The Single-Stranded DNA-Binding Gene Whirly (Why1) with a Strong Pathogen-Induced Promoter from Vitis pseudoreticulata Enhances Resistance to Phytophthora capsici.

Vitis vinifera plants are disease-susceptible while Vitis pseudoreticulata plants are disease-resistant; however, the molecular mechanism remains unclear. In this study, the single-stranded DNA- and RNA-binding protein gene Whirly (VvWhy1 and VpWhy1) were cloned from V. vinifera "Cabernet Sauvignon" and V. pseudoreticulata "HD1". VvWhy1 and VpWhy1 promoter sequences (pVv and pVp) were also isolated; however, the identity of the promoter sequences was far lower than that between the Why1 coding sequences (CDSs). Both Why1 gene sequences had seven exons and six introns, and they had a C-terminal Whirly conserved domain and N-terminal chloroplast transit peptide, which was then verified to be chloroplast localization. Transcriptional expression showed that VpWhy1 was strongly induced by Plasmopara viticola, while VvWhy1 showed a low expression level. Further, the GUS activity indicated pVp had high activity involved in response to Phytophthora capsici infection. In addition, Nicotiana benthamiana transiently expressing pVp::VvWhy1 and pVp::VpWhy1 enhanced the P. capsici resistance. Moreover, Why1, PR1 and PR10 were upregulated in pVp transgenic N. benthamiana leaves. This research presented a novel insight into disease resistance mechanism that pVp promoted the transcription of Why1, which subsequently regulated the expression of PR1 and PR10, further enhancing the resistance to P. capsici.

Temperature drives the assembly of Bacillus community in mangrove ecosystem.

Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO3-N and NH4-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.

Evansella halocellulosilytica sp. nov., an alkali-halotolerant and cellulose-dissolving bacterium isolated from bauxite residue.

An alkali and salt-tolerating strain FJAT-44876T was isolated from the bauxite residue sample. The 16S rRNA gene sequence and phylogenetic analysis suggest that strain FJAT-44876T was a member of the genus Evansella. It grew at 15-45 â„ƒ (optimum 20-25 â„ƒ) and pH 6.5-11.0 (optimum pH 8.0-9.0) with 0-20% (w/v) NaCl (optimum 6-8%). The major fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, iso-C17:0, and C16:0. The cell wall peptidoglycan contained meso-diaminopimelic acid and MK-7 as the menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G+C content was 38.2%. The average nucleotide identity values between strain FJAT-44876T and closely related members were below the cutoff level for species delineation. Thus, based on the above results, strain FJAT-44876T represents a novel species of the genus Evansella, for which the name Evansella halocellulosilytica sp. nov., is proposed. The type strain is FJAT-44876T (=CCTCC AB 2016264T = DSM 104633T).

Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov., isolated from the citrus rhizosphere soil.

Two Gram-staining positive strains, FJAT-49825T and FJAT-50051T were isolated from a citrus rhizosphere soil sample. Strains FJAT-49825T and FJAT-50051T showed the highest 16S rRNA gene sequence similarity with the type strain of Neobacillus cucumis (98.4-98.5%). The 16S rRNA gene sequence similarity between strains FJAT-49825T and FJAT-50051T was 99.8%. Strain FJAT-49825T optimally grew at 35 °C, pH 6.0 in the absence of NaCl while strain FJAT-50051T grew at 40 °C, pH 7.0 and in presence of 2% NaCl (w/v). Both strains contained meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The respiratory quinone of strains FJAT-49825T and FJAT-50051T was MK-7. The polar lipids of strain FJAT-49825T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified lipid whereas strain FJAT-50051T polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid and unidentified lipid. The major fatty acids (> 10%) in both strains were iso-C15:0 and anteiso-C15:0. The genomic DNA G + C content of strains FJAT-49825T and FJAT-50051T were 40.8 and 41.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization value between strains FJAT-49825T and FJAT-50051T and with other members of the genus Neobacillus were lower than the cut-off value (95-96/70%) for interspecies identity. Based on the results, strains FJAT-49825T and FJAT-50051T represent two novel species of the genus Neobacillus, for which the names Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov. are proposed. The type strains are FJAT-49825T (= GDMCC 1.2592T = JCM 34834T) and FJAT-50051T (= GDMCC 1.2593T = JCM 34835T).

