Microorganisms, or microbes, can function as threatening
pathogens that cause disease in humans, animals, and plants;
however, they also act as litter decomposers in natural ecosystems.
As the outermost barrier and interface with the environment,
the microbial cell surface is crucial for cell-to-cell
communication and is a potential target of chemotherapeutic
agents. Surface ultrastructures of microbial cells have typically
been observed using scanning electron microscopy (SEM)
and atomic force microscopy (AFM). Owing to its characteristics
of low-temperature specimen preparation and superb
resolution (down to 1 nm), cryo-field emission SEM has
revealed paired rodlets, referred to as hydrophobins, on the
cell walls of bacteria and fungi. Recent technological advances
in AFM have enabled high-speed live cell imaging in liquid
at the nanoscale level, leading to clear visualization of celldrug
interactions. Platinum-carbon replicas from freeze-fractured
fungal spores have been observed using transmission
electron microscopy, revealing hydrophobins with varying
dimensions. In addition, AFM has been used to resolve bacteriophages
in their free state and during infection of bacterial
cells. Various microscopy techniques with enhanced spatial
resolution, imaging speed, and versatile specimen preparation
are being used to document cellular structures and
events, thus addressing unanswered biological questions.
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Strain 63MJ-2T was isolated from the feces of broad-winged
katydid (Pseudorhynchus japonicus) collected in Korea. The
16S rRNA gene sequence of this strain showed the highest
sequence similarity with that of Siphonobacter aquaeclarae
P2T (96.1%) and had low similarities (below 86.3%) with those
of other members of family ‘Flexibacteraceae’. The strain
63MJ-2T is a strictly aerobic, Gram-stain-negative, non-motile,
rod-shaped bacterium. The strain grew at 4–35°C (optimum,
25–30°C), pH of 5.0–9.0 (optimum, 6.0–7.0), and
0–2.0% (optimum, 1.0–2.0) (w/v) NaCl. The DNA G+C content
of strain 63MJ-2T was 43.5 mol%. The major fatty acids
were C16:1 ω5c (42.5%), iso-C17:0 3-OH (18.7%), and summed
feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c, 18.0%). The major
menaquinone was MK-7 and polar lipids were phosphatidylethanolamine,
six unknown aminolipids, and five unknown
lipids. Based on the evidence from our polyphasic
taxonomic study, we conclude that strain 63MJ-2T should be
classified as a novel species of the genus Siphonobacter, and
propose the name Siphonobacter intestinalis sp. nov. The
type strain is 63MJ-2T (=KACC 18663T =NBRC 111883T).
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The increasing temperature in Arctic tundra deepens the
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of soil temperature and the deepening of active layer seem
to affect soil microbial communities. Therefore, information
on soil microbial communities at various soil depths is essential
to understand their potential responses to climate change
in the active layer soil. We investigated the community structure
of soil bacteria in the active layer from moist acidic tundra
in Council, Alaska. We also interpreted their relationship
with some relevant soil physicochemical characteristics along
soil depth with a fine scale (5 cm depth interval). The bacterial
community structure was found to change along soil
depth. The relative abundances of Acidobacteria, Gammaproteobacteria,
Planctomycetes, and candidate phylum WPS-2
rapidly decreased with soil depth, while those of Bacteroidetes,
Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly
increased. A structural shift was also found in the soil bacterial
communities around 20 cm depth, where two organic
(upper Oi and lower Oa) horizons are subdivided. The quality
and the decomposition degree of organic matter might
have influenced the bacterial community structure. Besides
the organic matter quality, the vertical distribution of bacterial
communities was also found to be related to soil pH and
total phosphorus content. This study showed the vertical
change of bacterial community in the active layer with a fine
scale resolution and the possible influence of the quality of soil
organic matter on shaping bacterial community structure.
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Fertilization and the response of the soil microbial community
to the process significantly affect crop yield and the environment.
In this study, the seasonal variation in the bacterial
communities in rice field soil subjected to different
fertilization treatments for more than 50 years was investigated
using 16S rRNA sequencing. The simultaneous application
of inorganic fertilizers and rice straw compost (CAPK)
maintained the species richness of the bacterial communities
at levels higher than that in the case of non-fertilization (NF)
and application of inorganic fertilizers only (APK) in the initial
period of rice growth. The seasonal variation in the bacterial
community structure in the NF and APK plots showed
cyclic behavior, suggesting that the effect of season was important;
however, no such trend was observed in the CAPK
plot. In the CAPK plot, the relative abundances of putative
copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria
were higher and those of putative oligotrophs such
as Acidobacteria and Plactomycetes were lower than those in
the other plots. The relative abundances of organotrophs with
respiratory metabolism, such as Actinobacteria, were lower
and those of chemoautotrophs that oxidize reduced iron and
sulfur compounds were higher in the CAPK plot, suggesting
greater carbon storage in this plot. Increased methane emission
and nitrogen deficiency, which were inferred from the
higher abundances of Methylocystis and Bradyrhizobium in
the CAPK plot, may be a negative effect of rice straw application;
thus, a solution for these should be considered to increase
the use of renewable resources in agricultural lands.
