Draft Genome Sequence of Rubricoccus marinus SG-29
 T
 , a Marine Bacterium within the Family
 Rhodothermaceae
 , Which Contains Two Different Rhodopsin Genes

Nakajima, Yu; Yoshizawa, Susumu; Park, Sanghwa; Kumagai, Yohei; Wong, Shu-Kuan; Ogura, Yoshitoshi; Hayashi, Tetsuya; Kogure, Kazuhiro

doi:10.1128/genomea.00990-17

Cited by 5 publications

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“…A previous study showed that R. marinus SG-29 T has a 4.43-Mbp chromosome encoding 3847 CDSs ( 24 ). The present genome sequence analysis of R. marina SAORIC-28 T and R. profundi SAORIC-476 T revealed that these strains have 4.98 Mbp and 4.48 Mbp chromosomes encoding 4267 and 3842 CDSs, respectively ( Table S1 ).…”

Section: Resultsmentioning

confidence: 99%

“…The genomic DNA of strains SAORIC-28 T and SAORIC-476 T was extracted using phenol-chloroform and ethanol precipitation ( 21 ). Library preparation was performed for strain SAORIC-28 T , as previously reported for strain SG-29 T ( 24 ). A KAPA HyperPlus Kit (Kapa Biosystems, Boston, MA, USA) was used for library preparation for strain SAORIC-476 T .…”

Section: Methodsmentioning

confidence: 99%

“…Following the genome information of Rubricoccus marinus SG-29 T ( 24 ), we herein report two genome sequences of Rubrivirga marina SAORIC-28 T and R. profundi SAORIC-476 T . A genomic analysis revealed that R. marinus SG-29 T and R. marina SAORIC-28 T have five rhodopsin genes belonging to two different clusters: one is included in the xenorhodopsin (XeR) cluster, and the other is a unique cluster consisting of rhodopsin containing a TSA motif (amino acid residues 85, 89, and 96 in BR numbering).…”

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confidence: 99%

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Presence of a Haloarchaeal Halorhodopsin-Like Cl− Pump in Marine Bacteria

et al. 2018

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Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl−-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl− pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl−-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl−-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.

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Section: Resultsmentioning

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Section: Methodsmentioning

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Presence of a Haloarchaeal Halorhodopsin-Like Cl− Pump in Marine Bacteria

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“…The main biomarkers of plant biomass in keystone bacterial and AMF taxa (Figure 6) have been described as salt‐tolerant or growth‐promoting taxa in global soils in a wide range of terrestrial ecosystems. For example, in saline–alkaline grasslands, the family Rhodothermaceae has been reported to harbor halophilic bacteria (Nakajima et al, 2017), and Conexibacter may improve plant uptake and utilization of P in soil (Deng et al, 2021). In non‐saline–alkaline grasslands, some species of Sphingomonas and Microvirga have been confirmed to be plant growth‐promoting rhizobacteria (Jiménez‐Gómez et al, 2019; Kim et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…The main biomarkers of plant biomass in keystone bacterial and AMF taxa (Figure 6) have been described as salt-tolerant or growth-promoting taxa in global soils in a wide range of terrestrial ecosystems. For example, in saline-alkaline grasslands, the family Rhodothermaceae has been reported to harbor halophilic bacteria (Nakajima et al, 2017),…”

Section: Response Strategies Of Bacteria and Amf Communities To Salin...mentioning

confidence: 99%

Microbial community in the Leymus chinensis rhizosphere associates with its high production in mild saline–alkaline grassland

Guo,

Hao

et al. 2023

Land Degrad Dev

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Leymus chinensis is a dominant grass widely distributed in Central Asia, in both saline−alkaline and non‐saline−alkaline grasslands. However, the mechanisms underlying its saline−alkaline tolerance have not been explored from the perspective of rhizosphere microbial communities. We investigated L. chinensis rhizosphere microbial communities in both saline–alkaline and non‐saline–alkaline grasslands. It was found that the biomass of L. chinensis was remarkably higher in saline–alkaline than in non‐saline–alkaline habitat and that changes in the rhizosphere bacterial and arbuscular mycorrhizal fungi (AMF) communities had a greater effect on biomass than climate, soil moisture, nutrients, and salinity. We demonstrated that the bacteria and AMF in the rhizosphere of L. chinensis grown in saline–alkaline grassland differed from those in non‐saline–alkaline grassland, and the differences were associated with soil salinity or alkalinity. The co‐occurrence networks of bacteria and AMF and bacteria–AMF interaction networks in rhizosphere were complex and connected, with more nodes and edges and a higher average degree of nodes and modularity in the saline–alkaline grassland. More complex networks promoted plant tolerance and growth under salt–alkali stress. High number of microbial keystone taxa was related to the nutrient concentration in the soil and L. chinensis leaves, and more remarkable direct effects of the bacterial and AMF keystone communities on plant nutrient concentrations were demonstrated in saline–alkaline grassland. This indicates that bacterial and AMF communities in saline–alkaline grasslands are favorable for plant growth and nutrient uptake. This study provides an accurate and beneficial source of soil microbial assemblages for future plant–microbial joint remediation of the saline–alkaline ecosystems.

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A Study of Sponge Symbionts from Different Light Habitats

Cleary,

de Voogd,

Stuij

et al. 2023

Microb Ecol

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The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.

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Draft Genome Sequence of Rubricoccus marinus SG-29 ^T , a Marine Bacterium within the Family Rhodothermaceae , Which Contains Two Different Rhodopsin Genes

Cited by 5 publications

References 8 publications

Presence of a Haloarchaeal Halorhodopsin-Like Cl<sup>−</sup> Pump in Marine Bacteria

Presence of a Haloarchaeal Halorhodopsin-Like Cl<sup>−</sup> Pump in Marine Bacteria

Microbial community in the Leymus chinensis rhizosphere associates with its high production in mild saline–alkaline grassland

A Study of Sponge Symbionts from Different Light Habitats

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Draft Genome Sequence of Rubricoccus marinus SG-29 T , a Marine Bacterium within the Family Rhodothermaceae , Which Contains Two Different Rhodopsin Genes

Cited by 5 publications

References 8 publications

Presence of a Haloarchaeal Halorhodopsin-Like Cl<sup>−</sup> Pump in Marine Bacteria

Presence of a Haloarchaeal Halorhodopsin-Like Cl<sup>−</sup> Pump in Marine Bacteria

Microbial community in the Leymus chinensis rhizosphere associates with its high production in mild saline–alkaline grassland

A Study of Sponge Symbionts from Different Light Habitats

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Draft Genome Sequence of Rubricoccus marinus SG-29 ^T , a Marine Bacterium within the Family Rhodothermaceae , Which Contains Two Different Rhodopsin Genes