Devosia honganensis sp. nov., isolated from the soil of a chemical factory

Devosia lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic Microcystis

A novel alphaproteobacterial strain JXJ CY 41T was isolated from a culture mass of Microcystis, collected from Lake Dianchi, south-west, China. Strain JXJ CY 41T was gram-strain-negative, aerobic, motile, with rod-shaped cells (0.4-1.0 × 1.7-3.5 μm). It was positive for catalase and starch hydrolysis, negative for oxidase and hydrolysis of Tweens (20, 40, and 80). Growth occurred at 10-44 °C, pH 5.0-10.0, and 0-5.0% (w/v) NaCl. Major fatty acids included C16:0 (28.1%), 11-methyl C18:1 ω7c (36.7%) and C18:1 ω7c (20.8%). Q10 was the sole ubiquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, and an unidentified lipid. The DNA G + C content was 63.1%. Its 16S rRNA gene sequence showed high similarities with Devosia oryziradicis G19T (99.5%; not validly published), D. yakushimensis Yak96BT (98.3%) and D. ginsengisoli Gsoil 520T (98.1%), and less than 98.1% similarities with other members of the genus Devosia. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain JXJ CY 41T and its 5 closest similar strains were 19.9-24.1% and 75.7-80.5%, respectively. Based on the data above, strain JXJ CY 41T was identified as a novel species of the genus Devosia, for which the epithet Devosia lacusdianchii sp. nov. was proposed. The type strain is JXJ CY 41T (= KCTC 72812T = CGMCC 1.17502T). Strain JXJ CY 41T exhibited different interactions with Microcystis aeruginosa FACHB-905 (Maf) under different conditions, and Maf could control the bacterial cellular density by secreting unknown specific chemical compounds according to its nutritional requirements.

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696^T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696^T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696^T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696^T contained C_16:0, C_18:0, C_18:1ω7c 11-methyl and C_18:1ω6c/ C_18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696^T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696^T=BCRC 81284^T=JCM 34167^T) is proposed.

Devosia aurantiaca sp. nov., Isolated from Mountain Soil and Proposal of Albitalea gen. nov. to Replace the Illegitimate Prokaryotic Genus Name Geomonas Khan et al. 2020

Strain H239^T, a gram-negative, strictly aerobic, and oxidase-positive, and catalase-negative bacterium, was isolated from mountain soil in Gangwon-do of South Korea. Colonies were orange colored, and cells were motile rods with a single polar flagellum. Growth was observed between 25 and 30 °C (optimum, 30 °C), between pH 7.0 and pH 9.0 (optimum, pH 7.5), and in the presence of 0-1.5% (w/v) NaCl (optimum 0.5-1%). Ubiquinone-10 was detected as the sole respiratory quinone. The major fatty acids (>10%) of strain H239^T were C_18:1 ω7c, C_18:0, and C_16:0. The polar lipids detected from strain H239^T consisted of two unidentified glycolipids, two unidentified phospholipids, and three unidentified polar lipids. The G+C content of strain H239^T based on its genome sequence was 62.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain H239^T was most closely related to Devosia chinhatensis IPL18^T (97.7%), Devosia submarina KMM 9415^T (97.7%), and Devosia yakushimensis Yak96B^T (97.3%). Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain H239^T formed a distinct phyletic lineage as a new species within the genus Devosia. Based on its physiological, chemotaxonomic, and molecular properties, strain H239^T represents a novel species of the genus Devosia, for which the name Devosia aurantiaca sp. nov. is proposed. The type strain is H239^T (=KACC 21662^T=JCM 33930^T). In addition, because the prokaryotic genus name Geomonas Khan et al. 2020 is a later homonym of Geomonas Xu et al. 2020, the name is illegitimate (Principle 6 in the International Code of Nomenclature of Prokaryotes). Therefore, we propose to replace the problematic prokaryotic names Geomonas and Geomonas soli with Albitalea with Albitalea terrae, respectively.

Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil

A Gram-stain-negative, strictly aerobic, motile, ivory-coloured and rod-shaped bacterium (designated Gsoil 520T) isolated from ginseng cultivation soil was characterized by using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 520T was observed to grow optimally at 30 °C and pH 7.0 on Reasoner's 2A agar medium. The results of phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that Gsoil 520T belongs to the genus Devosia of the family Hyphomicrobiaceae and was most closely related to Devosia epidermidihirudinis E84T (98.0 %), Devosia yakushimensis Yak96BT (97.7 %), Devosia neptuniae J1T (97.7 %) and Devosia chinhatensis IPL18T (96.8 %). The complete genome of strain Gsoil 520T is a presumptive circular chromosome of 4 480 314 base pairs having G+C content of 63.7 mol%. A total of 4 354 genes, 4 303 CDS and 43 rRNA genes were assigned a putative function. The major isoprenoid quinone was Q-10. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids (AL1 and AL3). The predominant fatty acids of strain Gsoil 520T were C18 : 1ω7c 11-methyl, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c (summed feature 8) supporting the affiliation of strain Gsoil 520T to the genus Devosia . The low values of DNA–DNA hybridization distinguished strain Gsoil 520T from the recognized species of the genus Devosia . Thus, the novel isolate represents a novel species of the genus Devosia , for which the name Devosia ginsengisoli sp. nov. is proposed, with the type strain Gsoil 520T (=KACC 19440T=LMG 30329T).

