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Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052T, HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24–48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10T, Agromyces aureus AR33T, Agromyces salentinus 20-5T, Agromyces allii UMS-62T, Agromyces lapidis CD55T, and Agromyces italicus CD1T. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac-1340T and Agromyces fucosus VKM Ac-1345T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95–96% threshold. Furthermore, the genome of strain HY052T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C15:0 and anteiso-C17:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052T. Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces, named Agromyces laixinhei. The type strain is HY052T (= CGMCC 1.17175T = JCM 33695T). Electronic Supplementary Material Supplementary material is available in the online version of this article at 10.1007/s12275-021-0546-5.

The Passaic River in New Jersey, USA is heavily polluted by chlorodibenzo-p-dioxins (CDDs). Highly chlorinated CDDs are dechlorinated by anaerobic bacteria from these sediments, producing lightly c...

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22T was able to grow at 10–40 °C (optimum 30 °C), pH 5.5–9.0 (optimum 7.0–8.0) and with 0–5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA–DNA hybridization values between strain Q22T and the reference strains were 79.7–88.9% and 22.6–37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids of strain Q22T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22T represents a novel species of the genus Agromyces , for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22T (=MCCC 1K03340T= KCTC 39961T).

A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).

Two aerobic, Gram-stain-positive, catalase-positive, non-motile and rod-shaped bacterial strains, designated MF30-AT and MF845, were isolated from the intestinal contents of plateau pika collected from the Qinghai–Tibet Plateau. Optimal growth of these two strains was observed under aerobic conditions at pH 7.0 and 28 °C. The 16S rRNA gene sequences of the isolates had highest similarities of 98.5 and 98.4 % to Agromyces fucosus , respectively. In the 16S rRNA gene and polygenetic trees, strains MF30-AT and MF845 were clearly distinct from other species. The two strains could not produce acid from arbutin, d-fructose, D-sucrose, glycogen, salicin or starch. Production of β-glucosidase by these strains was negative. The major fatty acids of these strains were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain MF30-AT contained galactose, rhamnose and ribose as cell wall sugars and MK-12 and MK-11 as predominant menaquinones. The major polar lipids in strain MF30-AT were diphosphatidylglycerol, phosphatidylglycerol and a glycolipid, while the peptidoglycan contained alanine, glutamic acid, glycine and 2,4-diaminobutyric acid. The G+C contents of the DNA of strains MF30-AT and MF845 were 69.8 mol% and 69.7 mol%, respectively. The average nucleotide identity and digital DNA–DNA relatedness values of the two strains with all available genomes of the genus Agromyces were far below the respective thresholds of 95 and 70 %, respectively. All genotypic and phenotypic data indicated that strains MF30-AT and MF845 should be classified as novel members of the genus Agromyces , for which the name Agromyces badenianii sp. nov. is proposed. The type strain is MF30-AT (=CGMCC 1.16469T=DSM 106183T).

An actinobacterial strain, designated FW100M-8T, was isolated from a gut sample of larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, South Korea. Cells were Gram-stain-positive, microaerophilic to aerobic, non-spore forming and non-motile. It grew at pH 7.0–9.0 (optimum, pH 8.0), at 15–35 °C (optimum, 28 °C) and 0–3.0 % (w/v) NaCl (optimum, 0 %). According to the 16S rRNA gene analysis, strain FW100M-8T shared the highest sequence similarity with Agromyces mediolanus DSM 20152T (98.4 %), Agromyces ulmi XIL01T (98.3 %), Agromyces indicus NIO-1018T (98.3 %), Agromyces soli MJ21T (98.3 %), and Agromyces arachidis AK-1T (97.9 %). Phylogenetic trees showed that strain FW100M-8T fell into the lineage of the genus Agromyces . The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The menaquinones of strain FW100M-8T were MK-12 (46 %), MK-11 (36 %), MK-10 (14 %) and MK-13 (4 %). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The peptidoglycan type was supposed to be the type B1, comprising d-Ala, d-Glu, Gly and l-A2bu. The G+C content of the genomic DNA is 70.5 mol%. On the basis of the genotypic and phenotypic data, we conclude that strain FW100M-8T represents a novel species of the genus Agromyces , for which the name Agromyces protaetiae sp. nov. is proposed with strain FW100M-8T (=KACC 19308T=NBRC 113048T) as the type strain.

A Gram-positive, aerobic, heterotrophic, non-endospore-forming, rod-shaped and indole-acetic acid-producing strain, designated NEAU-184T, was isolated from marine sand collected in Sanya, PR China, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NEAU-184T should be assigned to the genus Agromyces and formed a distinct branch with its closest neighbour, Agromyces iriomotensis NBRC 106452T (99.1 %). 2,4-Diaminobutyric acid, d-alanine, d-glutamic acid and glycine were detected in cell-wall hydrolysate and glucose, rhamnose and xylose were detected in whole-cell hydrolysate. The polar lipids were found to contain diphosphatidylglycerol, glycolipid, phosphatidylglycerol and two unidentified lipids. The major menaquinone was MK-12 and the minor menaquinones were MK-13 and MK-11. The predominant fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 71.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA–DNA hybridization results and some phenotypic characteristics. Meanwhile, the strain has the ability to produce indole-acetic acid (0.334mg ml−1). Therefore, strain NEAU-184T represents a novel species of the genus Agromyces , for which the name Agromyces mariniharenae sp. nov. is proposed, with strain NEAU-184T (=CGMCC 4.7505T=JCM 32546T) as the type strain.

Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g−1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%–194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.

