Using a soilless culture system mimicking tropical acidic peat soils, which contained 3 mg of gellan gum and 0.5 mg NO sub(3) super(-)-N per gram of medium, a greenhouse gas, N sub(2O emitting ...capability of microorganisms in acidic peat soil in the area of Palangkaraya, Central Kalimantan, Indonesia, was investigated. The soil sampling sites included a native swamp forest (NF), a burnt forest covered by ferns and shrubs (BF), three arable lands (A-1, A-2 and A-3) and a reclaimed grassland (GL) next to the arable lands. An acid-tolerant Janthinobacterium sp. strain A1-13 (Oxalobacteriaceae, beta -proteobacteria) isolated from A-1 soil was characterized as one of the most prominent N) sub(2)O-emitting bacteria in this region. Physiological characteristics of the N sub(2O emitter in the soilless culture system, including responses to soil environments, substrate concentration, C-source concentration, pH, and temperature, suggest that the N) sub(2)O emitting Janthinobacterium sp. strain A1-13 is highly adapted to reclaimed open peatland and primarily responsible for massive N sub(2O emissions from the acidic peat soils. Regulation of N) sub(2)O emitters in the reclaimed peatland for agricultural use is therefore one of the most important issues in preventing the greenhouse gas emission from acidic peat soil farmlands.
Purple pigment producing bacterium strains AMJK, AMJM, and AMRM were isolated from sediment in sinan-gun, Korea and their draft genomes were sequenced using Illumina Hiseq 4000 platform. The lengths ...of AMJK, AMJM, and AMRM genomes were 6,380,747 bp, 6,381,259 bp, and 6,380,870 bp, respectively and G+C contents were 62.82%, 64.15%, and 62.82%, respectively. Comparative analysis of genomic identity showed that three strains were closely related to the group of Janthinobacterium lividum. Functional analysis of AMJK, AMJM, and AMRM genomes showed that all strains harbor genes related to producing violacein (VioABCDE).
A bacterial strain designated JA-1, related to
Janthinobacterium lividum,
was isolated from glacier ice samples from the island Spitsbergen in the Arctic. The strain was tested for phenotypic traits ...and the most prominent appeared to be the dark red brown to black pigmentation different from the violet pigment of
Janthinobacterium, Chromobacterium
and
Iodobacter
. Phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA hybridization tests showed that strain JA-1 belongs to the genus
Janthinobacterium
but represents a novel lineage distinct from the two known species of this genus,
J. lividum
and
Janthinobacterium agaricidamnosum
. The DNA G + C content of strain JA-1 was determined to be 62.3 mol %. The isolate is a psychrotrophic Gram negative bacterium, rod-shaped with rounded ends, containing intracellular inclusions and one polar flagellum. On the basis of the presented results strain JA-1 is proposed as the type strain of a novel species of the genus
Janthinobacterium
, for which the name
Janthinobacterium svalbardensis
sp. nov. is proposed (JA-1
T
= DSM 25734, ZIM B637).
Phthalates esters (PAEs) are a kind of polymeric material additives widely been added into plastics to improve products’ flexibility. It can easily cause environmental pollution which are hazards to ...public health. In this study, we isolated an efficient PAEs degrading strain, Janthinobacterium sp. E1, and determined its degradation effect of di-2-ethylhexyl phthalate (DEHP) under stress conditions. Strain E1 showed an obvious advantage in pollutants degradation under various environmental stress conditions. Degradation halo clearly occurred around the colony of strain E1 on agar plate supplemented with triglyceride. Strain E1’s esterase is a constitutively expressed intracellular enzyme. The esterase purified from strain E1 showed a higher catalytic effect on short-chain PAEs than long-chain PAEs. The input of DEHP, DBP (dibutyl phthalate) and DMP (dimethyl phthalate) into the tested soil did not change the species composition of soil prokaryotic community, but altered the dominant species in specific environmental conditions. And the community diversity and richness decreased to a certain extent. However, the diversity and richness of the microbial community were improved after the contaminated soil was treated with the strain E1. Our results also suggested that strain E1 exhibited a tremendous potential in environmental bioremediation in the real environment, which provides a new insight into the elimination of the pollutants contamination in the urban environment.
