bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seeing Cooperation or Competition: Ecological Interactions in Cultural Perspectives
Authors: ojalehto bethany l. , Medin Douglas L. , Horton William S. , Garcia Salino G. , Kays Estefano G. 
Published: October 2015

AbstractDo cultural models facilitate particular ways of perceiving interactions in nature? We explore variability in folkecological principles of reasoning about interspecies interactions (specifically, competitive or cooperative). In two studies, Indigenous Panamanian Ngöbe and U.S. participants interpreted an illustrated, wordless nonfiction book about the hunting relationship between a coyote and badger. Across both studies, the majority of Ngöbe interpreted the hunting relationship as cooperative and the majority of U.S. participants as competitive. Study 2 showed that this pattern may reflect different beliefs about, and perhaps different awareness of, plausible interspecies interactions. Further probes suggest that these models of ecological interaction correlate with recognition of social agency (e.g., communication, morality) in nonhuman animals. We interpret our results in terms of cultural models of nature and nonhuman agency.
Effect of patch size on seed removal by harvester ants
Authors: Torra J , Atanackovic V , Blanco‐Moreno J M , Royo‐Esnal A , Westerman P R 
Published: October 2015

SummaryThe harvester ant Messor barbarus can be responsible for high weed seed losses in dry land cereals in Spain. Because weeds occur in patches, harvester ants have to be able to find and exploit patches. However, seed patches can differ in size and may, therefore, differ in the probability of being discovered and exploited. Here, 90 patches varying in size from 0.25 to 9 m2 were created in three 50 × 50 m subareas in a cereal field. Oat seeds were sown as weed seed surrogates in the patches at 2000 seeds m−2. After 24 h, those remaining were collected and the exploitation rate (the percentage of seeds removed per patch discovered by ants) was estimated. Harvester ant nests and the location of the seed patches were georeferenced and used to estimate distances between them. The patch encounter rate (the proportion of patches discovered by the ants) decreased slightly, but significantly, with decreasing patch size, though not the exploitation rate, which was lowest in the smallest patches (78–94%) and highest in the largest (99–100%). Seed patches that were not found or partially exploited were mostly located in subareas with a lower ant nest density or a longer distance away from the nearest nest than seed patches that were fully exploited. The results of this study indicate that the interaction between the spatial distribution of ant nests and the patchy distribution of seeds can create opportunities for seeds to be subjected to lower levels of predation.
Modelling interactive effects of herbicide application timing and dose for the control of Bromus japonicus in wheat in an arid environment
Authors: Sarani M , Oveisi M , Rahimian Mashhadi H , Alizadeh H 
Published: October 2015

SummaryTimely herbicide application is a key factor in herbicide efficiency that may provide some possibility of reducing herbicide dose. Field experiments were conducted to study the interactive effect of dose of the herbicide mesosulfuron‐methyl and application timing on the control of Bromus japonicas in wheat. Herbicide application timings were based on Zadoks growth stages of wheat. An empirical model was developed for deciding herbicide dose. Relationships between herbicide dose and weed biomass were described with the standard dose–response model at each application time. Parameter estimates suggested a linear increase in parameters W0 (weed biomass with no herbicide treatment) and ED50 (herbicide dose required for 50% reduction in W0) with thermal time. A combined dose–response (CDR) model, with W0 and ED50 being replaced by their linear relationships with thermal time, was used for weed biomass prediction. CDR was incorporated into the rectangular hyperbolic relationship to predict wheat yield with different herbicide doses and application timings simultaneously. The combined model was rearranged to give the minimum dose required to restrict weed competition and achieve an acceptable wheat yield. For example, to obtain a wheat grain yield of 4.4 kg h−1 (90% of the potential yield), the model suggests 75% of the recommended dose, if herbicide is applied prior to tillering. With delayed herbicide application to wheat jointing, the respective amount of wheat yield is achieved with herbicide rates higher than the recommended dose. The model developed in this study can be used to decide herbicide dose for controlling B. japonicus based on application timing.
Microbiological Oxidation of Antimony(III) with Oxygen or Nitrate by Bacteria Isolated from Contaminated Mine Sediments
Authors: Terry Lee R. , Kulp Thomas R. , Wiatrowski Heather , Miller Laurence G. , Oremland Ronald S. 
Published: October 2015