A Gram-stain-positive, aerobic, heterotrophic, non-spore-forming and rod-shaped strain, designated SJ-23T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) collected from Langfang, Hebei Province, central PR China and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Agromyces . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, glycolipid and three unidentified lipids. The predominant menaquinones detected were MK-12, MK-11 and MK-10. Major fatty acids were identified as anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The 16S rRNA gene sequence analysis showed that strain SJ-23T belongs to the genus Agromyces with high sequence similarities to Agromyces ramosus DSM 43045T (99.2 %), Agromycescerinus subsp. cerinus DSM 8595T (98.8 %) and Agromyces cerinus subsp. nitratus DSM 8596T (98.6 %). Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a separate branch in the genus Agromyces . Furthermore, the combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain SJ-23T could be distinguished from its closest relatives. Therefore, it is proposed that strain SJ-23T represents a novel species of the genus Agromyces , for which the name Agromyces tardus sp. nov. is proposed. The type strain is SJ-23T (=CGMCC 4.7419T=DSM 105049T).

We screened 15 Agromyces strains from the Microbacteriaceae family and 16 Gordonia strains from the Gordoniaceae family to investigate their biocatalytic ability to reduce carbonyl compounds. Two Agromyces strains (A. soli NBRC109063 and A. humatus NBRC109085) and two Gordonia strains (G. hydrophobica NBRC16057 and G. malaquae NBRC108250) grew well in 230 medium. The stereoselective reduction of various carbonyl compounds using these four strains was investigated. We discovered that these strains can reduce aliphatic and aromatic α-keto esters and an aromatic α-keto amide. On the basis of the conversion rate and stereoselectivity of the alcohols produced, G. hydrophobica NBRC16057 is a potential biocatalyst for the stereoselective reduction of α-keto esters and an aromatic α-keto amide to the corresponding chiral alcohols. Our results also suggest that the reduction of ethyl 2-methylacetoacetate by wet G. hydrophobica NBRC16057 cells in the presence of L-glutamate is useful for the production of chiral ethyl 3-hydroxy-2-methylbutanoate.

Two bacterial strains, FWR-8T and CFWR-9T, were isolated from the gut of larvae of Protaetia brevitarsis seulensis that were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Both strains were strictly aerobic, Gram-stain-positive and non-motile. Strain FWR-8T possessed the highest sequence similarity (98.7 %) to that of Protaetiibacter intestinalis 2DFWR-13T and the phylogenetic tree revealed that strain FWR-8T formed a cluster with Ptb. intestinalis 2DFWR-13T. Pseudolysinimonas kribbensis MSL-13T and Lysinimonas yzui N7XX-4T shared a high 16S rRNA gene sequence similarity (97.8 %) and formed a cluster adjacent to the cluster that included Ptb. intestinalis 2DFWR-13T. The 16S rRNA gene sequence of strain CFWR-9T exhibited the highest similarity (97.7 %) to that of Agromyces binzhouensis OAct353T and the phylogenetic tree indicated that strain CFWR-9T formed one independent cluster with A. binzhouensis OAct353T that was within the radius of the genus Agromyces . The peptidoglycan type, major fatty acids, major menaquinones and total polar lipids of strain FWR-8T were characterized as type B1, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, MK-15, MK-16 and MK-14, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Those from strain CFWR-9T were type B1, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, MK-11, MK-12 and MK-10, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Based on the phenotypic and genotypic data, strains FWR-8T and CFWR-9T each represent a novel species within the genera Protaetiibacter and Agromyces , respectively. For these species, the names Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov. have been proposed, with the type strains FWR-8T (=KACC 19322T=NBRC 113051T) and CFWR-9T (=KACC 19306T=NBRC 113046T), respectively. Our results also justify a reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and an emended description of the genus Pseudolysinimonas isprovided.

Soil ecosystem perturbation due to agronomic practices can negatively impact soil productivity by altering the diversity and function of soil health determinants. Currently, the influence of rice cultivation and off-season periods on the dynamics of soil health determinants is unclear. Therefore, soil enzyme activities (EAs) and bacterial community compositions in rice-cultivated fields at postharvest (PH) and after a 5-month off-season period (5mR), and fallow-fields (5-years-fallow, 5YF, 10-years-fallow, 10YF and/or one-year-fallow, 1YF) were assessed in two agroecological regions of Mozambique. EAs were mostly higher in fallow fields than in PH, with significant (p &lt, 0.05) differences detected for β-glucosidase and acid phosphatase activities. Only β-glucosidase activity was significantly (p &lt, 0.05) different between PH and 5mR, suggesting that β-glucosidase is responsive in the short-term. Bacterial diversity was highest in rice-cultivated soil and correlated with NO3−, NH4+ and electrical conductivity. Differentially abundant genera, such as Agromyces, Bacillus, Desulfuromonas, Gaiella, Lysobacter, Micromonospora, Norcadiodes, Rubrobacter, Solirubrobacter and Sphingomonas were mostly associated with fallow and 5mR fields, suggesting either negative effects of rice cultivation or the fallow period aided their recovery. Overall, rice cultivation and chemical parameters influenced certain EAs and shaped bacterial communities. Furthermore, the 5-month off-season period facilitates nutrient recovery and proliferation of plant-growth-promoting bacteria.

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the acdS gene. We stated the hypothesis that the relative phylogenetic distribution of acdS carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective rth3 mutant in the substrates loam and sand, and harvest was implemented from three depths. Most acdS sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. Variovorax, Acidovorax, and Ralstonia sequences dominated in loam, whereas Streptomyces and Agromyces were more abundant in sand. Soil depth caused strong variations in acdS sequence distribution, with differential levels in the relative abundances of acdS sequences affiliated to Tetrasphaera, Amycolatopsis, and Streptomyces in loam, but Burkholderia, Paraburkholderia, and Variovorax in sand. Maize genotype influenced the distribution of acdS sequences mainly in loam and only in the uppermost depth. Variovorax acdS sequences were more abundant in WT, but Streptomyces, Microbacterium, and Modestobacter in rth3 rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of acdS carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere acdS carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on acdS carrying bacterial populations.

