Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota.

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.

Response of microbial diversity and function to the degradation of Barkol Saline Lake.

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The ßNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

Chelativorans salis sp. nov., a slightly halophilic bacterium isolated from an enrichment system with saline lake sediment.

A Gram-stain-negative, non-motile, and slightly halophilic alphaproteobacterium, designated strain EGI FJ00035T, was isolated from enrichment sediment samples of a saline lake in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using the polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain EGI FJ00035T formed a distinct clade with 'Chelativorans alearense' UJN715 and 'Chelativorans xinjiangense' lm93 with sequence similarities of 98.44 and 98.22 %, respectively, while sharing less than 96.7 % with other valid type strains. The novel isolate could be distinguished from other species of the genus Chelativorans by its distinct phenotypic, physiological, and genotypic characteristics. Optimal growth of strain EGI FJ00035T occurred on marine agar 2216 at pH 7.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>5 %) were C19 : 0 cyclo ω8c, summed feature 8 (C17 : 1 ω6c and/or C17 : 1 ω7c), C16 : 0, C18 : 0, and iso-C17 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipids, unidentified glycolipids, and an unidentified lipid. Based on its genome sequence, the G+C content of strain EGI FJ00035T was 63.2 mol%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values of strain EGI FJ00035T against related members of the genus Chelativorans were below the thresholds for delineation of a novel species. According our polyphasic taxonomic data, strain EGI FJ00035T represents a new species of the genus Chelativorans, for which the name Chelativorans salis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI FJ00035T (=KCTC 92251T=CGMCC 1.19480T).

Dongia deserti sp. nov., Isolated from the Gurbantunggut Desert Soil.

A Gram-stain-negative, aerobic, short rod-shaped strain, designated as SYSU D60009T, was isolated from a dry sandy soil sample collected from the Gurbantunggut Desert in Xinjiang, northwest China. Strain SYSU D60009T was observed to grow at 15-42 °C (optimum at 37 °C), pH 4.0-10.0 (optimum at 7.0), and with 0-0.5% (w/v) NaCl (optimum, 0%). The strain grew well on R2A agar, and colonies were smooth, white-pigmented, and circular with low convexity. The polar lipids consisted of phosphatidylethanolamine, aminolipid, aminophospholipid, and unknown lipids. The major cellular fatty acid (> 10%) was C16:0 and the predominant respiratory quinone was Q-10. Whole genome sequencing of strain SYSU D60009T revealed 6,132,710 bp with a DNA G + C content of 63.6%. The ANI and dDDH values of strains SYSU D60009T to Dongia mobilis CGMCC 1.7660 T were 72.8% and 19.0%, respectively. Based on the phenotypic, phylogenetic, and chemotaxonomic properties, strain SYSU D60009T represents a novel species of the genus Dongia, for which the name Dongia deserti sp. nov. is proposed, the type strain is SYSU D60009T (= CGMCC 1.16441 T = KCTC 52790 T).

Pseudalkalibacillus salsuginis sp. nov., a novel salt-tolerant bacterium isolated from a saline lake sediment.

A salt-tolerant bacterium, designated strain EGI L200015T, was isolated from saline lake sediment in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that EGI L200015T formed a distinct clade with Pseudalkalibacillus berkeleyi KCTC 12718T with sequence identity of 98.3%. The novel isolate could be distinguished from species of the genus Pseudalkalibacillus by its distinct phenotypic, physiological and genotypic characteristics. Cells of EGI L200015T were aerobic, Gram-stain-positive, non-motile and rod-shaped. Optimal growth conditions for EGI L200015T occurred on marine agar 2216 at pH 8.0 at 30 °C. The major respiratory quinone was MK-7, while the major fatty acids (> 10 %) were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The detected polar lipids of included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the genome sequence data, the DNA G+C content of EGI L200015T was 41.6 %. On the basis of the phenotypic, physiological, genotypic and phylogenetic data, strain EGI L200015T represents a novel species of the genus Pseudalkalibacillus, for which the name Pseudalkalibacillus salsuginis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200015T (= KCTC 43363T = CGMCC 1.19260T).

The Metabolic Potential of Endophytic Actinobacteria Associated with Medicinal Plant Thymus roseus as a Plant-Growth Stimulator.

