Two Gram-stain-positive, oxidase-negative, non-motile, facultative anaerobic, α-hemolytic, coccus-shaped bacteria (zg-86T and zg-70) were isolated from the respiratory tracts of marmots (Marmota Himalayana) on the Qinghai-Tibet Plateau of China. Phylogenetic analysis of the 16S rRNA gene and 545 core genes revealed that these two strains belong to the Streptococcus genus. These strains were most closely related to Streptococcus respiraculi HTS25T, Streptococcus cuniculi CCUG 65085T, and Streptococcus marmotae HTS5T. The average nucleotide identity (ANI) and digital DNA‒DNA hybridization (dDDH) were below the threshold for species delineation. The predominant cellular fatty acids (CFAs) in this novel species were C16:0, C18:0, and C18:1ω9c, whereas the primary polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and an unknown phosphoglycolipid (PGL). The optimal growth conditions for the strains were 37 °C, pH 7.0, and 0.5% (w/v) NaCl on brain-heart infusion (BHI) agar supplemented with 5% defibrinated sheep blood. Comparative genomics analyses revealed the potential pathogenicity of strain zg-86T through comparisons with suis subclade strains in terms of virulence factors, pathogen-host interactions (PHIs) and mobile genetic factors (MGEs). Based on the phenotypic characteristics and phylogenetic analyses, we propose that these two isolates represent novel species in the genus Streptococcus, for which the names Streptococcus zhangguiae sp. nov. (the type strain zg-86T=GDMCC 1.1758T=JCM 34273T) is proposed.
Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges.
Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.
We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038(T), from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C(15:0) and iso-C(17:0). Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038(T) has the highest similarity with Spelaeicoccus albus DSM 26341( T) (96.02%). ZFBP1038(T) formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038(T) was 63.65 mol% and the genome size was 4.05 Mb.
Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038(T) and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively.
Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038(T) represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038(T) (= EE 014( T) = GDMCC 1.3024( T) = JCM 35335( T)).
Elevation gradients, often regarded as “natural experiments or laboratories”, can be used to study changes in the distribution
of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We
obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total
number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately
45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns
in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most
unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6
had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current
study. Ammonium nitrogen (
NH4
+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_
1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results
provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications
for microbial responses to environmental change in semiarid mountain ecosystems.
Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae
J. Microbiol. 2022;60(6):576-584. Published online April 18, 2022
Three aerobic, Gram-negative, and rod-shaped bacterial strains,
designated strains G4M1T, SM13T, and L12M9T, were isolated
from the gut of Batillaria multiformis, Cellana toreuma, and
Patinopecten yessoensis collected from the Yellow Sea in South
Korea. All the strains grew optimally at 25°C, in the presence
of 2% (w/v) NaCl, and at pH 7. These three strains, which
belonged to the genus Polaribacter in the family Flavobacteriaceae,
shared < 98.8% in 16S rRNA gene sequence and < 86.68%
in whole-genome sequence with each other. Compared with
the type strains of Polaribacter, isolates showed the highest
sequence similarity to P. haliotis KCTC 52418T (< 98.68%),
followed by P. litorisediminis KCTC 52500T (< 98.13%). All
the strains contained MK-6 as their predominant menaquinone
and iso-C15:0 as their major fatty acid. Moreover, all the
strains had phosphatidylethanolamine as their polar lipid
component. In addition, strain G4M1T had two unidentified
lipids and three unidentified aminolipids, strain SM13T had
three unidentified lipids and three unidentified aminolipids,
and strain L12M9T had three unidentified lipids and one unidentified
aminolipid. The DNA G + C contents of strains
G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%,
respectively. Based on phenotypic, phylogenetic, chemotaxonomic,
and genotypic findings, strains G4M1T (= KCTC 82388T
= DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T),
and L12M9T (= KCTC 62751T = DSM 112374T) were classified
into the genus Polaribacter as the type strains of novel
species, for which the names Polaribacter batillariae sp. nov.,
Polaribacter cellanae sp. nov., and Polaribacter pectinis sp.
nov., respectively, have been proposed.
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To date, all species in the genus Salicibibacter have been isolated
in Korean commercial kimchi. We aimed to describe
the taxonomic characteristics of two strains, NKC5-3T and
NKC21-4T, isolated from commercial kimchi collected from
various regions in the Republic of Korea. Cells of these strains
were rod-shaped, Gram-positive, aerobic, oxidase- and catalase-
positive, non-motile, halophilic, and alkalitolerant. Both
strains, unlike other species of the genus Salicibibacter, could
not grow without NaCl. Strains NKC5-3T and NKC21-4T
could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and
grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum
8.5), respectively; they showed 97.1% 16S rRNA gene sequence
similarity to each other and were most closely related
to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively).
The genome of strain NKC5-3T was nearly 4.6 Mb in
size, with 4,456 protein-coding sequences (CDSs), whereas
NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs.
OrthoANI values between the novel strains and S. kimchii
NKC1-1T were far lower than the species demarcation threshold.
NKC5-3T and NKC21-4T clustered together to form
branches that were distinct from the other Salicibibacter species.
The major fatty acids in these strains were anteiso-C15:0
and anteiso-C17:0, and the predominant menaquinone was
menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol
(DPG), phosphatidylglycerol (PG), and
five unidentified phospholipids (PL), and those of NKC21-4T
included DPG, PG, seven unidentified PLs, and an unidentified
lipid. Both isolates had DPG, which is the first case in
the genus Salicibibacter. The genomic G + C content of strains
NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively.