Lederbergia citri sp. nov., and Lederbergia citrisecundus sp. nov., isolated from citrus rhizosphere.

Two Gram-positive, rod-shaped, motile, endospore-forming strains, FJAT-49780T and FJAT-49732T were isolated from a citrus rhizosphere soil sample. The optimal growth temperatures for strains FJAT-49780T and FJAT-49732T were 45 and 35-40 °C, respectively. The optimal growth pH for strains FJAT-49732T and FJAT-49780T were pH 8.0 and pH 6.0, respectively. The 16S rRNA gene sequence similarity between FJAT-49780T and FJAT-49732T was 98.6%. Strains FJAT-49780T and FJAT-49732T shared 97.9-98.4% 16S rRNA gene sequence similarities to the type strain of Lederbergia wuyishanensis. In phylogenetic trees (based on 16S rRNA gene sequence), strains FJAT-49732T and FJAT-49780T clade with Lederbergia members. Both strains contained meso-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The major fatty acids of strains FJAT-49732T and FJAT-49780T were anteiso-C15:0 and iso-C15:0. The polar lipids of strain FJAT-49780T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, unidentified phospholipid and unidentified lipids while strain FJAT-49732T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, unidentified aminolipid and unidentified phospholipid. The genomic DNA G+C content of strains FJAT-49780T and FJAT-49732T were 37.0 and 36.7%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between strains FJAT-49780T and FJAT-49732T and with other members of the genus Lederbergia were below the cut-off level for species delineation. Thus, based on the above results, strains FJAT-49780T and FJAT-49732T represent two novel species of the genus Lederbergia, for which the names Lederbergia citri sp. nov., and Lederbergia citrisecundus sp. nov., are proposed. The type strains are FJAT-49780T (= CCTCC AB 2019242T = LMG 31583T) and FJAT-49732T (= CCTCC AB 2019246T = LMG 31584T).

Neobacillus sedimentimangrovi sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment.

Two Gram-stain positive, rod-shaped, endospore-forming, aerobic, thermophilic strains, designated FJAT-2464T and FJAT-52740, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequence similarity between strains FJAT-2464T and FJAT-52740 was 100%. The result suggests that strains FJAT-2464T and FJAT-52740 belong to the same genome species, hence only FJAT-2464T was considered for further analysis. Strain FJAT-2464T showed the highest 16S rRNA gene sequence similarities to the type strains of Neobacillus thermocopriae SgZ-7T (99.9%), Neobacillus cucumis AP-6T (97.6%) and Neobacillus drentensis LMG 21831T (97.5%). Growth was observed at 25-65 °C (optimum 60 °C), pH 7.0-8.0 (optimum 8.0) with NaCl tolerance up to 1.0% (w/v) (optimum without NaCl %). The cell-wall peptidoglycan contained meso-diaminopimelic acid and MK-7 was the only respiratory quinone. The major fatty acids were iso-C15:0 and anteiso-C15:0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid and unidentified lipids. The average nucleotide identity and digital DNA-DNA hybridization values between strain FJAT-2464T and the most closely related strain N. thermocopriae SgZ-7T was below the threshold value for species delineation. Based on the above results, strain FJAT-2464T represents a novel species of the genus Neobacillus, for which the name Neobacillus sedimentimangrovi sp. nov. is proposed. The type strain is FJAT-2464T (= MCCC 1K04406T = KCTC 43264T).

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting.

In this work, agricultural wastes were treated by composting in an ectopic fermentation bed system (EFBS) with a continuous nitrogen addition technique. With decreasing of NH4+-N concentration and increasing of NO3--N concentration were observed, and activities of protease, urease and nitrate reductase changed significantly during the fermentation process. To elucidate the key microbes and their function in nitrogen-transforming, microbial diversity and clusters of orthologous groups (COGs) in composting materials were evaluated using metagenomic technology. Comparing with ammonification, the COGs involved in nitrification and denitrification were predominant in the composts. The correlation heatmap revealed that Streptomyces predominant in ammonification was significantly affected by contents of N, NH4+-N and NO3--N. Meanwhile, ammonia-oxidizing archaea (AOA) had a positive relationship with moisture. The most abundant genera in denitrification had positive relationships with N and NO3--N. The results indicated that EFBS had functionally diverse microbes and COGs for NH3 removal.