Maize forms the basis of Mexican food. As a result, approximately six million tons of corncob are produced each year, which represents an environmental issue, as well as a potential feedstock for biogas production. This research aimed to analyze the taxonomic and functional shift in the microbiome of the fermenters using a whole metagenome shotgun approach. Two strategies were used to understand the microbial community at the beginning and the end of anaerobic digestion: (i) phylogenetic analysis to infer the presence and coverage of clade-specific markers to assign taxonomy and (ii) the recovery of the individual genomes from the samples using the binning of the assembled scaffolds. The results showed that anaerobic digestion brought some noticeable changes and the main microbial community was composed of Corynebacterium variable, Desulfovibrio desulfuricans, Vibrio furnissii, Shewanella spp., Actinoplanes spp., Pseudoxanthomonas spp., Saccharomonospora azurea, Agromyces spp., Serinicoccus spp., Cellulomonas spp., Pseudonocardia spp., Rhodococcus rhodochrous, Sphingobacterium spp. Methanosarcina mazei, Methanoculleus hydrogenitrophicus, Methanosphaerula spp., Methanoregula spp., Methanosaeta spp. and Methanospirillum spp. This study provides evidence of the drastic change in the microbial community structure in a short time and the functional strategy that the most representative microorganisms of the consortia used to carry out the process.

Transgenic Bacillus thuringiensis (Bt) rice extends significant protection against insect pests and meets the increasing demands for food and energy. Many studies have been conducted investigating the impacts of Bt rice to the agricultural ecosystem, but much less attention has been given to efforts attempting to determine how the presence of Bt rice influences and shapes the microbial community, especially the active microbes. Stable isotope probing and high-throughput sequencing were employed to explore the active microbes involved in Bt-containing straw decomposition. Compared to its near isoline, the Bt straw contained higher contents of total N, total P, total K, lignin, cellulose, and Cry1Ab toxin protein. These chemical differences did not affect the decomposition rate but significantly changed the active microbial decomposer communities. During the decomposition of Bt-containing straw, fungi were more affected than bacteria. Agromyces, Terrabacter, Microbacterium, Glycomyces, and Kribbella were the most representative unique (existed only in the Bt treatments and appeared at the early stage) bacterial genera, and Trichoderma was the most representative unique fungal genus in the Bt straw decomposition. By using similarity index calculation and function prediction, the significant differences between Bt straw and non-Bt straw treatments were found to be transient for both microbial taxa and functional traits. These results suggested that Bt rice has a significant but transient impact on soil microbes in terms of microbial straw decomposition.

Tioman Island is one of many sources for underexplored actinobacterial diversity in Malaysia. Selective isolation, molecular profiling, 16S rRNA gene sequencing and phylogenetic analyses were carried out to highlight the diversity of the marine actinobacterial community in a sediment collected off Tioman Island. A high number of diverse actinobacteria were recovered using skim milk/HEPES pre-treatment on a mannitol-based medium. A total of 123 actinobacterial strains were isolated, including thirty obligate marine actinobacteria putatively identified as Salinispora spp. Molecular fingerprinting profiles obtained with a double digestion approach grouped the remaining non-Salinispora-like strains into 24 different clusters, with Streptomyces and Blastococcus as the major clusters. A total of 17 strains were identified as novel actinobacterial species within the genera Streptomyces (n = 6), Blastococcus (n = 5), Marinactinospora (n = 3), Nocardiopsis (n = 1), Agromyces (n = 1) and Nonomuraea (n = 1) based on 16S rRNA gene sequence analyses. Polyphasic data from three putative Marinactinospora spp. showed that the strains represent a new genus in the Nocardiopsaceae family. Crude extracts from the strains were also found to inhibit the growth of Gram-positive (Staphylococcus aureus, Bacillus subtilis) and Gram-negative (Providencia alcalifaciens) pathogens. Hierarchical clustering of the bioactivities of an active fraction revealed a unique profile, which is closely related that of fosfomycin.

Mangrove is a rich and underexploited ecosystem with great microbial diversity for discovery of novel and chemically diverse antimicrobial compounds. The goal of the study was to explore the pharmaceutical actinobacterial resources from mangrove soil and gain insight into the diversity and novelty of cultivable actinobacteria. Consequently, 10 mangrove soil samples were collected from Futian and Maoweihai of China, and the culture-dependent method was employed to obtain actinobacteria. A total of 539 cultivable actinobacteria were isolated and distributed in 39 genera affiliated to 18 families of 8 orders by comparison analysis of partial 16S rRNA gene sequences. The dominant genus wasStreptomyces(16.0 %), followed byMicrobacterium(14.5 %),Agromyces(14.3 %), andRhodococcus(11.9 %). Other 35 rare actinobacterial genera accounted for minor proportions. Notably, 11 strains showed relatively low 16S rRNA gene sequence similarities (< 98.65 %) with validly described species. Based on genotypic analyses and phenotypic characteristics, 115 out of the 539 actinobacterial strains were chosen as representative strains to test their antibacterial activities against “ESKAPE” bacteria by agar well diffusion method and antibacterial mechanism by the double fluorescent protein reporter system. Fifty-four strains in 23 genera, including 2 potential new species, displayed antagonistic activity in antibacterial assay. Meanwhile, 5 strains in 3 genera exhibited inhibitory activity on protein biosynthesis due to ribosome stalling. These results demonstrate that cultivable actinobacteria from mangrove soil are potentially rich sources for discovery of new antibacterial metabolites and new actinobacterial taxa.