Bio-fertilizer practice considers not only economical but also environmentally friendly, sustainable agriculture. Endophytes can play important beneficiary roles in plant development, directly, indirectly, or synergistically. In this study, the majority of our endophytic actinobacteria were able to possess direct plant growth-promoting (PGP) traits, including auxin (88%), ammonia (96%), siderophore production (94%), and phosphate solubilization (24%), along with cell-wall degrading enzymes such as protease (75%), cellulase (81%), lipase (81%), and chitinase (18%). About 45% of tested strains have an inhibitory effect on the phytopathogen Fusarium oxysporum, followed by 26% for Verticillium dahlia. Overall, our results showed that strains XIEG63 and XIEG55 were the potent strains with various PGP traits that caused a higher significant increase (p ≤ 0.05) in length and biomass in the aerial part and roots of tomato and cotton, compared to the uninoculated plants. Our data showed that the greatest inhibition percentages of two phytopathogens were achieved due to treatment with strains XIEG05, XIEG07, XIEG45, and XIEG51. The GC-MS analysis showed that most of the compounds were mainly alkanes, fatty acid esters, phenols, alkenes, and aromatic chemicals and have been reported to have antifungal activity. Our investigation emphasizes that endophytic actinobacteria associated with medicinal plants might help reduce the use of chemical fertilization and potentially lead to increased agricultural productivity and sustainability.

Paracoccus salsus sp. nov., a novel slightly halophilic bacterium isolated from saline lake sediment.

A Gram-stain-negative, non-motile, slightly halophilic and non-endospore-forming alphaproteobacterium, designated strain EGI L200073T, was isolated from saline lake sediment sampled in Xinjiang Uygur Autonomous Region, China. The taxonomic position of the isolate was determined using the polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that strain EGI L200073T formed a distinct clade with Paracoccus seriniphilus DSM 14827T and shared sequence identity of 98.56 %. The novel isolate could be distinguished from other species of the genus Paracoccus by its distinct phenotypic, physiological and genotypic characteristics. Optimal growth of strain EGI L200073T occurred on marine agar 2216 at pH 8.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>10%) were summed feature 8 (C17 : 1 ω6c and/or C17 : 1 ω7c) and C18 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. Based on the genome sequence of strain EGI L200073T, the G+C content of the novel isolate was 65.7 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain EGI L200073T against related members in the genus Paracoccus were below the cut-off points proposed for delineation of a novel species. According our polyphasic taxonomic data, strain EGI L200073T represents a new species of the genus Paracoccus, for which the name Paracoccus salsus sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200073T (=KCTC 92045T=CGMCC 1.19242T).

Synergistic Plant-Microbe Interactions between Endophytic Actinobacteria and Their Role in Plant Growth Promotion and Biological Control of Cotton under Salt Stress.

Bacterial endophytes are well-acknowledged inoculants to promote plant growth and enhance their resistance toward various pathogens and environmental stresses. In the present study, 71 endophytic strains associated with the medicinal plant Thymus roseus were screened for their plant growth promotion (PGP), and the applicability of potent strains as bioinoculant has been evaluated. Regarding PGP traits, the percentage of strains were positive for the siderophore production (84%), auxin synthesis (69%), diazotrophs (76%), phosphate solubilization (79%), and production of lytic enzymes (i.e., cellulase (64%), lipase (62%), protease (61%), chitinase (34%), and displayed antagonistic activity against Verticillium dahliae (74%) in vitro. The inoculation of strain XIEG05 and XIEG12 enhanced plant tolerance to salt stress significantly (p < 0.05) through the promotion of shoot, root development, and reduced the activities of antioxidant enzymes (SOD, POD, and CAT), compared with uninoculated controls in vivo. Furthermore, inoculation of strain XIEG57 was capable of reducing cotton disease incidence (DI) symptoms caused by V. dahliae at all tested salt concentrations. The GC-MS analysis showed that many compounds are known to have antimicrobial and antifungal activity. Our findings provide valuable information for applying strains XIEG05 and XIEG12 as bioinoculant fertilizers and biological control agent of cotton under saline soil conditions.

Stripe order enhanced superconductivity in the Hubbard model.

Unidirectional ("stripe") charge density wave order has now been established as a ubiquitous feature in the phase diagram of the cuprate high-temperature superconductors, where it generally competes with superconductivity. Nonetheless, on theoretical grounds it has been conjectured that stripe order (or other forms of "optimal" inhomogeneity) may play an essential positive role in the mechanism of high-temperature superconductivity. Here, we report density matrix renormalization group studies of the Hubbard model on long four- and six-leg cylinders, where the hopping matrix elements transverse to the long direction are periodically modulated-mimicking the effect of putative period 2 stripe order. We find that even modest amplitude modulations can enhance the long-distance superconducting correlations by many orders of magnitude and drive the system into a phase with a substantial spin gap and superconducting quasi-long-range order with a Luttinger exponent, [Formula: see text].

