bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnitude and symmetry of seismic anisotropy in mica‐ and amphibole‐bearing metamorphic rocks and implications for tectonic interpretation of seismic data from the southeast Tibetan Plateau
Authors: Ji Shaocheng , Shao Tongbin , Michibayashi Katsuyoshi , Oya Shoma , Satsukawa Takako , Wang Qian , Zhao Weihua , Salisbury Matthew H.
Published: August 2015

We calibrated the magnitude and symmetry of seismic anisotropy for 132 mica‐ or amphibole‐bearing metamorphic rocks to constrain their departures from transverse isotropy (TI) which is usually assumed in the interpretation of seismic data. The average bulk Vp anisotropy at 600 MPa for the chlorite schists, mica schists, phyllites, sillimanite‐mica schists, and amphibole schists examined is 12.0%, 12.8%, 12.8%, 17.0%, and 12.9%, respectively. Most of the schists show Vp anisotropy in the foliation plane which averages 2.4% for phyllites, 3.3% for mica schists, 4.1% for chlorite schists, 6.8% for sillimanite‐mica schists, and 5.2% for amphibole schists. This departure from TI is due to the presence of amphibole, sillimanite, and quartz. Amphibole and sillimanite develop strong crystallographic preferred orientations with the fast c axes parallel to the lineation, forming orthorhombic anisotropy with Vp(X) > Vp(Y) > Vp(Z). Effects of quartz are complicated, depending on its volume fraction and prevailing slip system. Most of the mica‐ or amphibole‐bearing schists and mylonites are approximately transversely isotropic in terms of S wave velocities and splitting although their P wave properties may display orthorhombic symmetry. The results provide insight for the interpretation of seismic data from the southeast Tibetan Plateau. The N‐S to NW‐SE polarized crustal anisotropy in the Sibumasu and Indochina blocks is caused by subvertically foliated mica‐ and amphibole‐bearing rocks deformed by predominantly compressional folding and subordinate strike‐slip shear. These blocks have been rotated clockwise 70–90° around the east Himalayan Syntaxis, without finite eastward or southeastward extrusion, in responding to progressive indentation of India into Asia.
Source mechanism of small long‐period events at Mount St. Helens in July 2005 using template matching, phase‐weighted stacking, and full‐waveform inversion
Authors: Matoza Robin S. , Chouet Bernard A. , Dawson Phillip B. , Shearer Peter M. , Haney Matthew M. , Waite Gregory P. , Moran Seth C. , Mikesell T. Dylan
Published: August 2015

Long‐period (LP, 0.5‐5 Hz) seismicity, observed at volcanoes worldwide, is a recognized signature of unrest and eruption. Cyclic LP “drumbeating” was the characteristic seismicity accompanying the sustained dome‐building phase of the 2004–2008 eruption of Mount St. Helens (MSH), WA. However, together with the LP drumbeating was a near‐continuous, randomly occurring series of tiny LP seismic events (LP “subevents”), which may hold important additional information on the mechanism of seismogenesis at restless volcanoes. We employ template matching, phase‐weighted stacking, and full‐waveform inversion to image the source mechanism of one multiplet of these LP subevents at MSH in July 2005. The signal‐to‐noise ratios of the individual events are too low to produce reliable waveform inversion results, but the events are repetitive and can be stacked. We apply network‐based template matching to 8 days of continuous velocity waveform data from 29 June to 7 July 2005 using a master event to detect 822 network triggers. We stack waveforms for 359 high‐quality triggers at each station and component, using a combination of linear and phase‐weighted stacking to produce clean stacks for use in waveform inversion. The derived source mechanism points to the volumetric oscillation (∼10 m3) of a subhorizontal crack located at shallow depth (∼30 m) in an area to the south of Crater Glacier in the southern portion of the breached MSH crater. A possible excitation mechanism is the sudden condensation of metastable steam from a shallow pressurized hydrothermal system as it encounters cool meteoric water in the outer parts of the edifice, perhaps supplied from snow melt.
Microseismic sources during Hurricane Sandy
Authors: Chen Xiaohan , Tian Dongdong , Wen Lianxing
Published: August 2015

We find that microseisms generated by Hurricane Sandy exhibit coherent energy within 1 h time windows in the frequency band of 0.1–0.25 Hz, but with signals correlated among seismic stations aligned along close azimuths from the hurricane center. With the identification of this signal property, we show that travel time difference can be measured between the correlated stations. These correlated seismic signals can be attributed to two types of seismic sources, with one group of the seismic signals from the hurricane center and the other from coastal region. The seismic sources in coastal region are diffusive and move northward along the coastline as Sandy moves northward. We further develop a hurricane seismic source model, to quantitatively describe the coupling among sea level pressure fluctuations, ocean waves, and solid Earth in the region of hurricane center and determine the evolution of source's strength and pressure fluctuation in the region of hurricane center using seismic data. Strong seismic sources are also identified near the coastal region in New England after Sandy's dissipation, possibly related to subsequent storm surge in the area. The seismic method may be implemented as another practical means for hurricane monitoring, and seismological estimates of the hurricane seismic source model could be used as in situ proxy measurements of pressure fluctuation in the region of hurricane center for hurricane physics studies.
Critical evaluation of state evolution laws in rate and state friction: Fitting large velocity steps in simulated fault gouge with time‐, slip‐, and stress‐dependent constitutive laws
Authors: Bhattacharya Pathikrit , Rubin Allan M. , Bayart Elsa , Savage Heather M. , Marone Chris
Published: August 2015