Reclassification of Brevibacterium frigoritolerans DSM 8801T as Bacillus frigoritolerans comb. nov. Based on Genome Analysis.

16S rRNA gene sequence analysis showed that the type strain Brevibacterium frigoritolerans DSM 8801T had the highest similarity (99.7%) with the reference strain Bacillus simplex NBRC 15720T, followed by Bacillus muralis DSM 16288T (99.6%), Bacillus butanolivorans DSM 18926T (99.5%), and Bacillus loiseleuriae FJAT-27997T (97.9%). This relationship is confirmed by the phylogenetic analysis indicating that Bre. frigoritolerans DSM 8801T fell in the genus Bacillus group and formed a clade with the closely related Bacillus species. Average nucleotide identity and in silico DNA-DNA hybridization (isDDH) values between strain DSM 8801T and the most closed reference strain Bac. simplex NBRC 15720T were both much lower than species definition threshold values of 95% and 70%, respectively, which indicated strain DSM 8801T should not be affiliated to one of the validly named Bacillus species. The percentage of conserved protein (POCP) values between the strain DSM 8801T and the type strains of the above species were 80.7%, 69.2%, 72.2%, 53.6%, and 50.0%, respectively, higher than the genus definition threshold value of 50%. The main isoprenoid quinone of strain DSM 8801T was MK-7, the main polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidyl ethanolamine (PE), and the major fatty acids were anteiso-C15:0 and iso-C15:0. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, Bre. frigoritolerans DSM 8801T should belong to the genus Bacillus, and be proposed to reclassify as Bacillus frigoritolerans comb. nov., with the type strain DSM 8801T (=ATCC 25097T  = CCUG 43489T  = CIP 67.20T  = JCM 11681T).

Genome-based reclassification of Bacillus okuhidensis as a later heterotypic synonym of Bacillus halodurans.

The present study was carried out to clarify the taxonomic relationship between two closely related Bacillus species, Bacillus okuhidensis Li et al. 2002 and Bacillus halodurans (ex Boyer 1973) Nielsen et al. 1995. The maximum-likelihood tree based on the 16S rRNA gene sequence and the phylogenomic tree based on concatenation of 16 protein-marker genes showed that these species were similar. Average nucleotide identity (ANIm 99.25 %, ANIb 98.2 %) and digital DNA-DNA hybridization values (93.5 %) between B. okuhidensis DSM 13666T and B. halodurans DSM 497T were greater than the threshold values for bacterial species delineation, indicating that they belong to the same species. Therefore, B. okuhidensis Li et al. 2002 should be reclassified as a later heterotypic synonym of B. halodurans (ex Boyer 1973) Nielsen et al. 1995.

Genome-based reclassification of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995.

In the present study, phylogenetic and genome-based comparison was carried out to clarify the taxonomic positions of alkaliphilic Bacillus species, Bacillus plakortidis, Bacillus lehensis, Bacillus oshimensis, Bacillus rhizosphaerae and Bacillus clausii. Phylogenetic trees based on 16S rRNA gene sequences and concatenated protein marker genes were constructed. Average nucleotide identity (ANI) values were calculated to compare genetic relatedness. In phylogenetic trees, B. plakortidis DSM 19153T, B. lehensis DSM 19099T, and B. oshimensis DSM 18940T; B. rhizosphaerae DSM 21911T and B. clausii DSM 8716T clade together. The average nucleotide identity (ANI) values between B. oshimensis DSM 18940T, B. plakortidis DSM 19153T and B. lehensis DSM 19099T ranged from 98.7-98.8%, while the ANI values between B. rhizosphaerae DSM 21911T and B. clausii DSM 8716T were 95.2-95.5%. The ANI values were higher than the recognized threshold value for bacterial species delineation. Based on phylogenetic and genome comparison we propose reclassification of B. plakortidis and B. lehensis as a later heterotypic synonym of B. oshimensis; B. rhizosphaerae as a later heterotypic synonym of B. clausii.

