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Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H. Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales. THE ISME JOURNAL 2023; 17:2123-2133. [PMID: 37749300 PMCID: PMC10579370 DOI: 10.1038/s41396-023-01518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Anne Daebeler
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 7, 370 05, Budweis, Czech Republic
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | - Rasmus H Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Vienna, Austria.
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Daebeler A, Güell‐Bujons Q, Mooshammer M, Zechmeister T, Herbold CW, Richter A, Wagner M, Daims H. Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes. Environ Microbiol 2023; 25:1055-1067. [PMID: 36651641 PMCID: PMC10947350 DOI: 10.1111/1462-2920.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.
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Affiliation(s)
- Anne Daebeler
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Biology Centre CAS, BudweisInstitute of Soil Biology and BiogeochemistryCzechia
| | - Queralt Güell‐Bujons
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Institut de Ciències del Mar (ICM‐CSIC), Passeig Marítim de la Barceloneta 37‐49BarcelonaCataloniaSpain
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | | | - Craig W. Herbold
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | - Michael Wagner
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Holger Daims
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
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Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria. Microbiol Spectr 2023; 11:e0411022. [PMID: 36541777 PMCID: PMC9927469 DOI: 10.1128/spectrum.04110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.
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Csitári B, Bedics A, Felföldi T, Boros E, Nagy H, Máthé I, Székely AJ. Anion-type modulates the effect of salt stress on saline lake bacteria. Extremophiles 2022; 26:12. [PMID: 35137260 PMCID: PMC8825391 DOI: 10.1007/s00792-022-01260-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
Beside sodium chloride, inland saline aquatic systems often contain other anions than chloride such as hydrogen carbonate and sulfate. Our understanding of the biological effects of salt composition diversity is limited; therefore, the aim of this study was to examine the effect of different anions on the growth of halophilic bacteria. Accordingly, the salt composition and concentration preference of 172 strains isolated from saline and soda lakes that differed in ionic composition was tested using media containing either carbonate, chloride or sulfate as anion in concentration values ranging from 0 to 0.40 mol/L. Differences in salt-type preference among bacterial strains were observed in relationship to the salt composition of the natural habitat they were isolated from indicating specific salt-type adaptation. Sodium carbonate represented the strongest selective force, while majority of strains was well-adapted to growth even at high concentrations of sodium sulfate. Salt preference was to some extent associated with taxonomy, although variations even within the same bacterial species were also identified. Our results suggest that the extent of the effect of dissolved salts in saline lakes is not limited to their concentration but the type of anion also substantially impacts the growth and survival of individual microorganisms.
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Affiliation(s)
- Bianka Csitári
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117, Budapest, Hungary
- Department of Ecology and Genetics/Limnology, Uppsala University EBC, Norbyvägen 18D, 75236, Uppsala, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165, Stockholm, Sweden
| | - Anna Bedics
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117, Budapest, Hungary
- Depatment of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, 2100, Gödöllő, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117, Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina u. 29, 1113, Budapest, Hungary
| | - Emil Boros
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina u. 29, 1113, Budapest, Hungary
| | - Hajnalka Nagy
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117, Budapest, Hungary
| | - István Máthé
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104, Miercurea Ciuc, Romania
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Uppsala University EBC, Norbyvägen 18D, 75236, Uppsala, Sweden.
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden.
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Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432 T to highly alkaline stress. Extremophiles 2021; 25:459-470. [PMID: 34402982 DOI: 10.1007/s00792-021-01239-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
The haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T exhibits high adaptability to saline-alkaline environment. The salinity adaptation mechanism of E. halophilus EGI 80432T was fully understood based on transcriptome analyses and physiological responses; however, the alkaline response mechanism has not yet been investigated. Here, we investigated the alkaline response mechanism of E. halophilus EGI 80432T by a transcriptomic comparison. In this study, the genes involved in the glycolysis, TCA cycle, starch, and trehalose metabolism for energy production and storage, were up-regulated under highly alkaline condition. Furthermore, genes responsible for the production of acidic and neutral metabolites, i.e., acetate, pyruvate, formate, glutamate, threonine, and ectoine, showed increased expression under highly alkaline condition, compared with the control pH condition. In contrast, the opposite results were observed in proton capture or retention gene expression profiles, i.e., cation/proton antiporters and ATP synthases. The above results revealed that E. halophilus EGI 80432T likely tended to adopt an "acidic metabolites production" strategy in response to a highly alkaline condition. These findings would pave the way for further studies in the saline-alkaline adaptation mechanisms of E. halophilus EGI 80432T, and hopefully provide a new insight into the foundational theory and application in ecological restoration with saline-alkaline strains.