The variations in the response of different state evolution laws to large velocity increases can dramatically alter the style of earthquake nucleation in numerical simulations. But most velocity step friction experiments do not drive the sliding surface far enough above steady state to probe this relevant portion of the parameter space. We try to address this by fitting 1–3 orders of magnitude velocity step data on simulated gouge using the most widely used state evolution laws. We consider the Dieterich (Aging) and Ruina (Slip) formulations along with a stress‐dependent state evolution law recently proposed by Nagata et al. (2012). Our inversions confirm the results from smaller velocity step tests that the Aging law cannot explain the observed response and that the Slip law produces much better fits to the data. The stress‐dependent Nagata law can produce fits identical to, and sometimes slightly better than, those produced by the Slip law using a sufficiently large value of an additional free parameter c that controls the stress dependence of state evolution. A Monte Carlo search of the parameter space confirms analytical results that velocity step data that are well represented by the Slip law can only impose a lower bound on acceptable values of c and that this lower bound increases with the size of the velocity step being fit. We find that our 1–3 orders of magnitude velocity steps on synthetic gouge impose this lower bound on c to be 10–100, significantly larger than the value of 2 obtained by Nagata et al. (2012) based on experiments on initially bare rock surfaces with generally smaller departures from steady state.
High‐resolution modeling of atmospheric dynamics in the Nepalese Himalaya
Authors: Collier Emily , Immerzeel Walter W.
Published: August 2015

High‐altitude meteorological processes in the Himalaya are influenced by complex interactions between the topography and the monsoon and westerly circulation systems. In this study, we use the Weather Research and Forecasting model configured with high spatial resolution to understand seasonal patterns of near‐surface meteorological fields and precipitation processes in the Langtang catchment in the central Himalaya. Using a unique high‐altitude observational network, we evaluate a simulation from 17 June 2012 to 16 June 2013 and conclude that, at 1 km horizontal grid spacing, the model captures the main features of observed meteorological variability in the catchment. The finer representation of the complex terrain and explicit simulation of convection at this grid spacing give strong improvements in near‐surface air temperature and small improvements in precipitation, in particular in the magnitudes of daytime convective precipitation and at higher elevations. The seasonal differences are noteworthy, including a reversal in the vertical and along‐valley distributions of precipitation between the monsoon and winter seasons, with peak values simulated at lower altitudes (~3000 m above sea level (asl)) and in the upper regions (above 5000 m asl) in each season, respectively. We conclude that there is great potential for improving the local accuracy of climate change impact studies in the Himalaya by using high‐resolution atmospheric models to generate the forcing for such studies.
Future changes in autumn atmospheric river events in British Columbia, Canada, as projected by CMIP5 global climate models
Authors: Radić Valentina , Cannon Alex J. , Menounos Brian , Gi Nayeob
Published: August 2015

Atmospheric rivers (ARs) often trigger extreme precipitation events in British Columbia (BC), Canada. Here we analyze how well the autumn AR events with the highest probability for extreme precipitation over BC, henceforth called AR‐extreme events, are simulated in five Coupled Model Intercomparison Project Phase 5 (CMIP5) global climate models (GCMs) and how these AR‐extreme events are projected to change by the end of the century. We examine the daily synoptic patterns of integrated water vapor transport (IVT) over the Pacific Ocean that favor the formation of AR‐extreme events. Our analysis and comparison with AR‐extreme events in four reanalysis products for the period 1979–2010 reveal that the GCMs more successfully resolve their seasonality and interannual variability than their frequencies and amount of precipitation brought to BC. For the CMIP5 scenario's Representative Concentration Pathway (RCP) 4.5 and RCP8.5, the frequency of AR‐extreme events will increase for the period 2070–2100 with the largest increase in December. All models project an increase in total precipitation over BC, due to the increase in frequency and intensity of the AR‐extreme events; however, the dominant factor is the increase in frequency, especially of those events with precipitation exceeding 20 mmd−1. The path of the ARs during the AR‐extreme events is projected to move northward, bringing stronger IVT and more precipitation to the north coast of BC, while the south coast may become drier than at the present day. The shift in the ARs is driven by the northward shift in the Aleutian Low pressure system, especially in RCP8.5.
Trends of ice breakup date in south‐central Ontario
Authors: Fu Congsheng , Yao Huaxia
Published: August 2015

Large‐scale ice phenology studies have revealed overall patterns of later freeze, earlier breakup, and shorter duration of ice in the Northern Hemisphere. However, there have been few studies regarding the trends, including their spatial patterns, in ice phenology for individual waterbodies on a local or small regional scale, although the coherence of ice phenology has been shown to decline rapidly in the first few hundred kilometers. In this study, we extracted trends, analyzed affecting factors, and investigated relevant spatial patterns for ice breakup date time series at 10 locations with record length ≥90 years in south‐central Ontario, Canada. Wavelet methods, including the multiresolution analysis (MRA) method for nonlinear trend extraction and the wavelet coherence (WTC) method for identifying the teleconnections between large‐scale climate modes and ice breakup date, are proved to be effective in ice phenology analysis. Using MRA method, the overall trend of ice breakup date time series (1905–1991) varied from earlier ice breakup to later ice breakup, then to earlier breakup again from south to north in south‐central Ontario. Ice breakup date is closely correlated with air temperature during certain winter/spring months, as well as the last day with snow on the ground and number of snow‐on‐ground days. The influences of solar activity and Pacific North American on ice breakup were comparatively uniform across south‐central Ontario, while those of El Niño–Southern Oscillation, North Atlantic Oscillation, and Arctic Oscillation on ice phenology changed with distance of 50–100 km in the north‐south direction.
Evaluation of global impact models' ability to reproduce runoff characteristics over the central United States
Authors: Giuntoli Ignazio , Villarini Gabriele , Prudhomme Christel , Mallakpour Iman , Hannah David M.
Published: August 2015

