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).

Fundicoccus culcitae sp. nov., a novel potential bacteriocin producing bacterium isolated from a spoiled eye mask.

A Gram-positive, facultatively anaerobic, oval beaded-shape, oxidase-negative, and non-motile bacterium designated DM20194951T was isolated from a spoiled eye mask obtained from Guangdong, China. Based on the 16S rRNA gene sequence, phylogenetic analysis indicated that strain DM20194951T showed the highest sequence similarity (95.8%) to Fundicoccus ignavus WS4937T. Meanwhile, strain DM20194951T could be distinguished from the type strains in the genus Fundicoccus by distinct phenotypic and genotypic traits. Strain DM20194951T grew variably with 1-2% (w/v) NaCl and tolerated pH 6.0-10.0. Growth was observed from 28 to 37 °C. The diagnostic diamino acids in the cell-wall peptidoglycan consisted of aspartic and glutamic acids as well as alanine. The predominant fatty acids were C18:1 ω9c, C16:0, and C16:1 ω9c. In the polar lipid profile, two glycolipids, three phospholipids, one phosphatidylglycerol, and one diphosphatidylglycerol were found. No respiratory quinones were detected. The DM20194951T genome is 3.2 Mb in size and contains a G + C content of 38.1%. A gene cluster for lactococcin 972 family bacteriocin production was found in the DM20194951T genome. Based on morphological, genotypic, and phylogenetic data, strain DM20194951T should be considered to represent a novel species in the genus Fundicoccus, for which the name Fundicoccus culcitae sp. nov. is proposed with the type strain DM20194951T (= KCTC 43472T = GDMCC 1.3614T).

Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects.

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.

Aquiflexum gelatinilyticum sp. nov., isolated from river water.

Two Gram-stain-negative, strictly aerobic, rod-shaped, non-motile and non-gliding bacteria, designated as XJ19-10T and XJ19-11, were isolated from river water in Xinjiang Uygur Autonomous Region, PR China. Cells of these strains were catalase-, oxidase- and gelatinase-positive and contained carotenoids but no flexirubins. Growth occurred at 10-30 °C, pH 7.0-9.0 and with 0-2.5% (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence and genome analyses, the two isolates represented members of the genus Aquiflexum, and the closest relative was Aquiflexum aquatile Z0201T with 16S rRNA gene sequence pairwise similarities of 97.9-98.1%. Furthermore, the average nucleotide identities and digital DNA-DNA hybridization identities between the two isolates and other relatives were all less than 82.9 and 28.2 %, respectively, all below the species delineation thresholds. The results of pan-genomic analysis indicated that the type strain XJ19-10T shared 2813 core gene clusters with other three type strains of members of the genus Aquiflexum, as well as having 623 strain-specific clusters. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and unidentified lipids. The predominant fatty acids (>10% of the total contents) were iso-C15 : 0, iso-C15 : 1G, iso-C17 : 0 3-OH and summed feature 9, and MK-7 was the respiratory quinone. On the basis of the results of phenotypic, physiological, chemotaxonomic and genotypic characterization, strains XJ19-10T and XJ19-11 are considered to represent a novel species, for which the name Aquiflexum gelatinilyticum sp. nov. is proposed. The type strain is XJ19-10T (=CGMCC 1.19385T =KCTC 92266T).

Salinibacterium sedimenticola sp. nov., Isolated from Tidal Flat Sediment.

An actinobacterium, designated as SYSU T00001T, was isolated from a tidal flat sediment sample from Guangdong province, China. Cells were Gram-stain-positive, aerobic, motile and short rod-shaped. Colonies on marine agar 2216 were smooth, yellow-pigmented, and circular with low convexity. The isolate was able to grow at the temperature range 4-37 °C (optimum 30 °C), at pH 4.0-10.0 (optimum 7.0) and in the presence of 0-10% (w/v) NaCl. The major menaquinones were MK-11 and MK-10. The cell wall contained alanine, glutamic acid, lysine and ornithine. The major fatty acids were C19:0 cyclo ω8c (35.7%) and anteiso C15:0 (26.0%). The polar lipids consisted of one diphosphatidyl glycerol, one unidentified glycolipid and one unknown lipid. Whole genome sequencing of strain SYSU T00001T revealed 2,837,702 bp with a DNA G + C content of 67.8%. Phylogenetic analyses clearly demonstrated that strain SYSU T00001T belonged to the genus Salinibacterium, and the highest 16S rRNA gene similarity to Salinibacterium hongtaonis 194T (97.8%). The ANI and dDDH values of strain SYSU T00001T relative to Salinibacterium hongtaonis 194T were 74.5% and 19.5%, respectively. According to our data, strain SYSU T00001T represents a novel species of the genus Salinibacterium, for which the name Salinibacterium sedimenticola sp. nov. is proposed, the type strain is SYSU T00001T (= GDMCC 1.3283T = KCTC 49758T).

Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat.

The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO42-, Na+, CO32-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded saline lakes under environmental change.

Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems.

BACKGROUND: The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS: The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION: Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.

Insights into the effects of drying treatments on cultivable microbial diversity of marine sediments.