High Temperature Superconductivity in a Lightly Doped Quantum Spin Liquid.

We have performed density-matrix renormalization group studies of a square lattice t-J model with small hole doping, δ≪1, on long four and six-leg cylinders. We include frustration in the form of a second-neighbor exchange coupling, J_{2}=J_{1}/2, such that the undoped (δ=0) "parent" state is a quantum spin liquid. In contrast to the relatively short range superconducting (SC) correlations that have been observed in recent studies of the six-leg cylinder in the absence of frustration, we find power-law SC correlations with a Luttinger exponent, K_{SC}≈1, consistent with a strongly diverging SC susceptibility, χ∼T^{-(2-K_{SC})} as the temperature T→0. The spin-spin correlations-as in the undoped state-fall exponentially suggesting that the SC "pairing" correlations evolve smoothly from the insulating parent state.

Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress.

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.

Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria.

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

Orbital Chern Insulator and Quantum Phase Diagram of a Kagome Electron System with Half-Filled Flat Bands.

We study the quantum phase diagram of electrons on kagome lattice with half-filled lowest flat bands by considering the antiferromagnetic Heisenberg interaction J, and short-range Coulomb interaction V. In the weak J regime, we identify a fully spin-polarized phase. The presence of finite V drives a spontaneous chiral current, which makes the system an orbital Chern insulator by contributing an orbital magnetization. Such an out-of-plane orbital magnetization allows the presence of a Chern insulating phase independent of the spin orientation in contrast to the spin-orbit coupling induced Chern insulator that disappears with in-plane ferromagnetism constrained by symmetry. Such a symmetry difference provides a criterion to distinguish the physical origin of topological responses in kagome systems. The orbital Chern insulator is robust against small coupling J. By further increasing J, we find that the ferromagnetic topological phase is suppressed, which first becomes partially polarized and then enters a nonmagnetic phase with spin and charge nematicity. The frustrated flat band allows the spin and Coulomb interaction to play an essential role in determining the quantum phases.

Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

Lunatibacter salilacus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a saline and alkaline lake sediment.

A non-motile, Gram-staining negative, catalase- and oxidase-positive, crescent-rod shaped bacterium, designated strain CUG 91308T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. Colonies on OSM agar were round, smooth, flat and pinkish-orange in colour. Strain CUG 91308T could grow at 15-37 °C, pH 6-12 and in the presence of up to 7.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91308T belonged to the family Cyclobacteriaceae and formed a clade with the genus Lunatimonas in the phylogenetic tree, but separated from any species of the known genera within the family. The genomic DNA G+C content is about 42.1 %. The predominant fatty acids (>10 %) were iso-C15 : 0 (21.1 %), summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c / iso-C15 : 0 2OH) (14.3 %), iso-C17 : 0 3OH (12.3 %) and summed feature 9 (iso-C17 : 1 ω9c / C16 : 0 10-methyl) (10.6 %). The polar lipids of strain CUG 91308T were phosphatidylethanolamine (PE) and four unidentified polar lipids. Strain CUG 91308T contained MK-7 as the major respiratory quinone. On the basis of phenotypic, genotypic and phylogenetic data, strain CUG 91308T represents a novel species of a novel genus in the family Cyclobacteriaceae, for which the name Lunatibacter salilacus gen. nov., sp. nov. is proposed. The type strain of the proposed new isolate is CUG 91308T (=KCTC 62636T=CGMCC 1.13593T).

Materializing rival ground states in the barlowite family of kagome magnets: quantum spin liquid, spin ordered, and valence bond crystal states.