The central United States experiences a wide array of hydrological extremes, with the 1993, 2008, 2013, and 2014 flooding events and the 1988 and 2012 droughts representing some of the most recent extremes, and is an area where water availability is critical for agricultural production. This study aims to evaluate the ability of a set of global impact models (GIMs) from the Water Model Intercomparison Project to reproduce the regional hydrology of the central United States for the period 1963–2001. Hydrological indices describing annual daily maximum, medium and minimum flow, and their timing are extracted from both modeled daily runoff data by nine GIMs and from observed daily streamflow measured at 252 river gauges. We compare trend patterns for these indices, and their ability to capture runoff volume differences for the 1988 drought and 1993 flood. In addition, we use a subset of 128 gauges and corresponding grid cells to perform a detailed evaluation of the models on a gauge‐to‐grid cell basis. Results indicate that these GIMs capture the overall trends in high, medium, and low flows well. However, the models differ from observations with respect to the timing of high and medium flows. More specifically, GIMs that only include water balance tend to be closer to the observations than GIMs that also include the energy balance. In general, as it would be expected, the performance of the GIMs is the best when describing medium flows, as opposed to the two ends of the runoff spectrum. With regards to low flows, some of the GIMs have considerably large pools of zeros or low values in their time series, undermining their ability in capturing low flow characteristics and weakening the ensemble's output. Overall, this study provides a valuable examination of the capability of GIMs to reproduce observed regional hydrology over a range of quantities for the central United States.
An improved lightning flash rate parameterization developed from Colorado DC3 thunderstorm data for use in cloud‐resolving chemical transport models
Authors: Basarab B. M. , Rutledge S. A. , Fuchs B. R.
Published: August 2015

Accurate prediction of total lightning flash rate in thunderstorms is important to improve estimates of nitrogen oxides (NOx) produced by lightning (LNOx) from the storm scale to the global scale. In this study, flash rate parameterization schemes from the literature are evaluated against observed total flash rates for a sample of 11 Colorado thunderstorms, including nine storms from the Deep Convective Clouds and Chemistry (DC3) experiment in May‐June 2012. Observed flash rates were determined using an automated algorithm that clusters very high frequency radiation sources emitted by electrical breakdown in clouds and detected by the northern Colorado lightning mapping array. Existing schemes were found to inadequately predict flash rates and were updated based on observed relationships between flash rate and simple storm parameters, yielding significant improvement. The most successful updated scheme predicts flash rate based on the radar‐derived mixed‐phase 35 dBZ echo volume. Parameterizations based on metrics for updraft intensity were also updated but were found to be less reliable predictors of flash rate for this sample of storms. The 35 dBZ volume scheme was tested on a data set containing radar reflectivity volume information for thousands of isolated convective cells in different regions of the U.S. This scheme predicted flash rates to within 5.8% of observed flash rates on average. These results encourage the application of this scheme to larger radar data sets and its possible implementation into cloud‐resolving models.
Combined impacts of land cover changes and large‐scale forcing on Southern California summer daily maximum temperatures
Authors: Sequera Pedro , González Jorge E. , McDonald Kyle , Bornstein Robert , Comarazamy Daniel
Published: August 2015

California near‐surface air temperatures are influenced by large‐scale, regional and local factors. In that sense, a numerical model experiment was carried out to analyze the contribution of large‐scale (changes in atmospheric and oceanic conditions) and regional (increased urbanization) factors on the observed California South Coast Air Basin regional summer daily maximum temperature warming pattern from 1950 to 2013. The simulations were performed with past (1950–1954) and present (2009–2013) land cover and climate conditions. The past land cover was derived from historical digital maps, and the present land cover was updated with high‐resolution airborne remote sensing data. Results show that both factors contribute to the total change in daily maximum temperatures. Changes due to large‐scale climate conditions dominate in coastal (due to warming sea surface temperatures) and nonurban regions, while changes due to urbanization have an impact mainly in urban areas, especially inland where large‐scale warming weakens. Increased urbanization has also reduced sea‐breeze intensity due to changes in surface roughness. The model was able to reproduce the regional observed warming pattern, as it incorporates urban heat island effects, otherwise underestimated by large‐scale climate change only.
Effect of climate and land cover changes on watershed runoff: A multivariate assessment for storm water management
Authors: Ekness Paul , Randhir Timothy O.
Published: August 2015

Impact of climate change and land use on watershed runoff involves multiattribute ecohydrologic interactions. This information is critical to development of comprehensive storm water management policies. Watersheds in the continental United States have diverse temperatures and precipitation regimes and varying hydrogeomorphic features that influence runoff. This study investigates watershed‐scale runoff using statistical modeling for storm water policy optimization. Multivariate statistical modeling show that vegetative activity, annual evaporation, precipitation, temperature, and soil moisture significantly influenced watershed runoff. Soil moisture has a strong influence on runoff with each percent increase causing 5% increase in runoff. Nonlinear modeling with quadratic and interaction effects shows a significant interaction between soil moisture and other climatic variables in influencing annual runoff patterns. Changes in climate affect ecohydrologic characters by altering available soil moisture, evaporation, precipitation patterns, and runoff. Optimization of green infrastructure design can be a successful management tool for runoff with an understanding that changes to multiple attributes in ecohydrologic variables affect runoff. Multi‐attribute‐based green infrastructure and incentive policies can result in comprehensive storm water policies that incorporate climatic and ecohydrologic conditions of watershed systems.
New method for deriving the topside ionospheric Vary‐Chap scale height
Authors: Wang Sicheng , Huang Sixun , Fang Hanxian
Published: August 2015

An α‐Chapman function with a continuously varying scale height H(h) can be used to describe the topside ionosphere electron density profile that seamlessly connects the ionosphere with the plasmasphere. Huang and Reinisch () have derived the analytic expression of the scale height from the Vary‐Chap function, which can be applied to the topside F2 region. However, the H(h) is still difficult to obtain because H(h) is a function of the unknown value H(h) at hmF2. In this paper, the maximum entropy method is introduced to solve this ill‐posed problem, and the Vary‐Chap scale height for each electron density profile is derived. Then the average percentage errors that defined as the differences between the measured electron density profiles and the Vary‐Chap profiles obtained from the Vary‐Chap scale heights are calculated with the Alouette/ISIS satellites topside sounder database. The results reveal that the average percentage errors are generally less than 5% and the Vary‐Chap profiles can well represent the topside electron density profiles. What is more, the local time, seasonal, solar cycle, and latitudinal variations of the Vary‐Chap scale height are preliminarily analyzed.
Desulforhopalus
Authors: Kuever Jan , Rainey Fred A. , Widdel Friedrich
Published: August 2015

De.sul.fo.rho' pa.lus
. L. pref.
de
from; L. n.
sulfur
sulfur; L. n.
rhopalus
cudgel; M.L. masc. n.
Desulforhopalus
cudgel‐formed sulfate reducer.