Description of Agromyces salentinus 17J49-8 Cells are Gram-stain-positive, non-flagellated, and rod shaped. Colonies are circular, convex, smooth, and pale-yellow colored after 4 days on R2 A at 25° C. Nitrate is reduced and esculin is hydrolyzed. The strain shows positive reactions for enzyme activities of urease, arginine dihydrolase, and β -galactosidase, whereas the strain shows negative reaction for enzyme activity of gelatinase. Indole is not produced and glucose is not fermented. The strain utilizes D-glucose, L-arabinose, D-mannose, D-mannitol, N -acetyl-glucosamine, D-maltose, potassium gluconate, malic acid, and trisodium citrate, whereas the strain does not utilize adipic acid, capric acid, and phenylacetic acid. Strain 17J49-8 (= NIBRBAC000501344) was isolated from a soil sample, Jeju, Korea., Published as part of Kim, Mi-Sun, Jeong, Seong-Hwa, Kang, Joo-Won, Kim, Seung-Bum, Cho, Jang-Cheon, Cha, Chang-Jun, Im, Wan-Taek, Bae, Jin-Woo, Lee, Soon-Dong, Kim, Won-Yong, Kim, Myung-Kyum & Seong, Chi-Nam, 2019, Unrecorded prokaryotic species belonging to the class Actinobacteria in Korea, pp. 97-108 in Journal of Species Research 8 (1) on page 104, DOI: 10.12651/JSR.2019.8.1.097, http://zenodo.org/record/8120476

Description of Agromyces ulmi 17J49-11 Cells are Gram-stain-positive, non-flagellated, and rod shaped. Colonies are circular, convex, smooth, and yellow colored after 4 days on R2 A at 25° C. Nitrate is reduced and esculin is hydrolyzed. The strain shows positive reactions for enzyme activities of urease and β -galactosidase, whereas the strain shows negative reactions for enzyme activities of arginine dihydrolase and gelatinase. Indole is not produced and glucose is not fermented. The strain utilizes D-glucose, L-arabinose, D-mannose, D-mannitol, N -acetyl-glucosamine, D-maltose, potassium gluconate, adipic acid, malic acid, and trisodium citrate, whereas the strain does not utilize capric acid and phenylacetic acid. Strain 17J49-11 (= NIBRBAC000501345) was isolated from a soil sample, Jeju, Korea., Published as part of Kim, Mi-Sun, Jeong, Seong-Hwa, Kang, Joo-Won, Kim, Seung-Bum, Cho, Jang-Cheon, Cha, Chang-Jun, Im, Wan-Taek, Bae, Jin-Woo, Lee, Soon-Dong, Kim, Won-Yong, Kim, Myung-Kyum & Seong, Chi-Nam, 2019, Unrecorded prokaryotic species belonging to the class Actinobacteria in Korea, pp. 97-108 in Journal of Species Research 8 (1) on page 104, DOI: 10.12651/JSR.2019.8.1.097, http://zenodo.org/record/8120476

Dimethylamine (DMA) possesses an obnoxious odor which has resulted in public concern during the past several decades. A rare bacterial species proficient to degrade DMA, designated IR-26, was isolated from Indian Oil Corporation Limited (IOCL) and identified as Agromyces and Ochrobactrum sp., which has presented a rapid degradation when compared to other bacterial species which were capable to degrade DMA. The removal efficiency of 100% has been calculated in different concentration of DMA. The kinetic study reveals the maximum reduction rate of DMA was 0.11 per hour and the maximum growth rate of biomass was 0.013 per hour respectively. The saturation constant of DMA was around 1.96 mg/L which shows a high affinity of DMA. The importance of these analyses is offered and conversed in this paper.

Aquest projecte d'investigació estudia els processos de fitoremediació per a sòls contaminats amb cadmi, específicament la fitoextracció, on una espècie vegetal metalofita hiperacumula el metall objectiu. El disseny experimental es basa en Arabidopsis halleri, registrada com a la més alta hiperacumuladora per a cadmi, amb l'objectiu de determinar els mecanismes d'absorció i compartimentalització en solució hidropònica i comprovar la viabilitat de les seves capacitats de fitoextracció en sòls contaminats amb cadmi. també pretén validar les hipotètiques propietats de millora dels gèneres bacterians Streptomyces i Agromyces sobre els processos de fitoextracció d'Arabidopsis halleri. Este proyecto de investigación estudia los procesos de fitoremediación para suelos contaminados con cadmio, específicamente la fitoextracción, donde una especie vegetal metalofita hiperacumula el metal objetivo. El diseño experimental se basa en Arabidopsis halleri, registrada como la más alta hiperacumuladora para cadmio, con el objetivo de determinar los mecanismos de absorción y compartimentalización en solución hidropónica y comprobar la viabilidad de sus capacidades de fitoextracción en suelos contaminados con cadmio. También pretende validar las hipotéticas propiedades de mejora de los géneros bacterianos Streptomyces y Agromyces sobre los procesos de fitoextracción de Arabidopsis halleri. This research project studies phytoremediation processes for cadmium contaminated soils, specifically phytoextraction, where a metal-tolerant plant species hyperaccumulate the target metal. The experimental design is based on Arabidopsis halleri, recorded as the highest hyperaccumulator in cadmium, with the objective of determining absorption and compartmentalization mechanisms in hydroponic solution and test the viability of its phytoextraction capabilities in cadmium contaminated soils. Also aims to validate the hypothesized enhancing properties of Streptomyces and Agromyces bacteria genera over the phytoextraction process for Arabidopsis halleri.

