scholarly journals Aerobic carboxydotrophy under extremely haloalkaline conditions in Alkalispirillum/Alkalilimnicola strains isolated from soda lakes

Microbiology ◽  
2010 ◽  
Vol 156 (3) ◽  
pp. 819-827 ◽  
Author(s):  
Dimitry Yu. Sorokin ◽  
Tatjana P. Tourova ◽  
Olga L. Kovaleva ◽  
J. Gijs Kuenen ◽  
Gerard Muyzer
Keyword(s):  
Carbon Fixation ◽  
Soda Lakes ◽  
Large Subunit ◽  
Calvin Cycle ◽  
Soda Lake ◽  
Protein Profiling ◽  
Bacterial Strains ◽  
Gene Encoding ◽  
Respiration Activity ◽  
Ph Range

Aerobic enrichments from soda lake sediments with CO as the only substrate resulted in the isolation of five bacterial strains capable of autotrophic growth with CO at extremely high pH and salinity. The strains belonged to the Alkalispirillum/Alkalilimnicola cluster in the Gammaproteobacteria, where the ability to oxidize CO, but not growth with CO, has been demonstrated previously. The growth with CO was possible only at an oxygen concentration below 5 % and CO concentration below 20 % in the gas phase. The isolates were also capable of growth with formate but not with H2. The carboxydotrophic growth occurred within a narrow pH range from 8 to 10.5 (optimum at 9.5) and a broad salt concentration from0.3 to 3.5 M total Na+ (optimum at 1.0 M). Cells grown on CO had high respiration activity with CO and formate, while the cells grown on formate actively oxidized formate alone. In CO-grown cells, CO-dehydrogenase (CODH) activity was detectable both in soluble and membrane fractions, while the NAD-independent formate dehydrogenase (FDH) resided solely in membranes. The results of total protein profiling and the failure to detect CODH with conventional primers for the coxL gene indicated that the CO-oxidizing enzyme in haloalkaliphilic isolates might differ from the classical aerobic CODH complex. A single cbbL gene encoding the RuBisCO large subunit was detected in all strains, suggesting the presence of the Calvin cycle of inorganic carbon fixation. Overall, these results demonstrated the possibility of aerobic carboxydotrophy under extremely haloalkaline conditions.

scholarly journals Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils

2017 ◽  
Author(s):  
Dmitry Y. Sorokin ◽  
Tatiana V. Kolganova ◽  
Tatiana V. Khijniak ◽  
Brian E. Jones ◽  
Ilya V. Kublanov
Keyword(s):  
Soda Lakes ◽  
Soda Lake ◽  
Rrna Gene ◽  
Alkaline Soils ◽  
Present Information ◽  
Hydrolytic Activities ◽  
Hydrolytic Bacteria ◽  
Sequences Analysis ◽  
Ph Range ◽  
Soda Soils

Alkaline saline soils known also as “soda solonchaks” represent a natural soda habitat which differed from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we present information on the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia and Africa. In total, 180 isolates were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequences analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of both groups were active at a broad pH range from 6 to 11. Overall, this work demonstrated the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.

scholarly journals Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria

2020 ◽  
Vol 8 (12) ◽  
pp. 1880
Author(s):  
Marcela Hernández ◽  
Blanca Vera-Gargallo ◽  
Marcela Calabi-Floody ◽  
Gary M. King ◽  
Ralf Conrad ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Carbon Fixation ◽  
Large Subunit ◽  
Natural Habitat ◽  
Volcanic Rocks ◽  
Amino Acid Identity ◽  
Cellular Functions ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Successional Stages

Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

scholarly journals Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria

2020 ◽  
Author(s):  
Marcela Hernández ◽  
Blanca Vera-Gargallo ◽  
Marcela Calabi-Floody ◽  
Gary M King ◽  
Ralf Conrad ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Carbon Fixation ◽  
Large Subunit ◽  
Natural Habitat ◽  
Volcanic Rocks ◽  
Amino Acid Identity ◽  
Cellular Functions ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Successional Stages

AbstractMicroorganisms can potentially colonize volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilize H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

scholarly journals Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils

2017 ◽  
Author(s):  
Dmitry Y. Sorokin ◽  
Tatiana V. Kolganova ◽  
Tatiana V. Khijniak ◽  
Brian E. Jones ◽  
Ilya V. Kublanov
Keyword(s):  
Soda Lakes ◽  
Soda Lake ◽  
Rrna Gene ◽  
Alkaline Soils ◽  
Present Information ◽  
Hydrolytic Activities ◽  
Hydrolytic Bacteria ◽  
Sequences Analysis ◽  
Ph Range ◽  
Soda Soils

Alkaline saline soils known also as “soda solonchaks” represent a natural soda habitat which differed from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we present information on the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia and Africa. In total, 180 isolates were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequences analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of both groups were active at a broad pH range from 6 to 11. Overall, this work demonstrated the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.

scholarly journals A shared core microbiome in soda lakes separated by large distances

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jackie K. Zorz ◽  
Christine Sharp ◽  
Manuel Kleiner ◽  
Paul M. K. Gordon ◽  
Richard T. Pon ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Carbon Fixation ◽  
Soda Lakes ◽  
Soda Lake ◽  
Sequencing Data ◽  
Core Microbiome ◽  
Lake Ecology ◽  
Selection Principles ◽  
Globally Distributed ◽  
Insight Into

Abstract In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.

scholarly journals Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3796 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Tatiana V. Kolganova ◽  
Tatiana V. Khijniak ◽  
Brian E. Jones ◽  
Ilya V. Kublanov
Keyword(s):  
Soda Lakes ◽  
Soda Lake ◽  
Rrna Gene ◽  
Alkaline Soils ◽  
Gene Sequence Analysis ◽  
Hydrolytic Activities ◽  
Hydrolytic Bacteria ◽  
Pure Cultures ◽  
Ph Range ◽  
Soda Soils

Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged toFirmicutesandActinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.

scholarly journals A shared core microbiome in soda lakes separated by large distances

2019 ◽  
Author(s):  
Jackie K. Zorz ◽  
Christine Sharp ◽  
Manuel Kleiner ◽  
Paul M.K. Gordon ◽  
Richard T. Pon ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Global Climate ◽  
Soda Lakes ◽  
Soda Lake ◽  
Sequencing Data ◽  
Carbon Dioxide Conversion ◽  
Core Microbiome ◽  
Central Asian

AbstractIn alkaline soda lakes, high concentrations of dissolved carbonates establish an environment favouring productive phototrophic microbial mat communities. Here we show how different species of microbial phototrophs and autotrophs contribute to this exceptional productivity. Four years of amplicon and shotgun DNA sequencing data from microbial mats from four different lakes indicated the presence of over 2,000 different species of Bacteria and Eukaryotes. Metagenome-assembled-genomes were obtained for a core microbiome of <100 abundant bacteria, which was shared among lakes and accounted for half of the extracted DNA throughout the four year sampling period. Most of the associated species were related to similar microbes previously detected in sediments of Central Asian alkaline soda lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Dispersal events between the two distant lake systems were shown to be extremely rare, with dispersal rates a function of abundance in microbial mats, but not sediments. Detection of more than 7,000 expressed proteins showed how phototrophic populations allocated resources to specific processes and occupied complementary niches. Carbon fixation only proceeded by the Calvin-Benson-Bassham cycle, detected in Cyanobacteria, Alphaproteobacteria, and, suprisingly, Gemmatomonadetes. Our study not only provides new fundamental insight into soda lake ecology, but also provides a template, guiding future efforts to engineer robust and productive biotechnology for carbon dioxide conversion.ImportanceAlkaline soda lakes are among the most productive ecosystems worldwide, despite their high pH. This high productivity leads to growth of thick “mats” of filamentous cyanobacteria. Here, we show that such mats have very high biodiversity, but at the same time contain a core, shared set of only approximately 100 different bacteria that perform key functions, such as photosynthesis. This “core microbiome” occurs both in Canadian and Central Asian soda lakes, >8,000 km apart. We present evidence for (very rare) dispersion of some core microbiome members from Canadian mats to Central Asian soda lake sediments. The close similarity between distant microbial communities indicates that these communities share common design principles, that reproducibly lead to a high and robust productivity. We unravel a few examples of such principles and speculate that these might be applied to create robust biotechnology for carbon dioxide conversion, to mitigate of global climate change.

scholarly journals Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA).

1986 ◽  
Vol 261 (32) ◽  
pp. 14929-14935
Author(s):  
J W Chase ◽  
B A Rabin ◽  
J B Murphy ◽  
K L Stone ◽  
K R Williams
Keyword(s):  
Escherichia Coli ◽  
Large Subunit ◽  
Cloning And Sequencing ◽  
Gene Encoding ◽  
Exonuclease Vii

Direct cloning of genes encoding novel xylanases from the human gut

2005 ◽  
Vol 51 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Hidenori Hayashi ◽  
Takashi Abe ◽  
Mitsuo Sakamoto ◽  
Hiroki Ohara ◽  
Toshimichi Ikemura ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Fecal Microbiota ◽  
Coli Strain ◽  
Amino Acid Sequences ◽  
Self Organizing Map ◽  
Human Gut ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Ph Range ◽  
Self Organizing

The aim of this study was to identify a novel 1,4-β-xylanase gene from the mixed genome DNA of human fecal bacteria without bacterial cultivation. Total DNA was isolated from a population of bacteria extracted from fecal microbiota. Using PCR, the gene fragments encoding 5 different family 10 xylanases (xyn10A, xyn10B, xyn10C, xyn10D, and xyn10E) were found. Amino acid sequences deduced from these genes were highly homologous with those of xylanases from anaerobic intestinal bacteria such as Bacteroides spp. and Prevotella spp. Self-organizing map (SOM) analysis revealed that xynA10 was classified into Bacteroidetes. To confirm that one of these genes encodes an active enzyme, a full-length xyn10A gene was obtained using nested primers specific to the internal fragments and random primers. The xyn10A gene encoding the xylanase Xyn10A consists of 1146 bp and encodes a protein of 382 amino acids and a molecular weight of 43 552. Xyn10A was a single module novel xylanase. Xyn10A was purified from a recombinant Escherichia coli strain and characterized. This enzyme was optimally active at 40 °C and stable up to 50 °C at pH 6.5 and over the pH range 4.0–11.0 at 25 °C. In addition, 2 ORFs (ORF1 and ORF2) were identified upstream of xyn10A. These results suggested that many unidentified xylanolytic bacteria exist in the human gut and may contribute to the breakdown of xylan which contains dietary fiber.Key words: xylanase, human gut, fecal microbiota, phylogenetic analysis, self-organizing map.

scholarly journals Design and in vitro realization of carbon-conserving photorespiration

2018 ◽  
Vol 115 (49) ◽  
pp. E11455-E11464 ◽  
Author(s):  
Devin L. Trudeau ◽  
Christian Edlich-Muth ◽  
Jan Zarzycki ◽  
Marieke Scheffen ◽  
Moshe Goldsmith ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Computational Design ◽  
Carbon Loss ◽  
Fixation Rate ◽  
Bisphosphate Carboxylase ◽  
Stoichiometric Model ◽  
Synthetic Routes ◽  
Coa Reductase

Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO2. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO2. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO2 release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO2, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD+, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.

Sign in / Sign up

Export Citation Format

Share Document