Desulfobacterota / Desulfobulbia / Desulfobulbales / Desulfobulbaceae / Desulforhopalus

Cells are oval to rod shaped with rounded ends, 1.5–1.8 × 3–5 μm. Longer cells occur in the stationary phase. Cells may contain gas vesicles
. Occur singly, in pairs, or short chains. Spore formation is not observed. Gram negative and nonmotile. Strictly anaerobic, having both a respiratory and a fermentative type of metabolism.
Chemoorganotrophs
, using propionate, lactate, pyruvate, ethanol, and 1‐propanol

as electron donors and carbon sources. Organic substrates are incompletely oxidized to acetate and CO
2
. Chemolithoheterotrophic growth occurs with H
2
as the electron donor in the presence of acetate

as the organic carbon source.

Sulfate, sulfite, and thiosulfate serve as terminal electron acceptors and are reduced to H
2
S

. Sulfur and oxygen are not reduced; nitrate is reduced to ammonia only by
D. singaporensis
.
In the absence of an external electron acceptor, growth occurs by fermentation of pyruvate and lactate
.
D. singaporensis
can grow by fermentation of 2‐aminoethansulfonate (taurine) and by disproportionation of sulfite in the presence of acetate.

The mol
%
G
+
C of the DNA is
: 48.4–50.6.

Type species
:
Desulforhopalus vacuolatus
Isaksen and Teske 1999, 935 (Effective publication: Isaksen and Teske 1996, 167.)
Desulfonatronovibrio
Authors: Zavarzin George A. , Zhilina Tatjana N.
Published: August 2015

De.sul.fo.nat.ro.no.vib' rio
. L. pref.
de
from; L. n.
sulfur
sulfur; M.L. n.
natron
soda; M.L. masc. n.
vibrio
that which vibrates; L. n.
Desulfonatronovibrio
sulfate‐reducing vibrio from soda environment.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfohalobiaceae / Desulfonatronovibrio

Cells are minute vibrios, single or sigmoid in pairs, sometimes spirilloid
, 0.5 × 1.5–2 µm. Gram negative.
Motile by a single polar flagellum
. Endospores not formed.
Anaerobic. Possess a respiratory type of metabolism, with sulfate or other oxidized sulfur compounds serving as terminal electron acceptors and being reduced to sulfide. Extremely alkaliphilic
. No growth at pH 7; optimal pH 9.0–9.7; maximum pH 10.2.
Obligately dependent on sodium and carbonates in the growth medium
. Optimal temperature 37–40°C.
Lithoheterotrophic
. Utilize H
2
or formate for reduction of sulfur compounds. Utilize acetate plus vitamins or yeast extract for anabolism. Desulfoviridin is absent. Cells contain
c
‐type cytochromes. Habitat: soda lakes. The genus currently includes only a single species.

The mol
%
G
+
C of the DNA is
: 47.9–48.5.

Type species
:
Desulfonatronovibrio hydrogenovorans
Zhilina, Zavarzin and Rainey
in
Zhilina, Zavarzin, Rainey, Pikuta, Osipov and Kostrikina 1997, 149.
Desulfothermus gen. nov
Authors: Kuever Jan , Rainey Fred A. , Widdel Friedrich
Published: August 2015

De.sul.fo.ther' mus
. L. pref.
de
from; L. n.
sulfur
sulfur; Gr. adj.
thermus
hot; M.L. masc. n.
Desulfothermus
sulfate reducer living in hot places.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfohalobiaceae / Desulfothermus

Rod‐shaped to slightly curved cells, 0.8–1.0 × 2.0–3.5 μm
. Occur singly or in pairs. May grow as individual cells or as compact clumps. Cells tend to stick to hydrophobic surfaces. Spore formation is not observed. Gram negative. Slow motility may occur. Strict anaerobe with a respiratory type of metabolism.
Chemoorganotroph
, using alkanes (C
6
–C
14
), and long‐chain fatty acids (C
4
–C
18
)
as electron donors and as carbon sources
; these compounds are completely oxidized to CO
2
via the anaerobic C
1
‐pathway (carbon monoxide dehydrogenase [CO‐DH] pathway, Wood pathway) as indicated by CO–DH activity.

Sulfate and thiosulfate serve as terminal electron acceptors and are reduced to H
2
S

. The optimal pH range for growth is 6.5–6.8. The optimal temperature range for growth is 60–65°C. Mesophilic species have not been described. Anoxic media containing a reductant (usually sulfide), NaCl, and MgCl
2
are necessary for growth. Vitamins are not required. Occur in anoxic marine sediment rich in aliphatic hydrocarbons.

The mol
%
G
+
C of the DNA is
: 37.4.

Type species
:
Desulfothermus naphthae
sp. nov
.
Desulfomicrobium
Authors: Sharak Genthner Barbara R. , Devereux Richard
Published: August 2015

De.sul.fo.mi.cro' bi.um
. L. pref.
de
from; L. n.
sulfur
sulfur; G. adj.
micros
small; G. n.
bios
life; M.L. neut. n.
Desulfomicrobium
sulfate‐reducing, small life.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfomicrobiaceae / Desulfomicrobium

Short, straight rod‐ or ellipsoidal‐shaped cells, 0.5–0.9 × 1.3–2.9 μm
, with rounded ends, either singly or in pairs (Sharak Genthner et al., 1994).
Gram‐negative
stain reaction and cell‐wall structure. Cells are
motile, usually by a single polar flagellum
. Endospores not formed.
Anaerobic
. Pre‐reduced medium or reducing agent required in medium for growth.