A screening system using enrichment culture has been established with the aim of obtaining a novel enzyme for protein modification that has not been previously reported. This enzyme catalyzes deamidation of the side-chain amide group of asparagine in proteins. Enrichment culture of 390 soil samples was carried out with Z-Asn-Gly as the sole source of nitrogen, and the reaction product, Z-Asp-Gly, was detected in the culture supernatant of 102 strains. Strains with particularly high activity were Leifsonia sp., Luteimicrobium sp., Microbacterium sp., and Agromyces sp., all belonging to the class Actinobacteria. Of these, a protein-asparaginase (PA) was obtained from the culture supernatant of Luteimicrobium album 333B-h1, and its reactivity with different substrates and its basic enzymatic characteristics were investigated. Addition of the enzyme solution resulted in specific deamidation of only the asparagine residue in insulin chain B. The enzyme showed no reactivity with free asparagine or asparagine in low molecular weight peptides. It was demonstrated that the enzyme reacts with various protein substrates. In particular, proteins that have open structures, such as casein or gelatin, were good substrates. The activity and stability of PA at different temperatures and pH values were investigated. It was found that a temperature of 37°C and a roughly neutral pH are optimal conditions for the enzyme.

Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave “Grotte des Collemboles”. From the “tips and tricks” that were tested, separate autoclaving of the components of the International Streptomyces Project (ISP) medium number 5 (ISP5) medium, prolonged incubation time, and dilution of the moonmilk suspension were found to most effectively improve colony forming units. Taxonomic analyses of the 40 isolates revealed new representatives of the Agromyces, Amycolatopsis, Kocuria, Micrococcus, Micromonospora, Nocardia, and Rhodococcus species, as well as additional new streptomycetes. The applied methodologies allowed the isolation of strains associated with both the least and most abundant moonmilk-dwelling actinobacterial operational taxonomic units. Finally, bioactivity screenings revealed that some isolates displayed high antibacterial activities, and genome mining uncovered a strong potential for the production of natural compounds.

A novel actinobacterium, designated HIr16-25T, was isolated from the rhizosphere soil of a mangrove growing on Iriomote Island in Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HIr16-25T fell within the cluster of the members of the genus Agromyces and the highest sequence similarity value was observed with Agromyces rhizospherae IFO 16236T (98.6%). Strain HIr16-25T possessed l-2,4-diaminobutyric acid as a diagnostic diamino acid of the peptidoglycan, and MK-12 and MK-11 as the predominant menaquinones. The major fatty acids were identified as iso-C16:0, anteiso-C15:0 and anteiso-C17:0 and the principal polar lipids were phosphatidylglycerol and one glycolipid. These chemotaxonomic features matched well those described for the members of the genus Agromyces. Meanwhile, the result of DNA–DNA hybridization and the presence of differential phenotypic characteristics between strain HIr16-25T and the type strain of A. rhizospherae indicated that strain HIr16-25T be classified as a novel species of the genus Agromyces. Therefore, we propose strain HIr16-25T to represent a novel species of the genus Agromyces, with the name Agromyces mangrovi sp. nov. The type strain is HIr16-25T (= NBRC 112812T = TBRC 7760T).

Bacterial community and diversity in a long-term petroleum-contaminated soil of an oilfield were characterized using 16S rRNA gene-based Illumina MiSeq high-throughput sequencing. Results indicated that Proteobacteria (49.11%) and Actinobacteria (24.24%) were the most dominant phyla, and the most abundant genera were Pseudoxanthomonas (8.47%), Luteimonas (3.64%), Alkanindiges (9.76%), Acinetobacter (5.26%) and Agromyces (8.56%) in the soil. Meanwhile a series of cultivations were carried out for isolation of alkane degraders from petroleum-contaminated soil with gellan gum and agar as gelling agents. And the isolates were classified by their 16S rRNA genes. Nine of the isolates including Enterobacter, Pseudomonas,Acinetobacter, Rhizobium, Bacillus, Sphingomonas, Paenibacillus, Variovorax and Rhodococcus showed strong biodegradability of alkane mixture (C9-C30) in a wide range of chain-length, which could be potentially applied in enhancement of bioremediation.

The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction.

The high demand for new antibacterials fosters the isolation of new biologically active compounds producing actinobacteria. Here, we report the isolation and initial characterization of cultured actinobacteria from dominant benthic organisms' communities of Lake Baikal. Twenty-five distinct strains were obtained from 5 species of Baikal endemic macroinvertebrates of amphipods, freshwater sponges, turbellaria worms, and insects (caddisfly larvae). The 16S ribosomal RNA (rRNA)-based phylogenic analysis of obtained strains showed their affiliation to Streptomyces, Nocardia, Pseudonocardia, Micromonospora, Aeromicrobium, and Agromyces genera, revealing the diversity of actinobacteria associated with the benthic organisms of Lake Baikal. The biological activity assays showed that 24 out of 25 strains are producing compounds active against at least one of the test cultures used, including Gram-negative bacteria and Candida albicans. Complete dereplication of secondary metabolite profiles of two isolated strains led to identification of only few known compounds, while the majority of detected metabolites are not listed in existing antibiotic databases.

