scholarly journals Potential Rhodopsin- and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier

mBio ◽  
2020 ◽  
Vol 11 (6) ◽  
Author(s):  
Yonghui Zeng ◽  
Xihan Chen ◽  
Anne Mette Madsen ◽  
Athanasios Zervas ◽  
Tue Kjærgaard Nielsen ◽  
...  
Keyword(s):  
Solar Energy ◽  
Energy Production ◽  
Gene Clusters ◽  
High Arctic ◽  
Proton Pumping ◽  
The Other ◽  
Life Strategy ◽  
Metabolic Potential ◽  
Expression Control ◽  
Arctic Glacier

ABSTRACT Conserving additional energy from sunlight through bacteriochlorophyll (BChl)-based reaction center or proton-pumping rhodopsin is a highly successful life strategy in environmental bacteria. BChl and rhodopsin-based systems display contrasting characteristics in the size of coding operon, cost of biosynthesis, ease of expression control, and efficiency of energy production. This raises an intriguing question of whether a single bacterium has evolved the ability to perform these two types of phototrophy complementarily according to energy needs and environmental conditions. Here, we report four Tardiphaga sp. strains (Alphaproteobacteria) of monophyletic origin isolated from a high Arctic glacier in northeast Greenland (81.566° N, 16.363° W) that are at different evolutionary stages concerning phototrophy. Their >99.8% identical genomes contain footprints of horizontal operon transfer (HOT) of the complete gene clusters encoding BChl- and xanthorhodopsin (XR)-based dual phototrophy. Two strains possess only a complete XR operon, while the other two strains have both a photosynthesis gene cluster and an XR operon in their genomes. All XR operons are heavily surrounded by mobile genetic elements and are located close to a tRNA gene, strongly signaling that a HOT event of the XR operon has occurred recently. Mining public genome databases and our high Arctic glacial and soil metagenomes revealed that phylogenetically diverse bacteria have the metabolic potential of performing BChl- and rhodopsin-based dual phototrophy. Our data provide new insights on how bacteria cope with the harsh and energy-deficient environment in surface glacier, possibly by maximizing the capability of exploiting solar energy. IMPORTANCE Over the course of evolution for billions of years, bacteria that are capable of light-driven energy production have occupied every corner of surface Earth where sunlight can reach. Only two general biological systems have evolved in bacteria to be capable of net energy conservation via light harvesting: one is based on the pigment of (bacterio-)chlorophyll and the other is based on proton-pumping rhodopsin. There is emerging genomic evidence that these two rather different systems can coexist in a single bacterium to take advantage of their contrasting characteristics in the number of genes involved, biosynthesis cost, ease of expression control, and efficiency of energy production and thus enhance the capability of exploiting solar energy. Our data provide the first clear-cut evidence that such dual phototrophy potentially exists in glacial bacteria. Further public genome mining suggests this understudied dual phototrophic mechanism is possibly more common than our data alone suggested.

scholarly journals Potential Rhodopsin and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier

2020 ◽  
Author(s):  
Yonghui Zeng ◽  
Xihan Chen ◽  
Anne Mette Madsen ◽  
Athanasios Zervas ◽  
Tue Kjærgaard Nielsen ◽  
...  
Keyword(s):  
Solar Energy ◽  
Energy Production ◽  
High Arctic ◽  
Proton Pumping ◽  
Data Availability ◽  
The Other ◽  
Solar Irradiation ◽  
Metabolic Potential ◽  
Expression Control ◽  
Arctic Glacier

AbstractConserving additional energy from sunlight through bacteriochlorophyll (BChl)‐based reaction center or proton‐pumping rhodopsin is a highly successful life strategy in environmental bacteria. Rhodopsin and BChl based systems display contrasting characteristics in the size of coding operon, cost of biosynthesis, ease of expression control, and efficiency of energy production. This raises an intriguing question of whether a single bacterium has evolved the ability to perform these two types of phototrophy complementarily according to energy needs and environmental conditions. Here we report four Tardiphaga sp. strains (Alphaproteobacteria) of monophyletic origin isolated from a high Arctic glacier in northeast Greenland (81.566° N, 16.363° W) that are at different evolutionary stages concerning phototrophy. Their >99.8% identical genomes contain footprints of horizontal operon transfers (HOT) of the complete gene clusters encoding BChl and xanthorhodopsin (XR)‐based dual phototrophy. Two strains only possess a complete xanthorhodopsin (XR) operon, while the other two strains have both a photosynthesis gene cluster (PGC) and an XR operon in their genomes. All XR operons are heavily surrounded by mobile genetic elements and located close to a tRNA gene, strongly signaling that a HOT event of XR operon has occurred recently. Mining public genome databases and our High Arctic glacial and soil metagenomes revealed that phylogenetically diverse bacteria have the metabolic potential of performing BChl and rhodopsin‐based dual phototrophy. Our data provide new insights on how bacteria cope with the harsh and energy‐deficient environments in surface glaciers, possibly by maximizing the capability of exploiting solar energy.ImportanceOver billions of years of evolution, bacteria capable of light‐driven energy production have occupied every corner of surface Earth where solar irradiation can reach. Only two general biological systems have evolved in bacteria to be capable of net energy conservation via light‐harvesting: one is based on the pigment of (bacterio‐)chlorophyll and the other based on light‐sensing retinal molecules. There is emerging genomic evidence that these two rather different systems can co‐exist in a single bacterium to take advantage of their contrasting characteristics in the number of genes involved, biosynthesis cost, ease of expression control and efficiency of energy production, and thus enhance the capability of exploiting solar energy. Our data provide the first clear‐cut evidence that such dual phototrophy potentially exist in glacial bacteria. Further public genome mining suggests this understudied dual phototrophic mechanism is possibly more common than our data alone suggested.Sequence data availabilityGenomes, metagenomes and raw reads were deposited into GenBank under Bioprojects PRJNA548505 and PRJNA552582.