Growth can occur by anaerobic respiration with sulfate or sulfoxyanions as terminal electron acceptor, producing H
2
S

. Simple organic compounds that serve as electron donors during sulfate respiration include lactate, pyruvate, ethanol, formate, and hydrogen. Sulfate respiration with lactate as electron donor is incomplete, with the formation of acetate and CO
2
. Hydrogenase present.

Cells contain
b
‐ and
c
‐type cytochromes

.
Metabolism can also be fermentative
on simple organic substrates, including pyruvate, malate, or fumarate.
Carbohydrates are not fermented
. No specific vitamins required.
Nitrate not reduced
. No requirement for NaCl.
Desulfoviridin absent
. Optimal temperature 25–30°C. Found in freshwater to brackish to marine anaerobic sediments and mud, in anaerobic stratal or overlying water, and in saturated mineral or organic deposits.

The mol
%
G
+
C of the DNA is
: 52.5–59.6.

Type species
:
Desulfomicrobium baculatum
(Rozanova and Nazina 1976) Rozanova, Nazina and Galushko 1994, 370 (Effective publication: Rozanova, Nazina and Galushko 1988, 519) (
Desulfovibrio baculatus
Rozanova and Nazina 1976, 825;
Desulfomicrobium baculatus
(sic) Rozanova, Nazina and Galushko 1988, 519.)
Desulfonatronum
Authors: Zhilina Tatjana N.
Published: August 2015

De.sul.fo.na.tro' num
. L. pref.
de
from; L. n.
sulfur
sulfur; M.L. n.
natron
soda; M.L. masc. n.
Desulfonatronum
a sulfate reducer inhabiting soda lakes.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfonatronumaceae / Desulfonatronum

Cells are vibrios
0.7–0.9 × 2.0–3.0 µm, occurring singly or sigmoid in pairs. Cells may be spirilloid under suboptimal conditions. Asporogenous. Gram negative. Motile by a single polar flagellum.
Anaerobic. Possess a strictly respiratory type of metabolism with sulfate and other oxidized sulfur compounds serving as terminal electron acceptors
and being reduced to H
2
S.
Extremely alkaliphilic
. No growth at pH values below 8; pH optimum, 9.5; pH maximum, 10.
Obligately dependent on sodium and carbonates. Lithoheterotrophic
. Utilizes H
2
, formate, ethanol, or lactate for reduction of sulfur compounds. Utilizes acetate plus vitamin or yeast extract for anabolism. Desulfoviridin is not present. Cells contain
c
‐type cytochromes. The habitat is bottom sediments of alkaline lakes. The genus presently includes only a single species.

The mol
%
G
+
C of the DNA is
: 56–57.

Type species
:
Desulfonatronum lacustre
Pikuta, Zhilina and Rainey 1998a, 631 (Effective publication: Pikuta, Zhilina and Rainey
in
Pikuta, Zhilina, Zavarzin, Kostrikina, Osipov and Rainey 1998b, 112.)
Lawsonia
Authors: McOrist Steven , Gebhart Connie J.
Published: August 2015

Law.so' ni.a
. L. dim. ending ‐
ia
M.L. masc. n.
Lawsonia
named after Gordon H.K. Lawson, the Scottish veterinarian who first recognized the organism causing porcine proliferative enteropathy.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae / Lawsonia

Curved, vibrioid, or occasionally straight rods, 0.3–0.4 × 1.5–2.0 μm
. The morphology is influenced by age and environment; descriptions refer to organisms within naturally infected intestinal epithelial cells or freshly grown co‐cultures of intestinal epithelial cells. Gram negative. Single polar bacterial cell appendages have been observed in some preparations of co‐cultured strains, with rapid darting motion apparent in active cultures. Endospores not formed.
Obligately intracellular, cell‐dependent, and microaerobic
. Optimal temperature usually 35–37°C. Strains have demonstrated survival, but not growth, at lower temperatures. The organisms react with the IG4 monoclonal antibody shown to be specific for
Lawsonia
sp. Habitats: intestines of pigs and other animals; feces. The causal agent of proliferative enteropathy. Key aspects of the 16S rDNA sequence are given in McOrist et al., 1995a. A 16S rRNA signature sequence for the genus is 5′‐GAUUAAGAGGUGCCUUUCGGGGAGCCUCAA‐3′, corresponding to the nucleotide positions 1015–1042 of the
E. coli
16S rRNA sequence.

The mol
%
G
+
C of the DNA is
: 34; total genome length 1.713 Mbp.

Type species
:
Lawsonia intracellularis
McOrist, Gebhart, Boid and Barns 1995a, 824.
Pelobacter
Authors: Schink Bernhard
Published: August 2015

Pe.lo.bac' ter
. Gr. masc. n.
pelos
mud; M.L. masc. n.
bacter
the equivalent of Gr. neut. n.
bakterion
a small rod; M.L. masc. n.
Pelobacter
a mud‐inhabiting rod.

Proteobacteria / Deltaproteobacteria / Desulfuromonales / Desulfuromonaceae / Pelobacter

Rod‐shaped cells
, 0.5–1.0 × 1.5–6.0 µm, with rounded ends, single, in pairs, or in chains. Motile forms may occur in some species; other species are nonmotile. Gram negative. Endospores not formed. Anaerobic.
Have a chemoorganotrophic, fermentative type of metabolism, using few simple organic compounds as substrates. Carbohydrates not utilized
. Media containing a reductant, e.g., sulfide, are necessary for growth. Catalase negative. Isolated from sediments of limnic or marine origin.

The mol
%
G
+
C of the DNA is
: 50–58.

Type species
:
Pelobacter acidigallici
Schink and Pfennig 1983, 896 (Effective publication: Schink and Pfennig 1982, 200.)
Syntrophobacter
Authors: McInerney Michael J. , Stams Alfons J.M. , Boone David R.
Published: August 2015

Syn.tro.pho.bac' ter. Gr. adj.syntogether with; Gr. n.trophosone who feeds; M.L. n.bactermasc. equivalent of Gr. neut. n.bacterionsmall staff, rod; M.L. masc. n.Syntrophobacterrod which feeds together with (another species).