The nephridia (excretory organs) of lumbricid earthworms generally harbor symbiotic bacteria. In the compost worms Eisenia fetida and E. andrei, these comprise Verminephrobacter, Ca. Nephrothrix and an Agromyces-like symbiont. While diversity, transmission, and function of the first two symbionts has been unraveled in recent years, little is known about the biology of the uncultured Agromyces-like symbiont or about its distribution within lumbricid earthworms. In this study, we sequenced a cocoon metagenome of E. andrei and assembled a 96.3% complete genome of the Agromyces-like symbiont, which indicates a heterotrophic and potentially microaerophilic lifestyle. A 16S rRNA gene based survey showed that the Agromyces-like symbiont has a narrow host range (present in 10 out of 51 investigated lumbricid earthworm species) and is likely species-specific or at least specific for groups of closely related host species. The Agromyces-like symbionts form a monophyletic group and feature a reduced genome with AT-bias and very low genome-wide similarity to closely related Agromyces spp. (average amino acid identity of 64%); therefore, we suggest establishing a novel genus for the Agromyces-like symbionts of earthworms, for which we propose the name Candidatus Lumbricidophila, with the specific symbiont of Eisenia andrei as novel species Ca. L. eiseniae.

A novel, Gram-stain-positive, microaerophilic to aerobic, non-endospore-forming, no-motile and rod-shaped bacterium designated Q14T was isolated from mangrove soil samples collected on chengmai, Hainan province, China. Strain Q14T was able to grow at 10–40 °C (optimum 30 °C), pH 5.5–10.0 (optimum 6.5-8.0) and with 0.5–6% (w/v) NaCl (optimum 1%). The genomic DNA G+C content was 70.1%. The chemotaxonomic analysis showed that the predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C17:0 and anteiso-C17:0. The major polar lipids of strain Q14T were diphosphatidylglycerol, phosphatidylglycerol and one glycolipid. The strain Q14T contained 2,4-diaminobutylic acid (A2bu), alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and DNA–DNA hybridization, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q14T as a novel species of the genus Agromyces, for which the name Agromyces mangrovi sp. nov. is proposed. The type strain is Q14T (= MCCC 1K03191T = KCTC 39814T).

The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples.

The links between microbial taxa, in situ organic matter decomposition, and coupling of carbon (C) and nitrogen (N) cycles remain unresolved. Here, we used stable isotope probing (SIP) technique to investigate bacterial carbon assimilation and C and N coupling during decomposition of 13C-labeled maize residue in a black soil from Northeast China. Bacteria assimilating carbon from maize residue (16S rRNA analysis) were primarily distributed in the Phyla Actinobacteria, Firmicutes and Proteobacteria. These include the recognized stubble decomposing lineages of Arthrobacter, Streptomyces, Bacillus and Rhizobium, but also lineages not previously reported (Agromyces, Blastococcus, Gemmatimonas, Glycomyces, Heliobacillus, Lysobacter, Microlunatus, Mycoplasma, Natronocella, Ohtaekwangia, Paenibacillus, Schlegelella, Sorangium, Steroidobacter and Thermacetogenium). Analysis of nitrogen fixation (nifH) and denitrification (nirS) genes in heavy-fraction DNA was used to link microbial taxa involved in N cycling to C transformation of the maize residue. A cluster of nifH genotypes affiliated with Rhizobium and two other ‘uncultured’ clusters dominated the N-fixing clone library, and genotypes affiliated with Kocuria varians and an uncultured cluster dominated the library of nitrite reducing (nirS) taxa. The results suggest that plant residue decomposition may stimulate both N-fixation and denitrification through direct C-feeding of related microbes in soil.

Studies of nitrogen-fixing properties among the Gram-positive Actinobacteria revealed that some species of Arthrobacter, Agromyces, Corynebacterium, Mycobacterium, Micromonospora, Propionibacteria and Streptomyces have nitrogen-fixing capacity. This is also valid for Frankia that fix nitrogen both in free-living and in symbiotic conditions. Frankia symbiosis results from interaction between the Frankia bacteria and dicotyledonous plants, that is, actinorhiza. These plants, which are important in forestry and agroforestry, form, together with the legumes (Fabales), a single nitrogen-fixing clade. It has been shown that a receptor-like kinase gene, SymRK, is necessary for nodulation in actinorhizal plants as well as in legumes and arbuscular mycorrhizal fungi. Recently, the involvement of isoflavonoids as signal molecules during nodulation of an actinorhizal plant was shown. The genome sizes of three Frankia species, Frankia EANpec, ACN14a and CcI3, are different, revealing a relationship between genome size and geographical distribution. Recent genomic sequencing data of Frankia represent genomes from cluster I to IV, indicating that the genome of DgI is one of the smallest genomes in Frankia. In addition, nonsymbiotic Frankiales such as Acidothermus cellulolyticus, Blastococcus saxoobsidens, Geodermatophilus obscurus and Modestobacter marinus have a variety of genome sizes ranging from 2.4 to 5.57 Mb.

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

A Gram-reaction-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33T, was isolated from the rhizosphere of Salix caprea L. growing in a former zinc/lead mining and processing site in Austria. A polyphasic approach was applied to determine its taxonomic position. 16S rRNA gene sequence analysis, and morphological and chemotaxonomic properties showed that strain AR33T belongs to the genus Agromyces. Strain AR33T had peptidoglycan type B2γ and the major menaquinones were MK-11, MK-10 and MK-12. The main branched-chain fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain AR33T showed catalase and oxidase activity and multiple heavy metal resistances to zinc, lead and cadmium. The DNA G+C content was 70.1 mol%. Levels of 16S rRNA gene sequence similarity with closely related recognized species of the genus Agromyces ranged between 98 and 99 %. However, DNA-DNA hybridization between strain AR33T and the type strains of three Agromyces species showed values lower than 42 % relatedness. Therefore, differential phenotypic characteristics together with DNA-DNA relatedness suggested that strain AR33T can be recognized as representing a distinct Agromyces species, for which the name Agromyces aureus sp. nov. is proposed. The type strain is AR33T (=DSM 101731T=LMG 29235T).