scholarly journals Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 239
Author(s):  
Arshad Ali Shaikh ◽  
Louis-Felix Nothias ◽  
Santosh K. Srivastava ◽  
Pieter C. Dorrestein ◽  
Kapil Tahlan
Keyword(s):  
In Silico Analysis ◽  
Cost Effective ◽  
Gene Clusters ◽  
Streptomyces Clavuligerus ◽  
Strain Engineering ◽  
Ribosome Recycling Factor ◽  
Metabolic Potential ◽  
Putative Gene ◽  
Specialized Metabolites ◽  
Streptomyces Spp

Bacterial specialized metabolites are of immense importance because of their medicinal, industrial, and agricultural applications. Streptomyces clavuligerus is a known producer of such compounds; however, much of its metabolic potential remains unknown, as many associated biosynthetic gene clusters are silent or expressed at low levels. The overexpression of ribosome recycling factor (frr) and ribosome engineering (induced rpsL mutations) in other Streptomyces spp. has been reported to increase the production of known specialized metabolites. Therefore, we used an overexpression strategy in combination with untargeted metabolomics, molecular networking, and in silico analysis to annotate 28 metabolites in the current study, which have not been reported previously in S. clavuligerus. Many of the newly described metabolites are commonly found in plants, further alluding to the ability of S. clavuligerus to produce such compounds under specific conditions. In addition, the manipulation of frr and rpsL led to different metabolite production profiles in most cases. Known and putative gene clusters associated with the production of the observed compounds are also discussed. This work suggests that the combination of traditional strain engineering and recently developed metabolomics technologies together can provide rapid and cost-effective strategies to further speed up the discovery of novel natural products.

scholarly journals Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Hsing Liu ◽  
Yu-Chen Lin ◽  
Chen-Shuan Chung ◽  
Kevin Liu ◽  
Ya-Hui Chang ◽  
...  
Keyword(s):  
Markov Models ◽  
Protein Domains ◽  
Degradation Pathway ◽  
The Other ◽  
Carbohydrate Binding ◽  
Gram Stain ◽  
Active Protein ◽  
Metabolic Potential ◽  
Independent Validation ◽  
Carbohydrate Binding Modules

AbstractBowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97, p < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10−4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10−5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

scholarly journals Solute in high arctic glacier snow cover and its impact on runoff chemistry

1998 ◽  
Vol 26 ◽  
pp. 156-160 ◽  
Author(s):  
Richard Hodgkins ◽  
Martyn Tranter
Keyword(s):  
Chemical Composition ◽  
Atmospheric Transport ◽  
Total Concentration ◽  
High Arctic ◽  
Sea Salt ◽  
Acidic Ph ◽  
Sea Salt Aerosol ◽  
Wet Snow ◽  
Potential Contributor ◽  
Arctic Glacier

The chemical composition of snow and meltwater in the 13 km2 catchment of Scott Turnerbreen, Svalbard, was investigated during the spring and summer of 1993. This paper assesses the provenance of solute in the snowpack and its impact on runoff chemistry. Dry snow contains 420μeql-1 of solute, is slightly acidic (pH 5.4) and is dominated by Na+ and Cl-. Wet snow is more dilute (total concentration 340μeql-1), and less acidic (pH 5.9). This is consistent with the elution of ions from the snowpack by meltwater. Snowpack solute can be partitioned into the following fractions: sea-salt aerosol, acid aerosol and crustal. About 98% of snowpack solute is sea salt, yielding 22000 kg km-2a-1. The behaviour of snowpack-derived Cl- in runoff is distinctive, peaking at over 800 μeql-1 early in the melt season as runoff picks up, before declining quasi-exponentially. This represents the discharge of snowmelt concentrated by elution within the snowpack which subsequently becomes relatively dilute. A solute yield of 140 kg km-2 a-1 can be attributed to anthropogenically generated acid aerosols, representing long-range atmospheric transport of pollutants, a potential contributor to Arctic runoff acidification.

scholarly journals Effects of substrate differences on water availability for Arctic lichens during the snow-free summers in the High Arctic glacier foreland

Polar Science ◽  
2014 ◽  
Vol 8 (4) ◽  
pp. 397-412 ◽  
Author(s):  
Takeshi Inoue ◽  
Sakae Kudoh ◽  
Masaki Uchida ◽  
Yukiko Tanabe ◽  
Masakane Inoue ◽  
...  
Keyword(s):  
Water Availability ◽  
High Arctic ◽  
Glacier Foreland ◽  
Arctic Glacier
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