Proteobacteria / Deltaproteobacteria / Syntrophobacterales / Syntrophobacteraceae / Syntrophobacter

Straight rods with rounded ends, 0.6–1.2 × 1.0–4.5 µm, sometimes oval to ellipsoid, occur singly and in pairs. May form short chains and filamentous cells (up to 35 µm).Gram negative. Endospores not formed.Strictly anaerobic chemoorganotroph. Mesophilic. Growth occurs at neutral pH (6.2–8.0) in low salinity media.Growth occurs by syntrophic metabolism and sulfate reduction. Propionate oxidation to acetate and CO2requires the presence of either a H2/formate‐using organism (methanogen or sulfate reducer) or sulfate as the electron acceptor.Acetate and other fatty acids not oxidized. Some species grow fermentatively with pyruvate, malate, or fumarate. Lactate and propanol may serve as electron donors for syntrophic metabolism or sulfate reduction.Other common bacterial substrates such as sugars and aromatic compounds are not usedeither in coculture with a H2/formate‐using organism or in pure culture with sulfate as the electron acceptor. Sulfite or thiosulfate, but not nitrate, may be used as the electron acceptor. Habitat is sludge from anaerobic waste treatment facilities.

The mol%G+C of the DNA is: 57–61.

Type species:Syntrophobacter woliniiBoone and Bryant 1984, 355 (Effective publication: Boone and Bryant 1980, 631.)
Thermodesulforhabdus
Authors: Beeder Janiche
Published: August 2015

Ther.mo.de.sul.fo.rhab' dus
. Gr. adj.
thermos
warm, hot; L. pref.
de
from; L. n.
sulfur
sulfur; Gr. fem. n.
rhabdos
rod; M.L. fem. n.
Thermodesulforhabdus
thermophilic, rod‐shaped, sulfate reducer.

Proteobacteria / Deltaproteobacteria / Syntrophobacterales / Syntrophobacteraceae / Thermodesulforhabdus

Rod‐shaped cells 1
×
2.5 μm. Motile by means of a single polar flagellum
. Gram‐negative by staining and cell wall structure.
Anaerobic
. Chemoorganotrophic.

The mol
%
G
+
C of the DNA is
: 51.

Type species
:
Thermodesulforhabdus norvegica
Beeder, Torsvik and Lien 1996, 625 (Effective publication:
Thermodesulforhabdus norvegicus
(sic) Beeder, Torsvik and Lien 1995, 335.)
Photobacterium
Authors: Thyssen An , Ollevier Frans
Published: August 2015

Pho.to.bac.te' ri.um
. Gr. n.
phos
light; Gr. neut. dim. n.
bakterion
a small rod; M.L. neut. n.
Photobacterium
light (‐producing) bacterium.

Proteobacteria / Gammaproteobacteria / “Vibrionales” / Vibrionaceae / Photobacterium

Plump, straight rods, 0.8–1.3 × 1.8–2.4 μm
; some coccobacillary and bipolar. Involution forms are usually seen in old cultures or under adverse conditions of cultivation. Gram negative.
Motile by 1–3 unsheathed polar flagella
; some species nonmotile.
Facultative anaerobic
. Chemoorganotrophic, having
both a respiratory and a fermentative type of metabolism
. Optimal growth temperature range appears to be 18–25°C, except for the psychrophilic species
P. profundum
.
Sodium ions are required for growth
.
D
‐Glucose and
D
‐mannose are catabolized with the production of acid and, in the case of
P. damselae
subsp.
damselae, P. iliopiscarium
, and
P. phosphoreum
, with gas. Oxidase reaction is variable. Most strains are lysine decarboxylase and arginine di‐hydrolase positive. Ornithine decarboxylase negative.
Accumulate poly
‐β‐
hydroxybutyrate
(PBH) under certain conditions of cultivation;
do not use the exogenous monomer
β‐
hydroxybutyrate
. Most strains

grow in a minimal medium containing a seawater base,
d
‐glucose, and NH
4
Cl

; other strains also require
L
‐methionine. Utilize
D
‐glucose,
D
‐fructose, glycerol, and
D
‐mannose. Some species are bioluminescent.

The mol
%
G
+
C of the DNA is
: 39–44 (Baumann and Baumann, 1977).

Type species
:
Photobacterium phosphoreum
(Cohn 1878) Beijerinck 1889, 401 (
Micrococcus phosphoreus
Cohn 1878, 126.)
Incertae Sedis Tolumonas
Authors: Fischer‐Romero Carmen , Tindall Brian J.
Published: August 2015

To.lu.mo' nas
. L. n.
toluolum
toluol (German for toluene); Gr. n.
monas
unit; M.L. fem. n.
Tolumonas
toluene‐producing unit.

Proteobacteria / Gammaproteobacteria / Aeromonadales / Aeromonadaceae / Incertae Sedis Tolumonas

Cells are
nonmotile
, Gram‐negative rods (2.5–3.2 × 0.9–1.2 µm) that occur singly or in pairs.
Growth
occurs under
aerobic and anaerobic
conditions. Anaerobic cultures are catalase and oxidase negative; aerobic cultures are
catalase positive
and
oxidase negative. Toluene is produced from phenylalanine, phenylacetate, phenyllactate, and phenylpyruvate
only in the presence of an additional carbon source. Phenol is produced when phenylalanine is replaced by tyrosine. The optimum conditions for anaerobic growth are
22°C
and pH 7.2. The major fermentation products in peptone–yeast extract–glucose cultures are ethanol, acetic acid, and formic acid. Under anaerobic conditions
D
‐arabinose,
D
‐cellobiose,
D
‐fructose,
D
‐glucose, glycogen, inulin, maltose,
D
‐mannose,
D
‐melecitose, melibiose,
D
‐raffinose, l‐rhamnose,
D
‐ribose, salicin, sucrose,
D
‐trehalose,
D
‐mannitol, and
D
‐sorbitol are used as carbon sources. In the presence of air the following organic substances are used: Tween 40, Tween 80,
L
‐arabinose,
D
‐fructose,
D
‐galactose,
D
‐glucose, methyl‐pyruvate, monomethyl succinate, acetic acid,
cis
‐aconitic acid,
D
‐galacturonic acid,
D
‐gluconic acid,
D
‐glucuronic acid, β‐hydroxybutyric acid, α‐ketoglutaric acid,
DL
‐lactic acid, malonic acid, quinic acid, sebacic acid, succinic acid, glucuronamide,
L
‐alanine,
L
‐asparagine,
L
‐aspartic acid,
L
‐glutamic acid,
L
‐histidine,
L
‐threonine, urocanic acid, and inosine. The enzymes lipase, lecithinase, urease, and exoprotease are not produced. Indole, lipase, and H
2
S are not formed. According to the results of 16S rDNA sequence analysis this genus belongs to the
Gammaproteobacteria
.