A Gram-stain-positive, heterotrophic, non-spore-forming, rod-shaped strain, designated OAct353T, belonging to the genus Agromyces was isolated from a soil sample collected from a coastal wetland of the Yellow River delta, PR China. The strain was identified using a polyphasic taxonomic approach. The strain grew in the presence of 0-10 % (w/v) NaCl (optimum 2-3 %), at pH 5.0-8.0 (optimum pH 7.0) and 12-36 °C (optimum 28 °C). The isolate contained 2,4-diaminobutyric acid, glutamic acid and glycine in its peptidoglycan. The acyl type of the cell-wall muramic acid was N-acetyl. The whole-cell sugars of this novel strain were glucose, xylose and rhamnose. The predominant menaquinones were MK-12 (74 %) and MK-11 (21 %). The major phospholipids were phosphatidylglycerol, one unknown phospholipid, three unknown glycolipids and three unknown polar lipids. The major fatty acids were iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 69.6 mol %. DNA-DNA relatedness clearly separated strain OAct353T from its closest relatives. On the basis of phenotypic, phylogenetic and chemotaxonomic data, a novel species, Agromyces binzhouensis sp. nov., is proposed. The type strain is OAct353T (=CGMCC4.7180T=DSM 28305T=NRRL B-59115T).

A newly isolated strain Agromyces sp. MT-O could utilize various phthalates and efficiently degraded di-(2-ethylhexyl) phthalate (DEHP). Response surface methodology was successfully employed for the optimization of culture conditions including pH (7.2), temperature (29.6), and inoculum size (OD600 of 0.2), resulting in almost complete degradation of DEHP (200 mg L− 1) within 7 days. At different initial concentrations (50–1000 mg L− 1), DEHP degradation curves were fitted well with the first-order kinetic model, and the half-life of DEHP degradation ranged from 0.83 to 2.92 days. Meanwhile, the substrate inhibition model was used to describe the special degradation rate with qmax, Ks, and Ki of 0.6298 day− 1, 86.78 mg L− 1, and 714.3 mg L− 1, respectively. The GC–MS analysis indicated that DEHP was degraded into mono-ethylhexyl phthalate and phthalate acid before its complete mineralization. Bioaugmentation of DEHP-contaminated soils with strain MT-O has greatly enhanced DEHP disappearance rate in soils, providing great potential for efficiently remediating DEHP-contaminated environment.

A Gram-positive, aerobic to microaerophilic, non-motile bacterial strain, designated MJ21T, was isolated from farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain MJ21T was placed within the genus Agromyces, and exhibited relatively high levels of similarity to Agromyces ulmi XIL01T (97.8 %), Agromyces aurantiacus YIM 21741T (97.1 %), Agromyces mediolanus JCM 3346T (96.7 %), A. mediolanus JCM 1376 (99.1 %), A. mediolanus JCM 9632 (99.1 %), A. mediolanus JCM 9633 (98.9 %) and A. mediolanus JCM 9631 (96.5 %). Chemotaxonomic data also supported the classification of strain MJ21T within the genus Agromyces. The new isolate contained MK-12 as the predominant menaquinone and rhamnose, galactose and xylose as cell-wall sugars. The major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Cell-wall amino acids were 2,4-diaminobutyric acid, glutamic acid, glycine and alanine. Diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and one unidentified phospholipid were detected as polar lipids. The DNA G+C content of strain MJ21T was 73.4 mol%. However, levels of DNA–DNA relatedness between strain MJ21T and the seven phylogenetically closest Agromyces strains ranged from 14 to 56 %, showing clearly that the new isolate represents a novel genomic species. Strain MJ21T could be differentiated clearly from its phylogenetic neighbours on the basis of phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ21T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces soli sp. nov. is proposed. The type strain is MJ21T ( = KCTC 19549T = JCM 16247T).

Cyhalofop-butyl (CyB) is a widely used aryloxyphenoxy propanoate (AOPP) herbicide for control of grasses in rice fields. Five CyB-degrading strains were isolated from rice field soil and identified as Agromyces sp., Stenotrophomonas sp., Aquamicrobium sp., Microbacterium sp., and Pseudomonas azotoformans; the results revealed high biodiversity of CyB-degrading bacteria in rice soil. One strain, P. azotoformans QDZ-1, degraded 84.5% of 100 mg L(-1) CyB in 5 days of incubation in a flask and utilized CyB as carbon source for growth. Strain QDZ-1 could also degrade a wide range of other AOPP herbicides. An esterase gene, chbH, which hydrolyzes CyB to cyhalofop acid (CyA), was cloned from strain QDZ-1 and functionally expressed. A chbH-disrupted mutant dchbH was constructed by insertion mutation. Mutant dchbH could not degrade and utilize CyB, suggesting that chbH was the only esterase gene responsible for CyB degradation in strain QDZ-1. ChbH hydrolyzed all AOPP herbicides tested as well as permethrin. The catalytic efficiency of ChbH toward different AOPP herbicides followed the order quizalofop-P-ethyl ≈ fenoxaprop-P-ethyl > CyB ≈ fluazifop-P-butyl > diclofop-methyl ≈ haloxyfop-P-methyl; the results indicated that the chain length of the alcohol moiety strongly affected the biodegradability of the AOPP herbicides, whereas the substitutions in the aromatic ring had only a slight influence.