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Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes. mSystems 2021; 6:6/2/e01202-20. [PMID: 33906913 PMCID: PMC8092127 DOI: 10.1128/msystems.01202-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2T originated from a soda lake in southeast Siberia that is exposed to strong seasonal temperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B12 biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2T upregulated flagellin expression, whereas ALJ2 downregulated it. IMPORTANCE In addition to their haloalkaline conditions, soda lakes can also harbor a variety of other extreme parameters, to which their microbial communities need to adapt. However, for most of these supplementary stressors, it is not well known yet how haloalkaliphiles adapt and resist. Here, we studied the strategy for adaptation to low temperature in the haloalkaliphilic genus Thioalkalivibrio by using two strains isolated from soda lakes with different temperature regimes. Even though the strains showed a strong difference in growth rate at 10°C, they exhibited similar molecular and physiological adaptation responses. We hypothesize that they take advantage of resistance mechanisms against other stressors commonly found in soda lakes, which are therefore maintained in the bacteria living in the absence of low-temperature pressure. A major difference, however, was detected for their glycine betaine content at 10°C, highlighting the power of this osmolyte to also act as a key compound in cryoprotection. Author Video: An author video summary of this article is available.
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Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. THE ISME JOURNAL 2021; 15:732-745. [PMID: 33067588 PMCID: PMC8026999 DOI: 10.1038/s41396-020-00809-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Cameron R Strachan
- Department for Farm Animals and Public Health, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Rasmus H Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, Zechmeister T, Karst SM, Albertsen M, Nielsen PH, Wagner M, Daims H. Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira. THE ISME JOURNAL 2020; 14:2967-2979. [PMID: 32709974 PMCID: PMC7784846 DOI: 10.1038/s41396-020-0724-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.
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Affiliation(s)
- Anne Daebeler
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Max Planck Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Hanna Koch
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela Steinfeder
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jasmin Schwarz
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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Szuróczki S, Szabó A, Korponai K, Felföldi T, Somogyi B, Márialigeti K, Tóth E. Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses. FEMS Microbiol Ecol 2020; 96:5895321. [PMID: 32821929 DOI: 10.1093/femsec/fiaa159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/11/2020] [Indexed: 11/15/2022] Open
Abstract
Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.
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Affiliation(s)
- Sára Szuróczki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Boglárka Somogyi
- Centre for Ecological Research, Balaton Limnological Institute, Hungarian Academy of Sciences, Klebelsberg Kuno u. 3., 8237 Tihany, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
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Draft Genome Sequence of Alkalicoccus halolimnae BZ-SZ-XJ29 T, a Moderately Halophilic Bacterium Isolated from a Salt Lake. Microbiol Resour Announc 2020; 9:9/27/e00500-20. [PMID: 32616637 PMCID: PMC7330239 DOI: 10.1128/mra.00500-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The moderate halophile Alkalicoccus halolimnae BZ-SZ-XJ29T grows optimally in a relative broad range of 8.3% to 12.3% (wt/vol) NaCl. The draft genome consists of approximately 3.66 Mb and contains 3,534 putative genes. Various genes involved in osmotic stress were predicted, providing pertinent insights into specific adaptations to the hypersaline environment.
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11
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Nature and bioprospecting of haloalkaliphilics: a review. World J Microbiol Biotechnol 2020; 36:66. [DOI: 10.1007/s11274-020-02841-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/14/2020] [Indexed: 01/07/2023]
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Draft Genome Sequence of Alkalicoccus saliphilus DSM 15402 T, a Haloalkaliphilic Bacterium Isolated from a Mineral Pool. Microbiol Resour Announc 2019; 8:8/24/e00266-19. [PMID: 31196917 PMCID: PMC6588035 DOI: 10.1128/mra.00266-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The haloalkaliphilic bacterium Alkalicoccus saliphilus DSM 15402T was isolated from a mineral pool. It grows aerobically at an optimum of 15% (wt/vol) salinity and pH 9.0. The draft genome consists of approximately 3.52 Mb and contains 3,434 predicted genes. Various genes are potentially involved in the adaptation mechanisms for both osmotic stress and pH homeostasis, providing insight into specific adaptations to this double-extreme environment. The haloalkaliphilic bacterium Alkalicoccus saliphilus DSM 15402T was isolated from a mineral pool. It grows aerobically at an optimum of 15% (wt/vol) salinity and pH 9.0. The draft genome consists of approximately 3.52 Mb and contains 3,434 predicted genes. Various genes are potentially involved in the adaptation mechanisms for both osmotic stress and pH homeostasis, providing insight into specific adaptations to this double-extreme environment.
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Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake. Microbiol Resour Announc 2018; 7:MRA00882-18. [PMID: 30533910 PMCID: PMC6256447 DOI: 10.1128/mra.00882-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/10/2018] [Indexed: 11/20/2022] Open
Abstract
The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt lake. It grows optimally at 8% (wt/vol) NaCl (pH 9.0). The draft genome is composed of 4,006 predicted genes. Genomic analysis showed that various genes are potentially involved in the adaptation mechanisms for osmotic stress and pH homeostasis.