Microbes are widespread in the sea that covers more than two-thirds of the earth's surface and most microorganisms living in the marine environment have yet to be cultured. Previous studies showed that drying treatment, a strategy of sample pre-treatment widely applied in microbial isolation and incubation, may alter the cultivable microbial diversity, such as Actinomycetota, essential for exploring novel secondary metabolites from the marine environment, isolated from drying-treated samples. However, whether drying treatments actually can change microbial community diversity and how the drying treatments of samples influence the cultivable microbial diversity of marine samples have not yet adequately been evaluated. Here, three marine sediment samples were dried and incubated at 28 ºC, 37 ºC, and 45 ºC, and the microbial diversity was assessed with high-throughput sequencing. Our results suggested that drying treatments had different effects on different genera and some potential novel species could be cultured only from drying-treated samples, including the novel members from the families Paenibacillaceae and Thermoactinomycetaceae. Non-metric multidimensional scaling analysis showed that the treated samples were clustered according to the cultivation temperatures rather than the drying conditions at high cultivation temperatures. However, at the cultivation temperatures of 28 ºC, drying treatments were the larger separation between cultivable microbial communities in the process of microbial isolation. These results showed that the drying treatments influenced the cultivated microbes in a taxon-specific pattern and extended potential novel taxa. Combining high-throughput sequencing to various drying conditions and incubation temperatures, this study provides new insight into the effects of drying treatment on the cultivable microbial diversity of marine sediments.

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts.

BACKGROUND: Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. RESULTS: Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. CONCLUSIONS: Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.

Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.

BACKGROUND: Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. RESULTS: Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. CONCLUSIONS: This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.

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).

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).

Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae.

In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.

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).

Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan.

A novel actinobacterial strain, designated SYSU K20354T, was isolated from a soil sample collected from a karst cave in Shaoguan city, Guangdong province, southern China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K20354T was most closely related to Agromyces humatus JCM 14319T, and shared the highest sequence identity of 98.3 % based on NCBI database. In addition, 2,4-diaminobutyric acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose and ribose. The major isoprenoid quinone was MK-12, while the major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, three unknown glycolipids, three unknown phospholipids and two unknown lipids. The draft genome size of strain SYSU K20354T was 3.96 Mbp with G+C content of 69.7 mol%. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values between strain SYSU K20354T and A. humatus JCM 14319T were 90.3 and 55.6 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K20354T represents a novel species of the genus Agromyces, for which the name Agromyces cavernae sp. nov. is proposed. The type strain is SYSU K20354T (=KCTC 49499T= CGMCC 4.7691T).

Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov., two novel members of the phylum Pseudomonadota isolated from hot spring sediments.

Two novel species, designated strains SYSU G04041T and SYSU G04536T, were isolated from hot spring sediments collected in Yunnan, PR China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic positions of the candidate strains. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU G04041T showed the highest sequence similarity to Thermomonas haemolytica A50-7-3T (97.5 %), and SYSU G04536T showed the highest sequence similarity to Thermomonas hydrothermalis SGM-6T (98.2 %). The strains could be differentiated from other species of the genus Thermomonas by their distinct phenotypic and genotypic characteristics. Cells of strains SYSU G04041T and SYSU G04536T were aerobic, motile and Gram-stain-negative. Growth both occurred optimally at 45 °C and pH 7.0 for SYSU G04041T and SYSU G04536T. In addition, the predominant respiratory quinone in both isolates was ubiquinone Q-8. The major fatty acids (>10 %) of strain SYSU G04041T were C16 : 0, iso-C15 : 0 and iso-C16 : 0, while the major fatty acids (>10 %) of strain SYSU G04536T were iso-C15 : 0 and iso-C16 : 0. The main detected polar lipids in strains SYSU G04041T and SYSU G04536T included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The G+C contents of the genomic DNA of strains SYSU G04041T and SYSU G04536T based on draft genomic sequences were 72.5 and 68.3 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU G04041T and SYSU G04536T represent two novel species of the genus Thermomonas, for which the names Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov. are proposed, with the type strains SYSU G04041T (=CGMCC 1.19366T=KCTC 92228T) and SYSU G04536T (=CGMCC 1.19367T=KCTC 82839T), respectively.

Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment.

An actinobacterium, designated strain EGI L10124T, was isolated from saline lake sediment collected in Xinjiang province, PR China. The taxonomic position of the isolate was determined based on polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L10124T formed a distinct clade with Rhabdothermincola sediminis SYSU G02662T, with a shared sequence identity of 95.2 %. The novel isolate could be distinguished from species in the genus Rhabdothermincola by its distinct phenotypic, physiological and genotypic characteristics. The cells of strain EGI L10124T were aerobic, Gram-stain-positive and short rod-shaped. Optimal growth conditions of strain EGI L10124T on marine agar 2216 were registered at pH 8.0 at 37 °C. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major respiratory quinone was MK-9 (H8), while the major fatty acids were iso-C16 : 0, C17 : 0 and C16 : 0. The polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. Based on the genome sequence of strain EGI L10124T, it appears that the G+C content of the novel isolate was 71.8 mol%. According to our data, strain EGI L10124T represents a new species of the genus Rhabdothermincola, for which the name Rhabdothermincola salaria sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L10124T (=CGMCC 1.19113T=KCTC 49679T).

Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary.

Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO2-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.