The mol
%
G
+
C of the DNA is
: 49.

Type species
:
Tolumonas auensis
Fischer‐Romero, Tindall and Jüttner 1996 , 187.
Succinimonas
Authors: Bryant Marvin P.
Published: August 2015

Suc.ci.ni.mo' nas
. M.L. n.
acidum succinicum
succinic acid; Gr. n.
monas
a unit, monad; M.L. fem. n.
Succinimonas
succinic acid monad.

Proteobacteria / Gammaproteobacteria / Aeromonadales / Succinivibrionaceae / Succinimonas

Short, straight rods to coccobacilli, 1.0–1.5 μm × 1.0–3.0 μm, with rounded ends
. No spores or resting stages are produced. Gram negative.
Motile by a single polar flagellum
.

The mol
%
G
+
C of the DNA is
: unknown.

Type species
:
Succinimonas amylolytica
Bryant, Small, Bouma and Chu 1958, 21.
Psychromonas
Authors:   The Editorial Board
Published: August 2015

Psy.chro.mo' nas
. Gr. adj.
psychros
cold; Gr. fem. n.
monas
a unit; N.L. n.
Psychromonas
a cold monad.

Proteobacteria / Gammaproteobacteria / Alteromonadales / Alteromonadaceae / Psychromonas

Motile Gram‐negative rod‐shaped or oval cells; polar flagellum.
Grow at temperatures <22°C
. Catalase and oxidase positive. Major quinone Q‐8; major fatty acids are C
14:1
, C
16:0
, and C
16:1
.
Facultative anaerobes
; use carbohydrates for energy for growth.
Found in marine or high salinity environments
.

The mol
%
G
+
C of the DNA is
: 38.1–43.8.

Type species
:
Psychromonas antarctica
Mountfort, Rainey, Burghardt, Kaspar and Stackebrandt 1998b, 631 (Effective publication: Mountfort, Rainey, Burghardt, Kaspar and Stackebrandt 1998a, 237.)
Shewanella
Authors: Bowman John P.
Published: August 2015

Shew.a.nel' l.a
. M.L. dim. ending ‐
ella
;
Shewanella
named after James Shewan for his work in fisheries microbiology.

Proteobacteria / Gammaproteobacteria / Alteromonadales / Alteromonadaceae / Shewanella

Straight or curved rods
, 0.5–0.8 × 0.7–2.0 µm. Endospores and microcysts are not formed.
Motile by a single, unsheathed, polar flagellum
. Gram negative. Colonies are often pale tan to pink‐orange, due to cytochrome accumulation.
Oxidase and catalase positive
. Chemoheterotrophic.
Facultatively anaerobic. Oxygen is used as the electron acceptor during aerobic growth. Anaerobic growth is predominantly respiratory
; the oxidation of organic carbon compounds or H
2
is coupled to the reduction of various inorganic and organic electron acceptors, including NO
3
−
, NO
2
−
, Fe
3+
, trimethylamine‐
N
‐oxide, fumarate, various sulfur compounds, and Mn
4+
.
May also be fermentative
, producing acid (but usually no gas) from carbohydrates, such as d‐glucose and
N
‐acetylglucosamine. Constitutive arginine dihydrolase is usually absent. Most strains can form H
2
S from thiosulfate.

May require Na
+
ions

for growth.
Most species can grow at 4°C
. Some species are psychrophilic. One species is psychrophilic and barophilic. Major fatty acids are C
13:0 iso
, C
14:0
, C
15:0
, C
15:0 iso
, C
16:1 ω7c
, C
16:0
, and C
17:1 ω8c
. Several species can also form significant quantities of the omega‐3 fatty acid eicosapentaenoic acid (C
20:5 ω3c
). Isoprenoid quinone components include ubiquinone‐8, ubiquinone‐7, and menaquinone‐7, with smaller amounts of methylmenaquinone‐7. Major polyamines are putrescine and cadaverine. Member of the order
Alteromonadales
, family
Alteromonadaceae
, class
Gammaproteobacteria
. Isolated from clinical samples, chilled meats, butter, cutting oils, fresh water, freshwater sediment, estuaries, salt marshes, marine algae, seawater, marine sediment, fish, marine invertebrates, sea ice, marine snow, and abyssal ocean waters.

The mol
%
G
+
C of the DNA is
: 38–54.

Type species
:
Shewanella putrefaciens
(Lee, Gibson and Shewan 1977) MacDonell and Colwell 1986, 355 (Effective publication: MacDonell and Colwell 1985, 180) (
Alteromonas putrefaciens
Lee, Gibson and Shewan 1977, 449.)
Thiodictyon
Authors: Imhoff Johannes F.
Published: August 2015

Thi' o.dic' ty.on. Gr. n.thiossulfur; Gr. n.dictyona net; M.L. neut. n.Thiodictyonsulfur net.