Endophytic actinobacteria from medicinal plant may play a significant role in producing bioactive compounds. The information regarding their diversity is an important. Rhododendron are traditionally used for treating human disorders. One of the selected Rhododendron used in this study was R. zoelleri from Papua origin, which has been conserved and grown in Cibodas Botanical Garden, West Java, Indonesia. The aim of this study was to assess the existence of endophytic actinobacteria from R. zoelleri based on a culture-dependent and their community structure based on a culture-independent approach. Culturable actinobacteria were isolated and cultured on HV medium. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) targeting the metagenomic 16S rRNA was used to analyse the structure of the actinobacterial community. Six culturable endophytic actinobacteria (200 cfu/g fresh weight) from R. zoelleri were successfully isolated, three isolates from leaf, and the other isolates were obtained from stem. The six culturable isolates were RZP 1.3, RZP 1.1, RZP 2.2, RZPB 1.1, RZPB 7.1, RZPB 4.1. Based on their morphological characteristics, the endophytes have Streptomyces characters. The existence of Streptomyces spp. were also confirmed with molecular analysis based on 16S rRNA gene. The phylogenetic analysis based on 16S rRNA gene to the reference strains available in EzTaxon-e database showed that six isolates were closely related to S. djakartensis strains of NBRC 15409ᵀ(99.19%), S. tritolerans strains of DAS 165T(99.90%), S. coelicoflavus strains of NBRC 15399T(99.59). However, they showed differences in morphological characteristics as compared with the reference strains. The metagenomic analysis of the DGGE profile based on 16S rRNA gene showed the community structure of endophytic actinobacteria from R. zoelleri which was represented by 13 DGGE bands. The bands were closely related to Agromyces, Gordonia, Microbacterium, Micromonospora, Propionibacterium, Saccharomonospora, Streptomyces which have 93.18%-100% similarity. Based on the data, it showed diversity of endophytic actinobacteria from R. zoelleri which may be further assess for their novelty and bioprospecting.

A Gram-positive, non-motile, cream-coloured, curved or straight rod-shaped bacterial strain, DS-10(T), was isolated from soil of Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-10(T) grew optimally at 25 degrees C and pH 7.0-8.0 in the presence of 0.5-1.0 % (w/v) NaCl. Strain DS-10(T) had peptidoglycan type B2gamma [d-Glu-d-Dab (diaminobutyric acid)] and galactose and ribose as whole-cell sugars. Strain DS-10(T) contained MK-11, MK-12 and MK-10 as predominant menaquinones. Major cellular fatty acids (>10 % of total) were anteiso-C(15 : 0), anteiso-C(17 : 0), iso-C(16 : 0) and iso-C(15 : 0). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C content was 71.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-10(T) belonged to the genus Agromyces. Similarity values between the 16S rRNA gene sequence of strain DS-10(T) and those of the type strains of recognized Agromyces species ranged from 95.8 to 99.3 %. DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-10(T) could be differentiated from recognized Agromyces species. On the basis of the data presented, strain DS-10(T) is considered to represent a novel species of the genus Agromyces, for which the name Agromyces terreus sp. nov. is proposed. The type strain is DS-10(T) (=KCTC 19216(T) =JCM 14581(T)).

A variety of plants growing on metalliferous soils accumulate metals in their harvestable parts and have the potential to be used for phytoremediation of heavy metal polluted land. There is increasing evidence that rhizosphere bacteria contribute to the metal extraction process, but the mechanisms of this plant–microbe interaction are not yet understood. In this study ten rhizosphere isolates obtained from heavy metal accumulating willows affiliating with Pseudomonas, Janthinobacterium, Serratia, Flavobacterium, Streptomyces and Agromyces were analysed for their effect on plant growth, Zn and Cd uptake. In plate assays Zn, Cd and Pb resistances and the ability of the bacteria to produce indole-3-acetic acid (IAA), 1-amino-cyclopropane-1-carboxylic acid deaminase (ACC deaminase) and siderophores were determined. The isolates showed resistance to high Zn concentrations, indicating an adaptation to high concentrations of mobile Zn in the rhizosphere of Salix caprea. Four siderophore producers, two IAA producers and one strain producing both siderophores and IAA were identified. None of the analysed strains produced ACC deaminase. Metal mobilization by bacterial metabolites was assessed by extracting Zn and Cd from soil with supernatants of liquid cultures. Strain Agromyces AR33 almost doubled Zn and Cd extractability, probably by the relase of Zn and Cd specific ligands. The remaining strains, immobilized both metals. When Salix caprea plantlets were grown in γ-sterilized, Zn/Cd/Pb contaminated soil and inoculated with the Zn resistant isolates, Streptomyces AR17 enhanced Zn and Cd uptake. Agromyces AR33 tendentiously promoted plant growth and thereby increased the total amount of Zn and Cd extracted from soil. The IAA producing strains did not affect plant growth, and the siderophore producers did not enhance Zn and Cd accumulation. Apparently other mechanisms than the production of IAA, ACC deaminase and siderophores were involved in the observed plant–microbe interactions.

A 15-kb gene locus including nylon-oligomer-degrading genes from the chromosome of an alkalophilic bacterium, Agromyces sp. KY5R, was cloned and sequenced. The genetic organization was similar to the DNA region flanked by directly repeated IS6100 sequences on the nylon-oligomer-degradative plasmid pOAD2. However, we found several genetic rearrangements between the two DNA regions. Here, we discuss the possible mechanisms underlying the genetic rearrangements.

Alkalophilic, nylon oligomer-degrading strains, Agromyces sp. and Kocuria sp., were isolated from the wastewater of a nylon-6 factory and from activated sludge from a sewage disposal plant. The 6-aminohexanoate oligomer hydrolases (NylC) from the alkalophilic strains had 95.8 to 98.6% similarity to the enzyme in neutrophilic Arthrobacter sp. but had superior thermostability, activity under alkaline conditions, and affinity for nylon-related substrates, which would be advantageous for biotechnological applications.