Continuing Impacts of Selective Inhibition on Bacterial and Fungal Communities in an Agricultural Soil

Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g^-1). The microcosms were incubated for 6 weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-¹⁴C] anthracene, was spiked to all microcosms, and the derived CO₂ was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2 mg g^-1 bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6 weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended.

Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment

A Gram-stain-negative bacterium, designated CM5-1^T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain CM5-1^T belongs to the genus Devosia, with closely related type strains Devosia submarina KMM 9415^T (98.6 %), Devosia psychrophilaCr7-05^T (98.6 %) and Devosia psychrophilaE84^T (98.2 %). Up-to-date bacterial core gene set analysis revealed that strain CM5-1^T represents one independent lineage with D. submarina KMM 9415^T. The average nucleotide identity values of CM5-1^T with D. submarina KMM 9415^T and D. psychrophila Cr7-05^T are 80.1 and 77.9 %, respectively. In silico DNA-DNA hybridization values between strain CM5-1^T and D. submarina KMM 9415^T and D. psychrophila Cr7-05^T are 23.8 and 21.9 %, respectively. Strain CM5-1^T contains diphosphatidylglycerol, phosphatidylglycerol and glycolipid as major polar lipids. The sole isoprenoid quinone is ubiquinone-10, and C18 : 1ω7c and 11-methyl C18 : 1ω7c are the dominant cellular fatty acids. The G+C content of the genomic DNA is 61.4 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain CM5-1^T could be differentiated from closely related species. Therefore, we propose strain CM5-1^T as a novel species of the genus Devosia, for which the name Devosia naphthalenivorans sp. nov. is suggested. The type strain is CM5-1^T (=JCM32509^T=CGMCC 1.13553^T).

Rhizobium album sp. nov., isolated from a propanil-contaminated soil

A novel Gram-stain negative, facultatively anaerobic, non-spore-forming, motile and rod-shaped bacterium (NS-104^T) was isolated from a propanil-contaminated soil in Nanjing, China. Growth occurred at pH 5.0-9.0 (optimum 6.0), 16-37 °C (optimum 30 °C) and in the presence of 0-2.0% (w/v) NaCl (optimum, without NaCl). Strain NS-104^T showed high 16S rRNA gene sequence identity to Rhizobium azooxidifex DSM 100211^T (96.7%). The phylogenetic analysis of the 16S rRNA gene as well as the housekeeping genes recA, atpD and glnA demonstrated that strain NS-104^T belongs to the genus Rhizobium. Strain NS-104^T did not form nodules on six different legumes, and the nodD, nodC and nifH genes were neither amplified by PCR nor found in the draft genome of strain NS-104^T. The sole respiratory quinone was ubiquinone Q-10. The polar lipid profile included the major amounts phosphatidylmonomethylethanolamine, phosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and unidentified aminolipids. The major cellular fatty acids were C_18:1ω7c (39.6%), C_19:0 cyclo ω8c (29.8%) and C_16:0 (11.5%). The G + C content of strain NS-104^T was 61.9 mol%. Strain NS-104^T therefore represents a new species, for which the name Rhizobium album sp. nov. is proposed, with the type strain NS-104^T (= KCTC 62327^T = CCTCC AB 2017250^T).

Symbiont replacement between bacteria of different classes reveals additional layers of complexity in the evolution of symbiosis in the ciliate Euplotes

Symbiosis is a diverse and complex phenomenon requiring diverse model systems. The obligate relationship between a monophyletic group of Euplotes species ("clade B") and the betaproteobacteria Polynucleobacter and "Candidatus Protistobacter" is among the best-studied in ciliates, and provides a framework to investigate symbiont replacements. Several other Euplotes-bacteria relationships exist but are less understood, such as the co-dependent symbiosis between Euplotes magnicirratus (which belongs to "clade A") and the alphaproteobacterium "Candidatus Devosia euplotis". Here we describe a new Devosia inhabiting the cytoplasm of a strain of Euplotes harpa, a clade B species that usually depends on Polynucleobacter for survival. The novel bacterial species, "Candidatus Devosia symbiotica", is closely related to the symbiont of E. magnicirratus, casting a different light on the history of bacteria colonizing ciliates of this genus. The two Devosia species may have become symbionts independently or as the result of a symbiont exchange between hosts, in either case replacing a previous essential bacterium in E. harpa. Alternatively, both may be remnants of an ancient symbiotic relationship between Euplotes and Devosia, in which case Polynucleobacter and "Ca. Protistobacter" are recent invaders. Either way, symbiont replacement between bacteria belonging to different classes must be evoked to explain this fascinating system.