Proteobacteria / Gammaproteobacteria / Chromatiales / Chromatiaceae / Thiodictyon

Cells are rod shaped with rounded ends, sometimes appearing spindle‐shaped, multiply by binary fission,nonmotile under all conditions, may form aggregates in which the cells are arranged end‐to‐end in an irregular netlike structure, the shape of which is variable. May also form clumps that are more compact or break up into individual cells. Contain large,irregularly shaped gas vesiclesin the central part of the cell. Gram negative, belong to theGammaproteobacteria, and contain internalphotosynthetic membranes of vesicular typewith bacteriochlorophyllaand carotenoids as photosynthetic pigments.

The mol%G+C of the DNA is: 65.3–66.3.

Type species:Thiodictyon elegansWinogradsky 1888x, 82.
Brenneria
Authors: Hauben Lysiane , Swings Jean
Published: August 2015

Bren.ne' ri.a
. M.L. fem. n.
Brenneria
named after Don J. Brenner.

Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / Brenneria

Cells are 0.5–1.0 × 1.3–3.0 µm; have rounded ends; occur singly or rarely in pairs. Gram negative. Motile by peritrichous flagella. Facultatively anaerobic, but anaerobic growth by some species is weak. Optimum temperature, 27–30°C; maximum temperature for growth is 40°C. Oxidase negative. Catalase positive. Acid is produced from fructose,
D
‐galactose,
D
‐glucose,
D
‐mannose, salicin, and sucrose but not from adonitol or dulcitol. Do not possess arginine decarboxylases, arginine dihydrolase, lysine decarboxylases, ornithine decarboxylases, or starch hydrolase.

The mol
%
G
+
C of the DNA is
: 50.1–56.1 (

T
m

, Bd).

Type species
:
Brenneria salicis
(Day 1924) Hauben, Moore, Vauterin, Steenackers, Mergaert, Verdonck and Swings 1999a, 1 (Effective publication: Hauben, Moore, Vauterin, Steenackers, Mergaert, Verdonck and Swings 1998a, 394) (
Erwinia salicis
(Day 1924) Chester 1936, 406; “
Bacterium salicis
” Day 1924, 14.)
Buttiauxella
Authors: Kämpfer Peter
Published: August 2015

But.ti' aux' el.la
. M.L. dim. ending ‐
ella
; M.L. fem. n.
Buttiauxella
named after René Buttiaux, a French microbiologist for his numerous contributions to the taxonomy of
Enterobacteriaceae
.

Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / Buttiauxella

Straight rods, 0.5–0.7 × 2–3 μm
, conforming to the general definition of the family
Enterobacteriaceae
.
Gram negative, motile by peritrichous flagella
. Facultatively anaerobic. Chemoorganotrophic. Psychrotolerant, growing at 4°C.
D
‐Glucose is fermented with the production of acid and gas. Nitrate is reduced to nitrite. Oxidase negative, catalase positive.

Most strains are methyl red positive. The majority of strains are indole negative. Acids are produced from various carbohydrates, including
L
‐arabinose, cellobiose, maltose

,

D

‐
mannose
,

L

‐
rhamnose
,

D

‐
xylose, and salicin
. 16S rDNA sequence analysis of the type strain of
Buttiauxella agrestis
clearly places the genus in the family
Enterobacteriaceae
within the
Gammaproteobacteria
. Often isolated from fresh water, but also found in soil, and especially in the intestines of snails and slugs from various regions in the world.

The mol
%
G
+
C of the DNA is
: 47–51.

Type species
:
Buttiauxella agrestis
Ferragut, Izard, Gavini, Lefebvre and Leclerc 1982, 266, emend. Müller, Brenner, Fanning, Grimont and Kämpfer 1996, 60 (Effective publication: Ferragut, Izard, Gavini, Lefebvre and Leclerc 1981, 40).
Cedecea
Authors: Farmer J.J.
Published: August 2015

Ce.de' ce.a
. M.L. fem. n.
Cedecea
formed from the abbreviation
CDC
. The named was coined by P.A.D. Grimont and F. Grimont for the Centers for Disease Control, Atlanta, Georgia, where the organisms were originally recognized as a new group and named Enteric Group 15.

Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / Cedecea

Rod‐shaped cells 0.6–0.7 × 1.3–1.9 µm, conforming to the general definition of the family
Enterobacteriaceae
. Gram negative. Motile, with five to nine peritrichous flagella. Grow at 15°, 20°, and 37°C. Facultatively anaerobic.
Catalase positive, strong and rapid
. Oxidase negative. Nonpigmented. Reduce nitrate to nitrite.

The mol
%
G
+
C of the DNA is
: 48–52.

Type species
:
Cedecea davisae
Grimont, Grimont, Farmer and Asbury 1981a, 325.
Edwardsiella
Authors: Sakazaki Riichi
Published: August 2015

Ed.ward.si.el' la
. M.L. dim. ending ‐
ella;
M.L. fem. n.
Edwardsiella
named after the American bacteriologist
RR
. Edwards (1901–1966).

Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / Edwardsiella

Straight rods
, ~1.0 × 2.0–3.0 µm, conforming to the general definition of the family
Enterobacteriaceae
. Gram negative.
Motile by peritrichous flagella
, but nonmotile strains may occur. Facultatively anaerobic. Growth occurs on ordinary media with small colonies (0.5–1.0 mm in diameter) after 24 h incubation. Optimum temperature, 37°C, except for
E
.
ictaluri
, which prefers a lower temperature.
Nicotinamide and amino acids are required for growth
. Reduce nitrate to nitrite. Ferment
D
‐glucose with the production of acid and often gas. Also

ferment a few other carbohydrates but are inactive compared to many taxa in the family
Enterobacteriaceae
. Usually resistant to colistin but susceptible to most other antibiotics, including penicillin

. Frequently isolated from river fish and cold‐blooded animals and their environment, particularly fresh water. Pathogenic for eels, catfish, and other animals, sometimes causing economic losses; also opportunistic pathogen and possibly rare cause of gastroenteritis for humans. A member of the
Gammaproteobacteria
.

The mol
%
G
+
C of the DNA is
: 53–59.

Type species
:
Edwardsiella tarda
Ewing and McWhorter
in
Ewing, McWhorter, Escobar and Lubin 1965, 37.