Bacillus xiapuensis sp. nov., isolated from marine sediment.

A rod-shaped, endospore-forming, aerobic bacterium, designated FJAT-46582T, was isolated from a sediment sample of the coastal region in Xiapu County, Fujian Province in China. Growth was observed at 10-30 °C (optimum, 25 °C), in 0-7.0 % NaCl (0 %) and at pH 6.0-11.0 (pH 8.0), respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the isoprenoid quinone was MK-7. The main fatty acids were anteiso-C17 : 0 (26.5 %), anteiso-C15 : 0 (19.6 %), iso-C15 : 0 (14.4 %) and C16 : 0 (10.5 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidyl ethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain FJAT-46582T with the genus Bacillus, and showed the highest sequence similarity to Bacillus thermotolerans SGZ-8T (97.6 %) and Bacillus ectoinformans (97.1 %). The average nucleotide identity and in silico DNA-DNA hybridization values between strain FJAT-46582T and the most closely related species were 72.3 and 22.9 %, respectively, which were much lower than the thresholds commonly used to define species (96 and 70 %, respectively) indicating that it belonged to a different taxon. The DNA G+C content was 44.2 mol%. The phenotypic characters and taxono-genomics study revealed that strain FJAT-46582T represents a novel Bacillus species, for which the name Bacillus xiapuensis sp. nov. is proposed. The type strain is FJAT-46582T (=JCM 33155=CCTCC AB 2017047T).

Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field.

Bacillus sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper is the first report, to our knowledge, to demonstrate the fully sequenced and completely annotated genome of Bacillus sp. FJAT-18017. The genome size is 5,265,521 bp. The average G+C content was 42.42%.

Antifungal Lipopeptides Produced by Bacillus sp. FJAT-14262 Isolated from Rhizosphere Soil of the Medicinal Plant Anoectochilus roxburghii.

This study aimed to develop biocontrol Bacillus and explore bacterial biocontrol substances. According to the blood agar test, strain FJAT-14262 was screened as a biosurfactant-producer. The biosurfactant-producing ability of FJAT-14262 was further confirmed by the oil spreading tests because of its amphipathic character. Furthermore, its fermentation supernatant could decrease the surface tension from 74.1 to 32.7 mN m-1. Fourier transform infrared spectroscopy (FT-IR) analysis indicated that the biosurfactant produced by the strain FJAT-14262 was a kind of lipopeptides. Reverse-phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography-mass spectrometry (LC-MS) analysis demonstrated that this lipopeptide contained surfactin with polar amino acids and hydrophobic fatty acid chains. Moreover, bioinformatic analysis revealed that the nonribosomal peptide synthetases genes srfAA, srfAB, and srfAC were structurally conserved in the FJAT-14262 genome. Importantly, the crude surfactant exhibited strong inhibitory activities against Fusarium oxysporum, suggesting that strain FJAT-14262 could be a potential biological control agent against Fusarium wilt.

Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T.

Here, we report the draft genome sequences of Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T with 5,305,306 bp and 5,667,584 bp, respectively, which will provide useful information for the functional gene mining and application of these two species. The average DNA G+C contents were 38.91% and 40.01%, respectively.

Effects of Brevibacillus brevis FJAT-1501-BPA on growth performance, faecal microflora, faecal enzyme activities and blood parameters of weaned piglets.