ABSTRACT

Bacterial oxidation of arsenite [As(III)] is a well-studied and important biogeochemical pathway that directly influences the mobility and toxicity of arsenic in the environment. In contrast, little is known about microbiological oxidation of the chemically similar anion antimonite [Sb(III)]. In this study, two bacterial strains, designated IDSBO-1 and IDSBO-4, which grow on tartrate compounds and oxidize Sb(III) using either oxygen or nitrate, respectively, as a terminal electron acceptor, were isolated from contaminated mine sediments. Both isolates belonged to the
Comamonadaceae
family and were 99% similar to previously described species. We identify these novel strains as
Hydrogenophaga
taeniospiralis
strain IDSBO-1 and
Variovorax paradoxus
strain IDSBO-4. Both strains possess a gene with homology to the
aioA
gene, which encodes an As(III)-oxidase, and both oxidize As(III) aerobically, but only IDSBO-4 oxidized Sb(III) in the presence of air, while strain IDSBO-1 could achieve this via nitrate respiration. Our results suggest that expression of
aioA
is not induced by Sb(III) but may be involved in Sb(III) oxidation along with an Sb(III)-specific pathway. Phylogenetic analysis of proteins encoded by the
aioA
genes revealed a close sequence similarity (90%) among the two isolates and other known As(III)-oxidizing bacteria, particularly
Acidovorax
sp. strain NO1. Both isolates were capable of chemolithoautotrophic growth using As(III) as a primary electron donor, and strain IDSBO-4 exhibited incorporation of radiolabeled [
14
C]bicarbonate while oxidizing Sb(III) from Sb(III)-tartrate, suggesting possible Sb(III)-dependent autotrophy. Enrichment cultures produced the Sb(V) oxide mineral mopungite and lesser amounts of Sb(III)-bearing senarmontite as precipitates.
Improvement of Glucose Uptake Rate and Production of Target Chemicals by Overexpressing Hexose Transporters and Transcriptional Activator Gcr1 in Saccharomyces cerevisiae
Authors: Kim Daehee , Song Ji-Yoon , Hahn Ji-Sook 
Published: October 2015

ABSTRACT

Metabolic engineering to increase the glucose uptake rate might be beneficial to improve microbial production of various fuels and chemicals. In this study, we enhanced the glucose uptake rate in
Saccharomyces cerevisiae
by overexpressing hexose transporters (HXTs). Among the 5 tested HXTs (Hxt1, Hxt2, Hxt3, Hxt4, and Hxt7), overexpression of high-affinity transporter Hxt7 was the most effective in increasing the glucose uptake rate, followed by moderate-affinity transporters Hxt2 and Hxt4. Deletion of
STD1
and
MTH1
, encoding corepressors of
HXT
genes, exerted differential effects on the glucose uptake rate, depending on the culture conditions. In addition, improved cell growth and glucose uptake rates could be achieved by overexpression of
GCR1
, which led to increased transcription levels of
HXT1
and ribosomal protein genes. All genetic modifications enhancing the glucose uptake rate also increased the ethanol production rate in wild-type
S. cerevisiae
. Furthermore, the growth-promoting effect of
GCR1
overexpression was successfully applied to lactic acid production in an engineered lactic acid-producing strain, resulting in a significant improvement of productivity and titers of lactic acid production under acidic fermentation conditions.
Involutin Is an Fe
3+
Reductant Secreted by the Ectomycorrhizal Fungus Paxillus involutus during Fenton-Based Decomposition of Organic Matter
Authors: Shah Firoz , Schwenk Daniel , Nicolás César , Persson Per , Hoffmeister Dirk , Tunlid Anders 
Published: October 2015