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Lee Pei Lee Angel , Mohd Termizi Yusof , Intan Safinar Ismail , Bonnie Tay Yen Ping , Intan Nur Ainni Mohamed Azni , Norman Hj Kamarudin , Shamala Sundram
J. Microbiol. 2016;54(11):732-744. Published online October 29, 2016
Ganoderma boninense is the causal agent of a devastating disease
affecting oil palm in Southeast Asian countries. Basal
stem rot (BSR) disease slowly rots the base of palms, which
radically reduces productive lifespan of this lucrative crop.
Previous reports have indicated the successful use of Trichoderma
as biological control agent (BCA) against G. boninense
and isolate T. virens 7b was selected based on its initial screening.
This study attempts to decipher the mechanisms responsible
for the inhibition of G. boninense by identifying and
characterizing the chemical compounds as well as the physical
mechanisms by T. virens 7b. Hexane extract of the isolate
gave 62.60% ± 6.41 inhibition against G. boninense and
observation under scanning electron microscope (SEM) detected
severe mycelial deformation of the pathogen at the
region of inhibition. Similar mycelia deformation of G. boninense
was observed with a fungicide treatment, Benlate®
indicating comparable fungicidal effect by T. virens 7b. Fraction
4 and 5 of hexane active fractions through preparative
thin layer chromatography (P-TLC) was identified giving the
best inhibition of the pathogen. These fractions comprised of
ketones, alcohols, aldehydes, lactones, sesquiterpenes, monoterpenes,
sulphides, and free fatty acids profiled through gas
chromatography mass spectrometry detector (GC/MSD). A
novel antifungal compound discovery of phenylethyl alcohol
(PEA) by T. virens 7b is reported through this study. T.
virens 7b also proved to be an active siderophore producer
through chrome azurol S (CAS) agar assay. The study demonstrated
the possible mechanisms involved and responsible
in the successful inhibition of G. boninense.
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Marta O. Domingos , Keyde C.M. Melo , Irys Viana Neves , Cristiane M. Mota , Rita C. Ruiz , Bruna S. Melo , Raphael C. Lima , Denise S.P.Q. Horton , Monamaris M. Borges , Marcia R. Franzolin
J. Microbiol. 2016;54(11):745-752. Published online October 29, 2016
Using clonal phylogenetic methods, it has been demonstrated
that O111:H25 atypical enteropathogenic E. coli (aEPEC)
strains belong to distinct clones, suggesting the possibility
that their ability to interact with different hosts and abiotic
surfaces can vary from one clone to another. Accordingly, the
ability of O111:H25 aEPEC strains derived from human, cat
and dogs to adhere to epithelial cells has been investigated,
along with their ability to interact with macrophages and to
form biofilms on polystyrene, a polymer used to make biomedical
devices. The results demonstrated that all the strains
analyzed were able to adhere to, and to form pedestals on,
epithelial cells, mechanisms used by E. coli to become strongly
attached to the host. The strains also show a Localized-Adherence-
Like (LAL) pattern of adhesion on HEp-2 cells, a
behavior associated with acute infantile diarrhea. In addition,
the O111:H25 aEPEC strains derived either from human
or domestic animals were able to form long filaments,
a phenomenon used by some bacteria to avoid phagocytosis.
O111:H25 aEPEC strains were also encountered inside vacuoles,
a characteristic described for several bacterial strains
as a way of protecting themselves against the environment.
They were also able to induce TNF-α release via two routes,
one dependent on TLR-4 and the other dependent on binding
of Type I fimbriae. These O111:H25 strains were also able
to form biofilms on polystyrene. In summary the results suggest
that, regardless of their source (i.e. linked to human origin
or otherwise), O111:H25 aEPEC strains carry the potential
to cause human disease.
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may have an adjuvant anti-biofilm agent. However, the in
vivo efficacy of farnesol is very questionable. Therefore, the
in vitro and in vivo activity of fluconazole combined with farnesol
was evaluated against C. albicans biofilms using fractional
inhibitory concentration index (FICI) determination,
time-kill experiments and a murine vulvovaginitis model.
