bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production
Authors: Bongaerts Dries , Bouchez Arne , De Roos Jonas , Cnockaert Margo , Wieme Anneleen D. , Vandamme Peter , Weckx Stefan , De Vuyst Luc 
Published: March 2024

ABSTRACT

The production of gueuze beers through refermentation and maturation of blends of lambic beer in bottles is a way for lambic brewers to cope with the variability among different lambic beer batches. The resulting gueuze beers are more carbonated than lambic beers and are supposed to possess a unique flavor profile that varies over time. To map this refermentation and maturation process for gueuze production, a blend of lambic beers was made and bottled, whereby one of them was produced with the old wheat landrace
Zeeuwse Witte
. Through the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and high-throughput sequencing of bacterial and fungal amplicons, in combination with metabolite target analysis, new insights into gueuze production were obtained. During the initial stages of refermentation, the conditions in the bottles were similar to those encountered during the maturation phase of lambic beer productions in wooden barrels, which was also reflected microbiologically (presence of
Brettanomyces
species,
Pediococcus damnosus
, and
Acetobacter lambici
) and biochemically (ethanol, higher alcohols, lactic acid, acetic acid, volatile phenolic compounds, and ethyl esters). However, after a few weeks of maturation, a switch from a favorable environment to one with nutrient and dissolved oxygen depletion resulted in several changes. Concerning the microbiology, a sequential prevalence of three lactic acid bacterial species occurred, namely,
P. damnosus
,
Lentilactobacillus buchneri
, and
Lactobacillus acetotolerans
, while the diversity of the yeasts decreased. Concerning the metabolites produced, mainly those of the
Brettanomyces
yeasts determined the metabolic profiles encountered during later stages of the gueuze production.

IMPORTANCE
Gueuze beers are the result of a refermentation and maturation process of a blend of lambic beers carried out in bottles. These gueuze beers are known to have a long shelf life, and their quality typically varies over time. However, knowledge about gueuze production in bottles is scarce. The present study provided more insights into the varying microbial and metabolite composition of gueuze beers during the first 2 years of this refermentation and maturation process. This will allow gueuze producers to gain more information about the influence of the refermentation and maturation time on their beers. These insights can also be used by gueuze producers to better inform their customers about the quality of young and old gueuze beers.
Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone
Authors: Elbon Claire E. , Stewart Frank J. , Glass Jennifer B. 
Published: March 2024

ABSTRACT

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (
nod
) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed
nod
genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria
,
rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe
nod
, but at lower relative abundance than UBA11136 in the upper ODZ. The
nod
-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named
ptd
) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.

IMPORTANCE

In marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world’s largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (
nod
) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe
nod
at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.
Halocin H4 is activated through cleavage by halolysin HlyR4
Authors: Chen Shaoxing , Dai Yongpei , Ke Juntao , Luo Yuqing , Wang Chuangming , Hao Yuling , Zhang Aodi , Han Jing , Xiang Hua 
Published: March 2024

ABSTRACT

Halocins are antimicrobial peptides secreted by haloarchaea capable of inhibiting the growth of other haloarchaea or bacteria. Halocin H4 (HalH4) is secreted by the model halophilic archaeon
Haloferax mediterranei
ATCC 33500. Despite attempts to express
halH4
heterologously in
Escherichia coli
and subsequent careful renaturation procedures commonly employed for haloarchaeal proteins, no active halocin was obtained. However, it was discovered that the antihaloarchaeal activity of this halocin could be activated through cleavage by halolysin R4 (HlyR4), a serine protease also secreted by
Hfx. mediterranei
ATCC 33500. Replacement of the cysteine at the number 115 amino acid with glycine and deletion of the internal trans-membrane region (15 aa) markedly abolished HalH4’s antihaloarchaeal activity. Compared to the N-terminus, the C-terminal amino acid sequence was found to be more crucial for HalH4 to exert its antihaloarchaeal activity. Mass spectrometry analysis revealed that the biologically active antihaloarchaeal peptide produced after hydrolytic cleavage by HlyR4 was the C-terminus of HalH4, suggesting a potential mechanism of action involving pore formation within competitor species’ cell membranes. Taken together, this study offers novel insights into the interplay between halocins and secreted proteases, as well as their contribution to antagonistic interaction within haloarchaea.

IMPORTANCE

The antihaloarchaeal function of halocin H4 (HalH4) can be activated by extracellular proteases from haloarchaea, as demonstrated in this study. Notably, we report the first instance of halocin activation through proteolytic cleavage, highlighting its significance in the field. The C-terminus of HalH4 (CTH4) has been identified as the antihaloarchaeal peptide present in hydrolysates generated by HlyR4. The CTH4 exhibited inhibitory activity against a range of haloarchaeal species (
Haloarchaeobius
spp.,
Haloarcula
spp.,
Haloferax
spp.,
Halorubellus
spp., and
Halorubrum
spp.), as well as selected bacterial species (
Aliifodinibius
spp. and
Salicola
spp.), indicating its broad-spectrum inhibitory potential across domains. The encoding gene of halocin HalH4,
halH4
, from the model halophilic archaeon
Haloferax mediterranei
ATCC 33500 can be expressed in
Escherichia coli
without codon optimization.
Hopanoid lipids promote soybean
–Bradyrhizobium
symbiosis
Authors: Pan Huiqiao , Shim Ashley , Lubin Matthew B. , Belin Brittany J. 
Published: March 2024

ABSTRACT

The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote
Bradyrhizobium
symbioses with tropical legumes. To characterize hopanoids in
Bradyrhizobium
symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of
Bradyrhizobium
diazoefficiens USDA110, Pcu-
shc
::∆
shc
. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress.
In planta
, Pcu-
shc
::∆
shc
is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to
B. diazoefficiens
in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility.