Phthalates esters (PAEs) are a kind of polymeric material additives widely been added into plastics to improve products’ flexibility. It can easily cause environmental pollution which are hazards to ...public health. In this study, we isolated an efficient PAEs degrading strain, Janthinobacterium sp. E1, and determined its degradation effect of di-2-ethylhexyl phthalate (DEHP) under stress conditions. Strain E1 showed an obvious advantage in pollutants degradation under various environmental stress conditions. Degradation halo clearly occurred around the colony of strain E1 on agar plate supplemented with triglyceride. Strain E1’s esterase is a constitutively expressed intracellular enzyme. The esterase purified from strain E1 showed a higher catalytic effect on short-chain PAEs than long-chain PAEs. The input of DEHP, DBP (dibutyl phthalate) and DMP (dimethyl phthalate) into the tested soil did not change the species composition of soil prokaryotic community, but altered the dominant species in specific environmental conditions. And the community diversity and richness decreased to a certain extent. However, the diversity and richness of the microbial community were improved after the contaminated soil was treated with the strain E1. Our results also suggested that strain E1 exhibited a tremendous potential in environmental bioremediation in the real environment, which provides a new insight into the elimination of the pollutants contamination in the urban environment.
Four strains assigned the names FT13W
, FT14W, FT58W
and FT68W
were isolated from a subtropical stream in PR China. All the strains were Gram-stain-negative, catalase- and oxidase-positive, ...rod-shaped and motile with flagella. Comparisons based on 16S rRNA gene sequences showed that strains FT13W
, FT14W, FT58W
and FT68W
belonged to genus
and shared 16S rRNA gene similarities in the range of 98.8-99.7 % with
DSM 1522
,
DSM 9628
and '
JA-1', respectively. The calculated pairwise average nucleotide identity (ANI) values among the genomes of above seven strains were in the range of 79.0-92.2 %, except that the ANI value was 96.8 % between strain FT13W
and FT14W. The respiratory quinone of strains FT13W
, FT14W, FT58W
and FT68W
was determined to be Q-8. The major fatty acids were C
ω7
, C
, C
ω7
and C
. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genome sizes of strains FT13W
, FT14W, FT58W
and FT68W
were 6.45, 6.38, 5.73 and 6.37 Mbp with G+C contents of 63.4, 63.7, 61.6 and 63.1 mol%, respectively. Combining phenotypic, biochemical, genotypic and ANI data, strain FT13W
and FT14W should belong to the same species. The four strains were considered to represent three novel species within genus
, for which the names
sp. nov. (type strain FT13W
=GDMCC 1.1638
=KACC 21319
),
sp. nov. (FT58W
=GDMCC 1.1676
=KACC 21468
) and
sp. nov. (FT68W
=GDMCC 1.1677
=KACC 21469
) are proposed.
Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT81W
T
, FT82W, FT107W, FT3S
T
, LX20W
T
and LX47W
T
) sharing high 16S rRNA gene sequence similarities with ...species of the genera
Janthinobacterium
(97.0–98.3 %),
Duganella
(96.3–98.8 %),
Rugamonas
(97.8–98.6 %),
Pseudoduganella
(96.8–97.5 %) and
Massilia
(94.5–98.6 %) were isolated from subtropical streams in PR China. The phylogenetic trees reconstructed using the 16S rRNA gene sequences indicated that the species of above five genera often mix together, indicating that the taxonomic statuses of some species were questionable. Phylogenomic reconstruction based on 369 single-copy orthologous clusters indicated that the species of the genus
Janthinobacterium
form a distinct cluster, strains FT81W
T
, FT82W and FT107W form a tight cluster with the species of the genus
Duganella
, and strains FT3S
T
, LX20W
T
and LX47W
T
form a tight cluster with the species of genus
Rugamonas
, and the species of genus
Pseudoduganella
form a tight cluster with
Massilia guangdongensis
,
Massilia ginsengisoli
,
Massilia rivuli
,
Massilia namucuonensis
,
Massilia aquatica
sensu Lu
et al.
,
Massilia buxea
,
Massilia armeniaca
,
Massilia plicata
,
Massilia flava
,
Massilia lurida
,
Massilia dura
,
Massilia lutea
,
Massilia umbonata
,
Massilia albidiflava
and
Massilia violacea
. It should be noted that
Massilia aquatica
Lu
et al.
2020 non
Massilia aquatica
Holochová
et al.
2020 is a later homonym and an illegitimate name. The GTDB Release 202 also supported the proposal that
M. guangdongensis
,
M. ginsengisoli
,
M. rivuli
,
M. namucuonensis
,
M. aquatica
sensu Lu
et al.