The median biofilm MICs of fluconazole-sensitive C. albicans
isolates ranged between 4 -> 512 mg/L and 150–300 μM
for fluconazole and farnesol, respectively. These values were
512 -> 512 mg/L and > 300 μM for fluconazole-resistant clinical
isolates. Farnesol decreased the median MICs of fluconazole
by 2-64-fold for biofilms. Based on FICI, synergistic
interaction was observed only in the case of the sessile
SC5314 reference strain (FICIs: 0.16–0.27). In time-kill studies,
only the 512 mg/L fluconazole and 512 mg/L fluconazole
+ 75 μM farnesol reduced biofilm mass significantly at
each time point in the case of all isolates. The combination
reduced the metabolic activity of biofilms for all isolates in a
concentration- and time-dependent manner. Our findings
revealed that farnesol alone was not protective in a murine
vulvovaginitis model. Farnesol was not beneficial in combination
with fluconazole for fluconazole-susceptible isolates,
but partially increased fluconazole activity against one fluconazole-
resistant isolate, but not the other one.
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Pulmonary tuberculosis (TB) is caused by Mycobacterium
tuberculosis. The protein composition of sputum may reflect
the immune status of the lung. This study aimed to evaluate
the protein profiles in spontaneous sputum samples from
patients with active pulmonary TB. Sputum samples were
collected from patients with pulmonary TB and healthy controls.
Western blotting was used to analyze the amount of interleukin
10 (IL-10), interferon-gamma (IFN-γ), IL-25, IL-
17, perforin-1, urease, albumin, transferrin, lactoferrin, adenosine
deaminase (also known as adenosine aminohydrolase,
or ADA), ADA-2, granzyme B, granulysin, and caspase-
1 in sputum. Results of detection of IL-10, IFN-γ, perforin-
1, urease, ADA2, and caspase-1, showed relatively high
specificity in distinguishing patients with TB from healthy
controls, although sensitivities varied from 13.3% to 66.1%.
By defining a positive result as the detection of any two proteins
in sputum samples, combined use of transferrin and
urease as markers increased sensitivity to 73.2% and specificity
to 71.1%. Furthermore, we observed that the concentration of transferrin was proportional to the number of acidfast
bacilli detected in sputum specimens. Detection of sputum
transferrin and urease was highly associated with pulmonary
TB infection. In addition, a high concentration of
transferrin detected in sputum might correlate with active
TB infection. This data on sputum proteins in patients with
TB may aid in the development of biomarkers to assess the
severity of pulmonary TB.
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Turgor is very important for the invasive growth of fungal
pathogens. Glycerol, a highly osmotic solvent, is considered
to play an important role in turgor generation. The nematophagous
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formation. We demonstrated that deleting gph1, which encodes
glycogen phosphorylase, decreased the glycerol content,
compared with that of a wild-type strain. Although the
number of traps induced by nematodes was not affected in
the Δgph1 mutant, the capture rate was lower. Meanwhile,
deleting gph1 also affected the growth rate and conidiation
capacity of the fungus. These results indicate that glycerol
derived from GPH1 is essential for the full virulence of A.
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The need for new antibiotics has sparked a search for the
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potential of microbial communities in diverse environments
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product discovery in diverse ways. A relatively recent method
to search for the possible production of novel compounds
includes studying the diverse genes belonging to polyketide
synthase pathways (PKS), as these complex enzymes are an
important source of novel therapeutics. In order to explore
the biotechnological potential of the microbial community
from the largest underground aquifer in the world located
in the Yucatan, we used a polyphasic approach in which a
simple, non-computationally intensive method was coupled
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domains. Our results suggest that the bioinformatic method
proposed can indeed be used to assess the novelty of KS enzymes;
nevertheless, this in silico study did not identify some
of the KS diversity due to primer bias and stringency criteria
outlined by the metagenomics pipeline. Therefore, additionally
implementing a method involving the direct cloning of
KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably
less diversity in relation to known ketosynthase domains;
however, the metagenome included a family of KS
type I domains phylogenetically related, but not identical, to
those found in the curamycin pathway, as well as an outstanding
number of thiolases. Over all, this first look into the microbial
community found in this large Yucatan aquifer and
other fresh water free living microbial communities highlights
the potential of these previously overlooked environments
as a source of novel natural products.
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with drug resistance of bladder cancer cells. Some
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an anti-cancer drug, cisplatin, possibly as a result of downregulation
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