12 research outputs found
Backreaction in Axion Monodromy, 4-forms and the Swampland
Axion monodromy models can always be described in terms of an axion coupled
to 3-form gauge fields with non-canonical kinetic terms. The presence of the
saxions parametrising the kinetic metrics of the 3-form fields leads to
backreaction effects in the inflationary dynamics. We review the case in which
saxions backreact on the K\"ahler metric of the inflaton leading to a
logarithmic scaling of the proper field distance at large field. This behaviour
is universal in Type II string flux compactifications and consistent with a
refinement of the Swampland Conjecture. The critical point at which this
behaviour appears depends on the mass hierarchy between the inflaton and the
saxions. However, in tractable compactifications, such a hierarchy cannot be
realised without leaving the regime of validity of the effective theory,
disfavouring transplanckian excursions in string theory.Comment: Proceedings prepared for the "Workshop on Geometry and Physics",
November 2016, Ringberg Castl
Biochar Impacts Soil Microbial Community Composition and Nitrogen Cycling in an Acidic Soil Planted with Rape
Biochar
has been suggested to improve acidic soils and to mitigate
greenhouse gas emissions. However, little has been done on the role
of biochar in ameliorating acidified soils induced by overuse of nitrogen
fertilizers. In this study, we designed a pot trial with an acidic
soil (pH 4.48) in a greenhouse to study the interconnections between
microbial community, soil chemical property changes, and N<sub>2</sub>O emissions after biochar application. The results showed that biochar
increased plant growth, soil pH, total carbon, total nitrogen, C/N
ratio, and soil cation exchange capacity. The results of high-throughput
sequencing showed that biochar application increased α-diversity
significantly and changed the relative abundances of some microbes
that are related with carbon and nitrogen cycling at the family level.
Biochar amendment stimulated both nitrification and denitrification
processes, while reducing N<sub>2</sub>O emissions overall. Results
of redundancy analysis indicated biochar could shift the soil microbial
community by changing soil chemical properties, which modulate N-cycling
processes and soil N<sub>2</sub>O emissions. The significantly increased <i>nosZ</i> transcription suggests that biochar decreased soil
N<sub>2</sub>O emissions by enhancing its further reduction to N<sub>2</sub>
Application of Struvite Alters the Antibiotic Resistome in Soil, Rhizosphere, and Phyllosphere
Struvite recovered
from wastewater is a renewable source of phosphorus
and nitrogen and can be used as fertilizer for plant growth. However,
antibiotics and resistome can be enriched in the struvite derived
from wastewater. Robust understanding of the potential risks after
struvite application to soils has remained elusive. Here, we profiled
antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs)
in struvite, soil, rhizosphere and phyllosphere of <i>Brassica</i> using high-throughput quantitative PCR. A total of 165 ARGs and
10 MGEs were detected. Application of struvite was found to increase
both the abundance and diversity of ARGs in soil, rhizosphere and
phyllosphere. In addition, ARGs shared exclusively between <i>Brassica</i> phyllosphere and struvite were identified, indicating
that struvite was an important source of ARGs found in phyllosphere.
Furthermore, OTUs shared between rhizosphere and phyllosphere were
found to significantly correlate with ARGs, suggesting that microbiota
in leaf and root could interconnect and ARGs might transfer from struvite
to the surface of plants via rhizosphere using bacteria as spreading
medium. These findings demonstrated that struvite as an organic fertilizer
can facilitate the spread of antibiotic resistance into human food
chain and this environment-acquired antibiotic resistance should be
put into human health risk assessment system
Diversity and Abundance of Arsenic Biotransformation Genes in Paddy Soils from Southern China
Microbe-mediated
arsenic (As) biotransformation in paddy soils
determines the fate of As in soils and its availability to rice plants,
yet little is known about the microbial communities involved in As
biotransformation. Here, we revealed wide distribution, high diversity,
and abundance of arsenite (AsÂ(III)) oxidase genes (<i>aioA</i>), respiratory arsenate (AsÂ(V)) reductase genes (<i>arrA</i>), AsÂ(V) reductase genes (<i>arsC</i>), and AsÂ(III) <i>S</i>-adenosylmethionine methyltransferase genes (<i>arsM</i>) in 13 paddy soils collected across Southern China. Sequences grouped
with As biotransformation genes are mainly from rice rhizosphere bacteria,
such as some <i>Proteobacteria</i>, <i>Gemmatimonadales</i>, and <i>Firmicutes</i>. A significant correlation of gene
abundance between <i>arsC</i> and <i>arsM</i> suggests
that the two genes coexist well in the microbial As resistance system.
Redundancy analysis (RDA) indicated that soil pH, EC, total C, N,
As, and Fe, C/N ratio, SO<sub>4</sub><sup>2–</sup>-S, NO<sub>3</sub><sup>–</sup>-N, and NH<sub>4</sub><sup>+</sup>-N were
the key factors driving diverse microbial community compositions.
This study for the first time provides an overall picture of microbial
communities involved in As biotransformation in paddy soils, and considering
the wide distribution of paddy fields in the world, it also provides
insights into the critical role of paddy fields in the As biogeochemical
cycle
Antibiotic Resistome and Its Association with Bacterial Communities during Sewage Sludge Composting
Composting is widely
used for recycling of urban sewage sludge
to improve soil properties, which represents a potential pathway of
spreading antibiotic resistant bacteria and genes to soils. However,
the dynamics of antibiotic resistance genes (ARGs) and the underlying
mechanisms during sewage sludge composting were not fully explored.