ABSTRACT

Ectomycorrhizal fungi play a key role in mobilizing nutrients embedded in recalcitrant organic matter complexes, thereby increasing nutrient accessibility to the host plant. Recent studies have shown that during the assimilation of nutrients, the ectomycorrhizal fungus
Paxillus involutus
decomposes organic matter using an oxidative mechanism involving Fenton chemistry (Fe
2+
+ H
2
O
2
+ H
+
→ Fe
3+
+ ˙OH + H
2
O), similar to that of brown rot wood-decaying fungi. In such fungi, secreted metabolites are one of the components that drive one-electron reductions of Fe
3+
and O
2
, generating Fenton chemistry reagents. Here we investigated whether such a mechanism is also implemented by
P. involutus
during organic matter decomposition. Activity-guided purification was performed to isolate the Fe
3+
-reducing principle secreted by
P. involutus
during growth on a maize compost extract. The Fe
3+
-reducing activity correlated with the presence of one compound. Mass spectrometry and nuclear magnetic resonance (NMR) identified this compound as the diarylcyclopentenone involutin. A major part of the involutin produced by
P. involutus
during organic matter decomposition was secreted into the medium, and the metabolite was not detected when the fungus was grown on a mineral nutrient medium. We also demonstrated that in the presence of H
2
O
2
, involutin has the capacity to drive an
in vitro
Fenton reaction via Fe
3+
reduction. Our results show that the mechanism for the reduction of Fe
3+
and the generation of hydroxyl radicals via Fenton chemistry by ectomycorrhizal fungi during organic matter decomposition is similar to that employed by the evolutionarily related brown rot saprotrophs during wood decay.
Two Pathways for Glutamate Biosynthesis in the Syntrophic Bacterium Syntrophus aciditrophicus
Authors: Kim Marie , Le Huynh M. , Xie Xiulan , Feng Xueyang , Tang Yinjie J. , Mouttaki Housna , McInerney Michael J. , Buckel Wolfgang 
Published: October 2015

ABSTRACTThe anaerobic metabolism of crotonate, benzoate, and cyclohexane carboxylate bySyntrophus aciditrophicusgrown syntrophically withMethanospirillum hungateiprovides a model to study syntrophic cooperation. Recent studies revealed thatS. aciditrophicuscontainsRe-citrate synthase but lacks the commonSi-citrate synthase. To establish whether theRe-citrate synthase is involved in glutamate synthesis via the oxidative branch of the Krebs cycle, we have used [1-13C]acetate and [1-14C]acetate as well as [13C]bicarbonate as additional carbon sources during axenic growth ofS. aciditrophicuson crotonate. Our analyses showed that labeled carbons were detected in at least 14 amino acids, indicating the global utilization of acetate and bicarbonate. The labeling patterns of alanine and aspartate verified that pyruvate and oxaloacetate were synthesized by consecutive carboxylations of acetyl coenzyme A (acetyl-CoA). The isotopomer profile and13C nuclear magnetic resonance (NMR) spectroscopy of the obtained [13C]glutamate, as well as decarboxylation of [14C]glutamate, revealed that this amino acid was synthesized by two pathways. Unexpectedly, only the minor route usedRe-citrate synthase (30 to 40%), whereas the majority of glutamate was synthesized via the reductive carboxylation of succinate. This symmetrical intermediate could have been formed from two acetates via hydration of crotonyl-CoA to 4-hydroxybutyryl-CoA. 4-Hydroxybutyrate was detected in the medium ofS. aciditrophicuswhen grown on crotonate, but an active hydratase could not be measured in cell extracts, and the annotated 4-hydroxybutyryl-CoA dehydratase (SYN_02445) lacks key amino acids needed to catalyze the hydration of crotonyl-CoA. BesidesClostridium kluyveri, this study reveals the second example of a microbial species to employ two pathways for glutamate synthesis.
Facultative Control of Matrix Production Optimizes Competitive Fitness in Pseudomonas aeruginosa PA14 Biofilm Models
Authors: Madsen Jonas S. , Lin Yu-Cheng , Squyres Georgia R. , Price-Whelan Alexa , de Santiago Torio Ana , Song Angela , Cornell William C. , Sørensen Søren J. , Xavier Joao B. , Dietrich Lars E. P. 
Published: October 2015