A feeding expriment was performed to investigate the effects of dietary supplementation with Brevibacillus brevis FJAT-1501-BPA fermentation on the growth performance, faecal microflora, faecal enzyme activities and blood parameters of weaned piglets. A total of 150 weaned piglets were randomly assigned to different treatments groups, which were fed the same basic diet supplemented with 10, 1, 0.1, 0.01 and 0 % B. brevis FJAT-1501-BPA fermentation. The results showed that a diet supplemented with 10 % B. brevis FJAT-1501-BPA fermentation could significantly increase the final body weight (P < 0.05) and decrease feed to gain ratio, which was 37.1 % lower than that of the control group. The addition of B. brevis FJAT-1501-BPA exhibited a trend of reducing the contents of the Escherichia coli, Lactobacillus and Salmonella compared with the control. During the 35 day experimental period, cellulase and protease activities were significantly increased by the dietary inclusion of the B. brevis FJAT-1501-BPA fermentation (P < 0.05). The cellulase activity for piglets fed diet containing 1 % B. brevis FJAT-1501-BPA fermentation, 21.8 U/g, was highest among the different treatments. The protease activity for piglets fed diet containing 10 % B. brevis FJAT-1501-BPA fermentation, 50.4 U/g, was highest among the different treatments. The amylase and hemicellulase activities for piglets fed diet containing 10 % B. brevis FJAT-1501-BPA fermentation were significantly higher than those on the control diet and other treatments (P < 0.05). Moreover, usage of feed dietary supplementation with B. brevis FJAT-1501-BPA had positive effects on levels of enzymes and minerals in blood. The alkaline phosphatase, alanine aminotransferase, Fe and Mg concentrations for weaned piglets fed diet containing B. brevis FJAT-1501-BPA fermentation were significantly higher than for those on the control diet (P < 0.05). Furthermore, concentration of IgG in serum was higher in weaned piglets fed diet containing 1 % B. brevis FJAT-1501-BPA fermentation compared to other treatments. These results indicated that feeding with B. brevis FJAT-1501-BPA has the potential to improve growth performance, faecal microflora, faecal enzyme activities and blood parameters of weaned piglets.

Draft Genome Sequence of Bacillus mesonae FJAT-13985T (=DSM 25968T) for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.

Bacillus mesonae FJAT-13985(T) is a Gram-positive, spore-forming, and aerobic bacterium. Here, we report the draft genome sequence of B. mesonae FJAT-13985(T) with 5,807,726 bp, which will provide useful information for setting up phylogenomics in the genomic taxonomy of the Bacillus-like bacteria, as well as for the functional gene mining and application of B. mesonae FJAT-13985(T).

Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.

Bacillus simplex DSM 1321 is a Gram-positive, spore-forming, and aerobic bacterium. Here, we report the draft genome sequence of B. simplex DSM 1321, with 6,494,937 bp, which will provide useful information for setting up phylogenomics in genomic taxonomy of the Bacillus-like bacteria as well as for the functional gene mining and application of B. simplex DSM 1321.

Bacillus loiseleuriae sp. nov., isolated from rhizosphere soil from a loiseleuria plant.

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium, designated strain FJAT-27997T, was isolated from the rhizosphere soil of a Loiseleuria plant collected from Sichuan province in China. Growth was observed aerobically between 20 and 35 °C (optimum 30 °C), between 0 and 3.0 % (w/v) NaCl (optimum at 0 %) concentration and pH in the range 6.0-9.0 (optimum at pH 7.0). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was menaquinone MK-7. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and C14 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolate FJAT-27997T was a member of the genus Bacillus and was related most closely to Bacillus simplex DSM 1321T (97.95 % similarity), followed by Bacillushuizhouensis GSS03T (97.9 %). The average nucleotide identity value between strain FJAT-27997T and the most closely related species, B. simplex DSM 1321T, was 71.60 % (JSpecies), less than the previously proposed cut-off value of 96 % for differentiating species within the genus. The in silico DNA-DNA hybridization values between strain FJAT-27997T and its most closely related species were <70 %, again indicating they belong to different taxa. The main fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The novel strain could be differentiated from other known Bacillus species on the basis of several phenotypic characters and fatty acid profiles. This taxononomic/genomic study revealed that strain FJAT-27997T represents a novel Bacillus species, for which the name Bacillus loiseleuriae sp. nov. (type strain FJAT-27997T =CCTCC AB 2015285T=DSM 101776T) is proposed.

Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier.

Bacillus cecembensis PN5(T) is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 4.72-Mb draft genome sequence of B. cecembensis PN5(T), the first genome sequence of this species, which will promote its fundamental research.