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Fox-Powell MG, Cockell CS. Building a Geochemical View of Microbial Salt Tolerance: Halophilic Adaptation of Marinococcus in a Natural Magnesium Sulfate Brine. Front Microbiol 2018; 9:739. [PMID: 29713317 PMCID: PMC5911959 DOI: 10.3389/fmicb.2018.00739] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/29/2018] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of life in hypersaline habitats is mostly limited to sodium and chloride-dominated environments. This narrow compositional window does not reflect the diversity of brine environments that exist naturally on Earth and other planetary bodies. Understanding the limits of the microbial biosphere and predicting extraterrestrial habitability demands a systematic effort to characterize ionic specificities of organisms from a representative range of saline habitats. Here, we investigated a strain of Marinococcus isolated from the magnesium and sulfate-dominated Basque Lakes (British Columbia, Canada). This organism was the sole isolate obtained after exposure to exceptionally high levels of Mg2+ and SO42- ions (2.369 and 2.840 M, respectively), and grew at extremes of ionic strength not normally encountered in Na+/Cl- brines (12.141 mol liter-1). Its association at the 16S rDNA level with bacterial halophiles suggests that ancestral halophily has allowed it to adapt to a different saline habitat. Growth was demonstrated in media dominated by NaCl, Na2SO4, MgCl2, and MgSO4, yet despite this plasticity the strain was still restricted; requiring either Na+ or Cl- to maintain short doubling times. Water activity could not explain growth rate differences between media, demonstrating the importance of ionic composition for dictating microbial growth windows. A new framework for understanding growth in brines is required, that accounts for the geochemical history of brines as well as the various stresses that ions impose on microbes. Studies such as this are required to gain a truly universal understanding of the limits of biological ion tolerance.
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Affiliation(s)
- Mark G Fox-Powell
- UK Centre for Astrobiology, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom.,School of Earth and Environmental Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
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Draft Genome Sequence of Natronolimnobius baerhuensis CGMCC 1.3597 T, an Aerobic Haloalkaliphilic Archaeon Isolated from a Soda Lake. GENOME ANNOUNCEMENTS 2017; 5:5/38/e00710-17. [PMID: 28935723 PMCID: PMC5609402 DOI: 10.1128/genomea.00710-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The haloalkaliphilic archaeon Natronolimnobius baerhuensis was isolated from a soda lake in Inner Mongolia (China), growing optimally at about 20% NaCl and pH 9.0. The draft genome consists of approximately 3.91 Mb and contains 3,810 predicted genes. Some genes that regulate intracellular osmotic stress and pH homeostasis were identified, providing insight into specific adaptations to this double-extreme environment.
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Draft Genome Sequence of Natranaerobius trueperi DSM 18760
T
, an Anaerobic, Halophilic, Alkaliphilic, Thermotolerant Bacterium Isolated from a Soda Lake. GENOME ANNOUNCEMENTS 2017; 5:5/36/e00785-17. [PMID: 28883132 PMCID: PMC5589526 DOI: 10.1128/genomea.00785-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The anaerobic, halophilic, alkaliphilic, thermotolerant bacterium
Natranaerobius trueperi
was isolated from a soda lake in Wadi An Natrun, Egypt. It grows optimally at 3.7 M Na
+
, pH 9.5, and 43°C. The draft genome consists of 2.63 Mb and is composed of 2,681 predicted genes. Genomic analysis showed that various genes are potentially involved in the adaptation mechanisms for osmotic stress, pH homeostasis, and high temperatures.
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Harrison JP, Dobinson L, Freeman K, McKenzie R, Wyllie D, Nixon SL, Cockell CS. Aerobically respiring prokaryotic strains exhibit a broader temperature-pH-salinity space for cell division than anaerobically respiring and fermentative strains. J R Soc Interface 2016; 12:0658. [PMID: 26354829 DOI: 10.1098/rsif.2015.0658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological processes on the Earth operate within a parameter space that is constrained by physical and chemical extremes. Aerobic respiration can result in adenosine triphosphate yields up to over an order of magnitude higher than those attained anaerobically and, under certain conditions, may enable microbial multiplication over a broader range of extremes than other modes of catabolism. We employed growth data published for 241 prokaryotic strains to compare temperature, pH and salinity values for cell division between aerobically and anaerobically metabolizing taxa. Isolates employing oxygen as the terminal electron acceptor exhibited a considerably more extensive three-dimensional phase space for cell division (90% of the total volume) than taxa using other inorganic substrates or organic compounds as the electron acceptor (15% and 28% of the total volume, respectively), with all groups differing in their growth characteristics. Understanding the mechanistic basis of these differences will require integration of research into microbial ecology, physiology and energetics, with a focus on global-scale processes. Critical knowledge gaps include the combined impacts of diverse stress parameters on Gibbs energy yields and rates of microbial activity, interactions between cellular energetics and adaptations to extremes, and relating laboratory-based data to in situ limits for cell division.
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Affiliation(s)
- Jesse P Harrison
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Luke Dobinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Kenneth Freeman
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Ross McKenzie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Dale Wyllie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Sophie L Nixon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
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Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Front Microbiol 2016; 7:211. [PMID: 26941731 PMCID: PMC4766312 DOI: 10.3389/fmicb.2016.00211] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/08/2016] [Indexed: 11/13/2022] Open
Abstract
Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.
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Affiliation(s)
- Charlotte D. Vavourakis
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
- Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of HydrobiologyČeské Budějovice, Czech Republic
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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