Here, we used high-throughput quantitative PCR and 16S rRNA gene based
illumina sequencing to investigate the dynamics of ARGs and bacterial
communities during a lab-scale in-vessel composting of sewage sludge.
A total of 156 unique ARGs and mobile genetic elements (MGEs) were
detected encoding resistance to almost all major classes of antibiotics.
ARGs were detected with significantly increased abundance and diversity,
and distinct patterns, and were enriched during composting. Marked
shifts in bacterial community structures and compositions were observed
during composting, with Actinobacteria being the dominant phylum at
the late phase of composting. The large proportion of Actinobacteria
may partially explain the increase of ARGs during composting. ARGs
patterns were significantly correlated with bacterial community structures,
suggesting that the dynamic of ARGs was strongly affected by bacterial
phylogenetic compositions during composting. These results imply that
direct application of sewage sludge compost on field may lead to the
spread of abundant ARGs in soils
Electron Shuttles Enhance Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction
Anaerobic
ammonium oxidation coupled to ironÂ(III) reduction, termed
Feammox, is a newly discovered nitrogen cycling process. However,
little is known about the roles of electron shuttles in the Feammox
reactions. In this study, two forms of FeÂ(III) (oxyhydr)Âoxide ferrihydrite
(ex situ ferrihydrite and in situ ferrihydrite) were used in dissimilatory
FeÂ(III) reduction (DIR) enrichments from paddy soil. Evidence for
Feammox in DIR enrichments was demonstrated using the <sup>15</sup>N-isotope tracing technique. The extent and rate of both the <sup>30</sup>N<sub>2</sub>–<sup>29</sup>N<sub>2</sub> and FeÂ(II)
formation were enhanced when amended with electron shuttles (either
9,10-anthraquinone-2,6-disulfonate (AQDS) or biochar) and further
simulated when these two shuttling compounds were combined. Although
the Feammox-associated FeÂ(III) reduction accounted for only a minor
proportion of total FeÂ(II) formation compared to DIR, it was estimated
that the potentially Feammox-mediated N loss (0.13–0.48 mg
N L<sup>–1</sup> day<sup>–1</sup>) was increased by
17–340% in the enrichments by the addition of electron shuttles.
The addition of electron shuttles led to an increase in the abundance
of unclassified Pelobacteraceae, Desulfovibrio, and denitrifiers but a decrease in Geobacter. Overall, we demonstrated a stimulatory effect of electron shuttles
on Feammox that led to higher N loss, suggesting that electron shuttles
might play a crucial role in Feammox-mediated N loss from soils
Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with <sup>15</sup>N<sub>2</sub> Labeling
Nitrogen (N) fixation
is the conversion of inert nitrogen gas (N<sub>2</sub>) to bioavailable
N essential for all forms of life. N<sub>2</sub>-fixing microorganisms
(diazotrophs), which play a key role
in global N cycling, remain largely obscure because a large majority
are uncultured. Direct probing of active diazotrophs in the environment
is still a major challenge. Herein, a novel culture-independent single-cell
approach combining resonance Raman (RR) spectroscopy with <sup>15</sup>N<sub>2</sub> stable isotope probing (SIP) was developed to discern
N<sub>2</sub>-fixing bacteria in a complex soil community. Strong
RR signals of cytochrome c (Cyt c, frequently present in diverse N<sub>2</sub>-fixing bacteria), along with a marked <sup>15</sup>N<sub>2</sub>-induced Cyt c band shift, generated a highly distinguishable
biomarker for N<sub>2</sub> fixation. <sup>15</sup>N<sub>2</sub>-induced
shift was consistent well with <sup>15</sup>N abundance in cell determined
by isotope ratio mass spectroscopy. By applying this biomarker and
Raman imaging, N<sub>2</sub>-fixing bacteria in both artificial and
complex soil communities were discerned and imaged at the single–cell
level. The linear band shift of Cyt c versus <sup>15</sup>N<sub>2</sub> percentage allowed quantification of N<sub>2</sub> fixation extent
of diverse soil bacteria. This single-cell approach will advance the
exploration of hitherto uncultured diazotrophs in diverse ecosystems
Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome
Land applications of municipal sewage
sludge may pose a risk of
introducing antibiotic resistance genes (ARGs) from urban environments
into agricultural systems. However, how the sewage sludge recycling
and application method influence soil resistome and mobile genetic
elements (MGEs) remains unclear. In the present study, high through-put
quantitative PCR was conducted on the resistome of soils from a field
experiment with past (between 1994 and 1997) and annual (since 1994)
applications of five different sewage sludges. Total inputs of organic
carbon were similar between the two modes of sludge applications.
Intrinsic soil resistome, defined as the ARGs shared by the soils
in the control and sludge-amended plots, consisted of genes conferring
resistance to multidrug, β-lactam, Macrolide-Lincosamide-Streptogramin
B (MLSB), tetracycline, vancomycin, and aminoglycoside, with multidrug
resistance genes as the most abundant members. There was a strong
correlation between the abundance of ARGs and MGE marker genes in
soils. The composition and diversity of ARGs in the five sludges were
substantially different from those in soils. Considerable proportions
of ARGs and MGE marker genes in the sludges attenuated following the
application, especially aminoglycoside and tetracycline resistance
genes. Annual applications posed a more significant impact on the
soil resistome, through both continued introduction and stimulation
of the soil intrinsic ARGs. In addition, direct introduction of sludge-specific
ARGs into soil was observed especially from ARG-rich sludge. These
results provide a better insight into the characteristics of ARG dissemination
from urban environment to the agricultural system through sewage sludge
applications
16S analysis
R script for analysis of 16S rRNA gene sequence