The spin- 1 2 kagome antiferromagnet is considered an ideal host for a quantum spin liquid (QSL) ground state. We find that when the bonds of the kagome lattice are modulated with a periodic pattern, new quantum ground states emerge. Newly synthesized crystalline barlowite (Cu4(OH)6FBr) and Zn-substituted barlowite demonstrate the delicate interplay between singlet states and spin order on the spin- 1 2 kagome lattice. Comprehensive structural measurements demonstrate that our new variant of barlowite maintains hexagonal symmetry at low temperatures with an arrangement of distorted and undistorted kagome triangles, for which numerical simulations predict a pinwheel valence bond crystal (VBC) state instead of a QSL. The presence of interlayer spins eventually leads to an interesting pinwheel q = 0 magnetic order. Partially Zn-substituted barlowite (Cu3.44Zn0.56(OH)6FBr) has an ideal kagome lattice and shows QSL behavior, indicating a surprising robustness of the QSL against interlayer impurities. The magnetic susceptibility is similar to that of herbertsmithite, even though the Cu2+ impurities are above the percolation threshold for the interlayer lattice and they couple more strongly to the nearest kagome moment. This system is a unique playground displaying QSL, VBC, and spin order, furthering our understanding of these highly competitive quantum states.

Topological Superconductivity in the Doped Chiral Spin Liquid on the Triangular Lattice.

It has long been proposed that doping a chiral spin liquid (CSL) or fractional quantum Hall state can give rise to topological superconductivity. Despite intensive effort, definitive evidences still remain lacking. We address this problem by studying the t-J model supplemented by time-reversal symmetry breaking chiral interaction J_{χ} on the triangular lattice using density-matrix renormalization group with a finite concentration δ of doped holes. It has been established that the undoped, i.e., δ=0, system has a CSL ground state in the parameter region 0.32≤J_{χ}/J≤0.56. Upon light doping, we find that the ground state of the system is consistent with a Luther-Emery liquid with power-law superconducting and charge-density-wave correlations but short-range spin-spin correlations. In particular, the superconducting correlations, whose pairing symmetry is consistent with d±id wave, are dominant at all hole doping concentrations. Our results provide direct evidences that doping the CSL on the triangular lattice can naturally give rise to topological superconductivity.

Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats.

The perplexity of the complex multispecies community interactions is one of the many reasons why majority of the microorganisms are still uncultivated. We analyzed the entire co-occurrence networks between the OTUs of Tibet and Yunnan hot spring samples, and found that less abundant OTUs such as genus Tepidimonas (relative abundant <1%) had high-degree centricity (key nodes), while dominant OTUs particularly genus Chloroflexus (relative abundant, 13.9%) formed the peripheral vertexes. A preliminary growth-promotion assay determined that Tepidimonas sp. strain SYSU G00190W enhanced the growth of Chloroflexus sp. SYSU G00190R. Exploiting this result, an ameliorated isolation medium containing 10% spent-culture supernatant of Tepidimonas sp. strain SYSU G00190W was prepared for targeted isolation of Chloroflexi in the Tibet and Yunnan hot spring samples. 16S rRNA gene fingerprinting characterized majority of the colonies isolated from these media as previously uncultivated Chloroflexi, of which 36 are potential novel species (16S rRNA sequence identity <98.5%). Metabolomes studies indicated that the spent-culture supernatant comprises several low-molecular-weight organic substrates that can be utilized as potential nutrients for the growth of these bacteria. These findings suggested that limited knowledge on the interaction of microbes provide threshold to traditional isolation method.

Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov., isolated from a saline lake.

Two novel strains, designated SYSU L10167T and SYSU L10180T, were isolated from sediment sampled at Dabancheng saline lake in Xinjiang, PR China. A polyphasic approach was used to clarify the taxonomic positions of the two strains. Cells of the isolates were curved ring-like, horseshoe-shaped or rod-shaped, non-motile and non-spore-forming. Cells were Gram-stain-negative, aerobic, heterotrophic and rose-pigmented. The phylogenetic trees based on 16S rRNA gene sequences showed that strains SYSU L10167T and SYSU L10180T formed a distinct lineage within the genus Cyclobacterium. Strains SYSU L10167T and SYSU L10180T showed highest similarities to Cyclobacterium jeungdonense KCTC 23150T (98.0 and 97.4%, respectively). Results of genomic analyses (including average nucleotide identity, digital DNA-DNA hybridization and the marker gene tree) and pan-genome analysis further confirmed that strains SYSU L10167T and SYSU L10180T were separate from each other and other species of the genus Cyclobacterium. The draft genomes of the isolates had sizes of 5.5-5.7 Mb and reflected their major physiological capabilities. Based on phenotypic, physiological, chemotaxonomic and genotypic characterization, we propose that the isolates represent two novel species, for which the names Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov. are proposed. The type strains of the species are SYSU L10167T (=KCTC 72390T=CGMCC 1.17521T) and SYSU L10180T (=KCTC 72391T=CGMCC 1.17278T).