,
M. buxea
,
M. armeniaca
,
M. plicata
,
M. flava
,
M. lurida
,
M. dura
,
M. lutea
,
M. umbonata
,
M. albidiflava
and
M. violacea
should be transferred into the genus
Pseudoduganella
. The calculated pairwise orthologous average nucleotide identity by
usearch
(OrthoANIu) values were between 95.0 % and 95.6 % among strains FT81W
T
, FT82W and FT107W, but were less than 91.5 % among strains FT3S
T
, LX20W
T
, LX47W
T
and other related strains. Combining the results of phylogenomic analyses, phenotypic, biochemical and genotypic characteristics, strains FT81W
T
, FT82W and FT107W should represent a novel species of the genus
Duganella
, and strains FT3S
T
, LX20W
T
and LX47W
T
should represent three novel species of the genus
Rugamonas
, for which the names
Duganella vulcania
sp. nov. (type strain FT81W
T
=GDMCC 1.1679
T
=KACC 21471
T
),
Rugamonas fusca
sp. nov. (type strain FT3S
T
=GDMCC 1.1907
T
=KACC 21952
T
),
Rugamonas brunnea
sp. nov. (type strain LX20W
T
=GDMCC 1.1911
T
=KACC 21956
T
) and
Rugamonas apoptosis
sp. nov. (type strain LX47W
T
=GDMCC 1.1914
T
=KACC 21959
T
) are proposed.
The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but ...the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam–resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam–resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the bla CEP₋₀₄ gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis , also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.
Significance The increasing prevalence of antibiotic-resistant bacteria is one of the most serious threats to public health in the 21st century. One route by which resistance genes enter the food system is through amendment of soils with manure from antibiotic-treated animals, which are considered a reservoir of such genes. Previous studies have associated application of pig manure with the dispersal of sulfonamide-resistance genes to soil bacteria. In this study, we found that dairy cow manure amendment enhanced the proliferation of resident antibiotic-resistant bacteria and genes encoding β-lactamases in soil even though the cows from which the manure was derived had not been treated with antibiotics. Our findings provide previously unidentified insight into the mechanism by which amendment with manure enriches antibiotic-resistant bacteria in soil.
•Coldness resistant microorganism, Janthinobacterium sp. M-11 was isolated from surface water.•M-11 could remove ammonium, nitrite and nitrate at 2 °C.•M-11 could remove N at low C/N ratio with a ...small inoculation.•M-11 displayed different pathway of anaerobic denitrification from conversional aerobic denitrification bacteria.•Denitrification genes of napA and narG were both found in M-11.
A novel heterotrophic nitrification-aerobic denitrification bacterium, identified as Janthinobacterium sp. M-11, was isolated from the Songhua River. When the initial ammonium concentration was 5 mg·L−1, 98% of ammonium was removed under cold condition (2 °C) with the C/N ratio of 5 at initial pH 7 and aerobic condition, which demonstrated the significant ammonium removal capacity of M-11 with low nutrient consumption at cold temperature. Denitrification processes under aerobic and anaerobic conditions were also investigated. 89% of nitrite and 89% of nitrate were removed under aerobic condition. Under anaerobic condition, 93% of nitrite and 98% of nitrate were removed. Interestingly, a high amount of nitrite accumulation was observed in the mid-stage of anaerobic denitrification for nitrate. This special phenomenon was probably because of the existence of narG gene amplified in the strain M-11, which would encode membrane-bound nitrate reductase and accelerate the nitrate conversion rate of M-11 under anaerobic condition.
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•A co-culture of marine strains ZZ145 and ZZ148 induced novel natural products.•New janthinopolyenemycins A and B were isolated from the co-culture.•Janthinopolyenemycins A and B are ...rare compounds found from the natural resources.•Janthinopolyenemycins A and B showed antifungal activity.
Two rare polyketides, named as janthinopolyenemycins A (1) and B (2), were isolated from a co-culture of two marine-sourced bacteria Janthinobacterium spp. ZZ145 and ZZ148. Their structures were established by a combination of extensive NMR spectroscopic analyses, HRESIMS data, and ECD calculation. Both janthinopolyenemycins A and B showed activity in inhibiting the growth of Candida albicans with a MIC value of 15.6 μg/mL and a MBC value of 31. 25 μg/mL.
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