02.007)
Feinstein, L. M., Sul, W. J. & Blackwood, C. B. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl. Environ. Microbiol. 75, 5428–5433 (2009). (PMID: 19561189272546910.1128/AEM.00120-09)
Loy, A. et al. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68, 5064–5081 (2002). (PMID: 1232435812640510.1128/AEM.68.10.5064-5081.2002)
Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129–137 (2015). (PMID: 10.3354/ame01753)
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016). (PMID: 2627176010.1111/1462-2920.13023)
Nikolenko, S. I., Korobeynikov, A. I. & Alekseyev, M. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 14, S7 (2013). (PMID: 23368723354981510.1186/1471-2164-14-S1-S7)
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013). (PMID: 2319328310.1093/nar/gks1219)
Szymanski, M., Barciszewska, M. Z., Barciszewski, J. & Erdmann, V. A. 5S ribosomal RNA database Y2K. Nucleic Acids Res. 28, 166–167 (2000). (PMID: 1059221210247310.1093/nar/28.1.166)
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014). (PMID: 2422767710.1093/bioinformatics/btt656)
McKinney, W. Data structures for statistical computing in python. In Proc. 9th Python in Science Conference 56–61 (2010).
Waskom, M. seaborn: statistical data visualization. J. Open Source Softw. 6, 3021 (2021). (PMID: 10.21105/joss.03021)
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014). (PMID: 25516281430204910.1186/s13059-014-0550-8)
Ramnarine, R., Wagner-Riddle, C., Dunfield, K. E. & Voroney, R. P. Contributions of carbonates to soil CO 2 emissions. Can. J. Soil Sci. 92, 599–607 (2012). (PMID: 10.4141/cjss2011-025)
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 11, 119 (2010). (PMID: 10.1186/1471-2105-11-119)
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011). (PMID: 22039361319763410.1371/journal.pcbi.1002195)
Søndergaard, D., Pedersen, C. N. S. & Greening, C. HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6, 34212 (2016). (PMID: 27670643503745410.1038/srep34212)
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014). (PMID: 24451623399814410.1093/bioinformatics/btu033)
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020). (PMID: 32011700718220610.1093/molbev/msaa015)
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019). (PMID: 31730192770375910.1093/bioinformatics/btz848)
Minh, B. Q., Nguyen, M. A. T. & von Haeseler, A. Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013). (PMID: 23418397367074110.1093/molbev/mst024)
معلومات مُعتمدة: 636928 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council); MAINTAIN DOC 69 doc.fund Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung); DK Plus project W1257-B20 Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)
المشرفين على المادة: 0 (Soil)
تواريخ الأحداث: Date Created: 20240417 Date Completed: 20240419 Latest Revision: 20240419
رمز التحديث: 20240419
DOI: 10.1038/s41467-024-46920-6
PMID: 38632260
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-46920-6