Based on phenotypic, genomic, phylogenetic, and chemotaxonomic
analyses, strains NKC5-3T (= KACC 22040T
= DSM 111417T) and NKC21-4T (= KACC 22041T = DSM
111418T) represent two novel species of the genus Salicibibacter,
for which the names Salicibibacter cibarius sp. nov.
and Salicibibacter cibi sp. nov. are proposed.
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Valid publication of new names and new combinations effectively published outside the IJSEM Aharon Oren, George M. Garrity
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Intestinal diseases caused by physiological stress have become
a severe public health threat worldwide. Disturbances in the
gut microbiota-host relationship have been associated with
irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory
and antioxidant effects. The objective of this
study was to investigate the mechanisms by which MT-mediated
protection mitigated stress-induced intestinal microbiota
dysbiosis and inflammation. We successfully established a
murine restraint stress model with and without MT supplementation.
Mice subjected to restraint stress had significantly
elevated corticosterone (CORT) levels, decreased MT levels
in their plasma, elevated colonic ROS levels and increased bacterial
abundance, including Bacteroides and Tyzzerella, in
their colon tract, which led to elevated expression of Toll-like
receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation
with 20 mg/kg MT reversed the elevation of the plasma
CORT levels, downregulated the colon ROS levels and inhibited
the changes in the intestinal microbiota induced by
restraint stress. These effects, in turn, inhibited the activities
of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory
reaction induced by restraint stress. Our results
suggested that MT may mitigate “restraint stress”-induced
colonic microbiota dysbiosis and intestinal inflammation by
inhibiting the activation of the NF-κB pathway.
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Ammonia oxidation, performed by ammonia-oxidizing archaea
(AOA) and bacteria (AOB), plays a critical role in the cycle
of nitrogen in the ocean. For now, environmental variables
controlling distribution of ammonia-oxidizing microbes are
still largely unknown in oceanic environments. In this study,
we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity
of AOA and AOB from sediment and water in Zhanjiang Bay.
Phylogenic analysis revealed that the majority of AOA amoA
sequences in water and sediment were affiliated with the genus
Nitrosopumilus, whereas the Nitrosotalea cluster was only detected
with low abundance in water. Nitrosomonas and Nitrosospira
dominated AOB amoA sequences in water and sediment,
respectively. The amoA copy numbers of both AOA and
AOB varied significantly with month for both sediment and
water. When water and sediment temperature dropped to 17–
20°C in December and February, respectively, the copy number
of AOB amoA genes increased markedly and was much
higher than for AOA amoA genes. Also, AOA abundance in
water peaked in December when water temperature was lowest
(17–20°C). Stepwise multiple regression analyses revealed that
temperature was the most key factor driving monthly changes
of AOA or AOB abundance. It is inferred that low water temperature
may inhibit growth of phytoplankton and other microbes
and so reduce competition for a common substrate,
ammonium.
The genome sequences of two pyrene-degrading bacterial
strains of Mycobacterium spp. PYR10 and PYR15, isolated
from the estuarine wetland of the Han river, South Korea,
were determined using the PacBio RS II sequencing platform.
The complete genome of strain PYR15 was 6,037,017 bp in
length with a GC content of 66.5%, and contained 5,933 protein-
coding genes. The genome of strain PYR10 was 5,999,427
bp in length with a GC content of 67.7%, and contained
5,767 protein-coding genes. Based on the average nucleotide
identity values, these strains were designated as M. gilvum
PYR10 and M. pallens PYR15. A genomic comparison
of these pyrene-degrading Mycobacterium strains with pyrene-
non-degrading strains revealed that the genomes of
pyrene-degrading strains possessed similar repertoires of ringhydroxylating
dioxygenases (RHDs), including the pyrenehydroxylating
dioxygenases encoded by nidA and nidA3,
which could be readily distinguished from those of pyrenenon-
degraders. Furthermore, genomic islands, containing
catabolic gene clusters, were shared only among the pyrenedegrading
Mycobacterium strains and these gene clusters
contained RHD genes, including nidAB and nidA3B3. Our
genome data should facilitate further studies on the evolution
of the polycyclic aromatic hydrocarbon-degradation
pathways in the genus Mycobacterium.
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Members of the family Clostridiaceae within phylum Firmicutes
are ubiquitous in various iron-reducing environments.
However, genomic data on iron-reducing bacteria of the family
Clostridiaceae, particularly regarding their environmental
distribution, are limited. Here, we report the analysis and
comparison of the genomic properties of Geosporobacter
ferrireducens IRF9, a strict anaerobe that ferments sugars
and degrades toluene under iron-reducing conditions, with
those of the closely related species, Geosporobacter subterraneus
DSM 17957. Putative alkyl succinate synthase-encoding
genes were observed in the genome of strain IRF9 instead
of the typical benzyl succinate synthase-encoding genes.
Canonical genes associated with iron reduction were not
observed in either genome. The genomes of strains IRF9 and
DMS 17957 harbored genes for acetogenesis, that encode two
types of Rnf complexes mediating the translocation of H+
and Na+ ions, respectively. Strain IRF9 harbored two different
types of ATPases (Na+-dependent F-type ATPase and H+-
dependent V-type ATPase), which enable full exploitation
of ion gradients. The versatile energy conservation potential
of strain IRF9 promotes its survival in various environmental
conditions.
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In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2~3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor-it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.