ABSTRACT

As biofilms grow, resident cells inevitably face the challenge of resource limitation. In the opportunistic pathogen
Pseudomonas aeruginosa
PA14, electron acceptor availability affects matrix production and, as a result, biofilm morphogenesis. The secreted matrix polysaccharide Pel is required for pellicle formation and for colony wrinkling, two activities that promote access to O
2
. We examined the exploitability and evolvability of Pel production at the air-liquid interface (during pellicle formation) and on solid surfaces (during colony formation). Although Pel contributes to the developmental response to electron acceptor limitation in both biofilm formation regimes, we found variation in the exploitability of its production and necessity for competitive fitness between the two systems. The wild type showed a competitive advantage against a non-Pel-producing mutant in pellicles but no advantage in colonies. Adaptation to the pellicle environment selected for mutants with a competitive advantage against the wild type in pellicles but also caused a severe disadvantage in colonies, even in wrinkled colony centers. Evolution in the colony center produced divergent phenotypes, while adaptation to the colony edge produced mutants with clear competitive advantages against the wild type in this O
2
-replete niche. In general, the structurally heterogeneous colony environment promoted more diversification than the more homogeneous pellicle. These results suggest that the role of Pel in community structure formation in response to electron acceptor limitation is unique to specific biofilm models and that the facultative control of Pel production is required for PA14 to maintain optimum benefit in different types of communities.
Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed
Authors: Du Zhe , Riveros-Iregui Diego A. , Jones Ryan T. , McDermott Timothy R. , Dore John E. , McGlynn Brian L. , Emanuel Ryan E. , Li Xu 
Published: October 2015

ABSTRACT

Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (
R
= 0.72,
P
< 0.001) and negatively with soil oxygen (
R
= −0.53,
P
= 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.
Avian Migrants Facilitate Invasions of Neotropical Ticks and Tick-Borne Pathogens into the United States
Authors: Cohen Emily B. , Auckland Lisa D. , Marra Peter P. , Hamer Sarah A. 
Published: October 2015

ABSTRACT

Migratory birds have the potential to transport exotic vectors and pathogens of human and animal health importance across vast distances. We systematically examined birds that recently migrated to the United States from the Neotropics for ticks. We screened both ticks and birds for tick-borne pathogens, including
Rickettsia
species and
Borrelia burgdorferi
. Over two spring seasons (2013 and 2014), 3.56% of birds (
n
= 3,844) representing 42.35% of the species examined (
n
= 85) were infested by ticks. Ground-foraging birds with reduced fuel stores were most commonly infested. Eight tick species were identified, including seven in the genus
Amblyomma
, of which only
Amblyomma maculatum/Amblyomma triste
is known to be established in the United States. Most ticks on birds (67%) were neotropical species with ranges in Central and South America. Additionally, a single
Ixodes
genus tick was detected. A total of 29% of the ticks (
n
= 137) and no avian blood samples (
n
= 100) were positive for infection with
Rickettsia
species, including
Rickettsia parkeri
, an emerging cause of spotted fever in humans in the southern United States, a species in the group of
Rickettsia
monacensis
, and uncharacterized species and endosymbionts of unknown pathogenicity. No avian tick or blood samples tested positive for
B. burgdorferi
, the etiologic agent of Lyme disease. An extrapolation of our findings suggests that anywhere from 4 to 39 million exotic neotropical ticks are transported to the United States annually on migratory songbirds, with uncertain consequences for human and animal health if the current barriers to their establishment and spread are overcome.
Adaptation of the Cecal Bacterial Microbiome of Growing Pigs in Response to Resistant Starch Type 4
Authors: Metzler-Zebeli Barbara U. , Schmitz-Esser Stephan , Mann Evelyne , Grüll Dietmar , Molnar Timea , Zebeli Qendrim 
Published: October 2015

ABSTRACT

Resistant starch (RS) exacerbates health benefits on the host via modulation of the gut bacterial community. By far, these effects have been less well explored for RS of type 4. This study aimed at gaining a community-wide insight into the impact of enzymatically modified starch (EMS) on the cecal microbiota and hindgut fermentation in growing pigs. Castrated male pigs (
n
= 12/diet; 29-kg body weight) were fed diets with either 70% EMS or control starch for 10 days. The bacterial profile of each cecal sample was determined by sequencing of the V345 region of the 16S rRNA gene using the Illumina MiSeq platform. EMS diet reduced short-chain fatty acid concentrations in cecum and proximal colon compared to the control diet. Linear discriminant analyses and
K
means clustering indicated diet-specific cecal community profiles, whereby diversity and species richness were not different among diets. Pigs showed host-specific variation in their most abundant phyla,
Firmicutes
(55%),
Proteobacteria
(35%), and
Bacteroidetes
(10%). The EMS diet decreased abundance of
Ruminococcus
,
Parasutterella
,
Bilophila
,
Enterococcus
, and
Lactobacillus
operational taxonomic units (OTU), whereas
Meniscus
and
Actinobacillus
OTU were increased compared to those with the control diet (
P
< 0.05). Quantitative PCR confirmed results for host effect on
Enterobacteriaceae
and diet effect on members of the
Lactobacillus
group. The presence of less cecal short-chain fatty acids and the imputed metabolic functions of the cecal microbiome suggested that EMS was less degradable for cecal bacteria than the control starch. The present EMS effects on the bacterial community profiles were different than the previously reported RS effects and can be linked to the chemical structure of EMS.
Comparison of Switching and Biofilm Formation between
MTL
-Homozygous Strains of Candida albicans and Candida dubliniensis
Authors: Pujol Claude , Daniels Karla J. , Soll David R. 
Published: October 2015

ABSTRACT

Candida albicans
and
Candida dubliniensis
are highly related species that share the same main developmental programs. In
C. albicans
, it has been demonstrated that the biofilms formed by strains heterozygous and homozygous at the mating type locus (
MTL
) differ functionally, but studies rarely identify the
MTL
configuration. This becomes a particular problem in studies of
C. dubliniensis
, given that one-third of natural strains are
MTL
homozygous. For that reason, we have analyzed
MTL
-homozygous strains of
C. dubliniensis
for their capacity to switch from white to opaque, the stability of the opaque phenotype, CO
2
induction of switching, pheromone induction of adhesion, the effects of minority opaque cells on biofilm thickness and dry weight, and biofilm architecture in comparison with
C. albicans
. Our results reveal that
C. dubliniensis
strains switch to opaque at lower average frequencies, exhibit a far lower level of opaque phase stability, are not stimulated to switch by high CO
2
, exhibit more variability in biofilm architecture, and most notably, form mature biofilms composed predominately of pseudohyphae rather than true hyphae. Therefore, while several traits of
MTL
-homozygous strains of
C. dubliniensis
appear to be degenerating or have been lost, others, most notably several related to biofilm formation, have been conserved. Within this context, the possibility is considered that
C. dubliniensis
is transitioning from a hypha-dominated to a pseudohypha-dominated biofilm and that aspects of
C. dubliniensis
colonization may provide insights into the selective pressures that are involved.
Major sinks of the Changjiang (Yangtze River)-derived sediments in the East China Sea during the late Quaternary
Authors: Yang Shouye , Bi Lei , Li Chao , Wang Zhongbo , Dou Yanguang 
Published: October 2015

Abstract
The East China Sea (ECS) is a typical marginal sea located between the Eurasian continent and west Pacific Ocean. In this study, we review state-of-the-art research progress on the possible sinks of the Changjiang-derived sediments in the ECS during the late Quaternary. The major sinks of these sediments in the ECS are on the outer shelf and the Okinawa Trough during the last glacial maximum corresponding to a lowstand of sea level. During the deglacial marine transgression, the gently dipping shelf was rapidly inundated and strong tides prevented fine sediment from deposition on the open shelf, resulting in the development of a unique tidal sand ridge system. With sea level reaching the present situation and the modern marine environment being completed in the early Holocene, the Changjiang sediments mostly accumulated in the river's estuary to build a large delta, with only a fraction reaching the inner shelf and coastal embayments. The late-Quaternary changes in monsoon-climate-induced river flux, sea level and oceanic circulation primarily controlled the source-to-sink transport of the Changjiang sediments in the ECS, and further determined the stratigraphic framework and sedimentary facies on the shelf.