IMPORTANCE

A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between
Bradyrhizobium diazoefficiens
USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
Whole-genome sequences of
Campylobacter coli
and
Campylobacter jejuni
isolates from rhesus macaques (
Macaca mulatta
) with and without intestinal disease
Authors: Bacon Rebecca L. , Norman Keri N. , Nickodem Colette A. , Vinasco Javier A. , Gray Stanton B. , Hodo Carolyn L. , Lawhon Sara D. 
Published: March 2024

ABSTRACT

Campylobacter jejuni
or
Campylobacter coli
infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (
Macaca mulatta
). We report the complete genomes of 8
C
.
jejuni
isolates and 103
C
.
coli
isolates obtained from rhesus macaques with and without intestinal disease.
Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient
Authors: Cai Miaomiao , Zhang Caifang , Ndungu Caroline Njambi , Liu Guihua , Liu Wenzhi , Zhang Quanfa 
Published: March 2024

ABSTRACT

Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.

IMPORTANCE
Ecosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.
Evolutionary trends in antifungal resistance: a meta-analysis
Authors: Niu Xueke , Al-Hatmi Abdullah M. S. , Vitale Roxana G. , Lackner Michaela , Ahmed Sarah A. , Verweij Paul E. , Kang Yingqian , de Hoog Sybren 
Published: March 2024

ABSTRACT

The present paper includes a meta-analysis of literature data on 318 species of fungi belonging to 34 orders in their response to 8 antifungal agents (amphotericin B, caspofungin, fluconazole, itraconazole, ketoconazole, posaconazole, terbinafine, and voriconazole). Main trends of MIC results at the ordinal level were visualized. European Committee on Antimicrobial Susceptibility Testing and Clinical & Laboratory Standards Institute (CLSI) clinical breakpoints were used as the staff gauge to evaluate MIC values ranging from resistance to susceptibility, which were subsequently compared with a phylogenetic tree of the fungal kingdom. Several orders (
Hypocreales, Microascales
, and
Mucorales
) invariably showed resistance. Also the basidiomycetous orders
Agaricales, Polyporales, Sporidiales, Tremellales
, and
Trichosporonales
showed relatively high degrees of azole multi-resistance, while elsewhere in the fungal kingdom, including orders with numerous pathogenic and opportunistic species, that is,
Onygenales, Chaetothyiales, Sordariales
, and
Malasseziales
, in general were susceptible to azoles. In most cases, resistance vs susceptibility was consistently associated with phylogenetic distance, members of the same order showing similar behavior.

IMPORTANCE
A kingdom-wide the largest set of published wild-type antifungal data comparison were analyzed. Trends in resistance in taxonomic groups (monophyletic clades) can be compared with the phylogeny of the fungal kingdom, eventual relationships between fungus–drug interaction and evolution can be described.
Multiscale structures of crust-mantle beneath the South China block and their geodynamic implication
Authors: Cheng Siyuan , Shen Xuzhang , Dong Shuwen , Gao Rui , Cui Jianjun , Huang He , Li Minjuan , Shao Ruotong 
Published: March 2024

Abstract
The South China block is an ideal location in which to study the impact of paleo-Pacific plate subduction on the upper mantle and crustal structures of the overriding plate, as well as the mechanism of lithospheric thinning. By integrating data from permanent seismic stations of the China Seismic Network and a dense seismic array at Xuefeng Mountain, this study employed P- and S-wave receiver functions (RFs) to image multiscale structures of crust-mantle across the South China block, thereby providing constraints for a comprehensive understanding of its tectonic evolution. The main findings are as follows: (1) The thickness of lithosphere and crust gradually decreases from northwest (NW) to southeast (SE). (2) Beneath the Xuefeng Mountain uplift zone, the P-to-S conversion from the 660 km discontinuity arrives earlier than that predicted from a one-dimensional model, other weak discontinuities can be traced in the upper mantle, including the lithosphere-asthenosphere boundary, the crust becomes thinner, and the Conrad discontinuity becomes deeper. Referring to previous results from tomography and geological reconstructions, we deduce that lithospheric delamination might have occurred beneath the Xuefeng Mountain uplift zone, and the delaminated lithosphere penetrated the upper mantle and reached the mantle transition zone.
Protocol for venoarterial ExtraCorporeal Membrane Oxygenation to reduce morbidity and mortality following bilateral lung TransPlantation: the ECMOToP randomised controlled trial
Authors: Messika Jonathan , Eloy Philippine , Boulate David , Charvet Aude , Fessler Julien , Jougon Jacques , Lacoste Philippe , Mercier Olaf , Portran Philippe , Roze Hadrien , Sage Edouard , Thes Jacques , Tronc Francois , Vourc'h Mickael , Montravers Philippe , Castier Yves , Mal Herve , Mordant Pierre 
Published: March 2024

IntroductionLung transplantation (LTx) aims at improving survival and quality of life for patients with end-stage lung diseases. Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is used as intraoperative support for LTx, despite no precise guidelines for its initiation. We aim to evaluate two strategies of VA-ECMO initiation in the perioperative period in patients with obstructive or restrictive lung disease requiring bilateral LTx. In the control ‘on-demand’ arm, high haemodynamic and respiratory needs will dictate VA-ECMO initiation; in the experimental ‘systematic’ arm, VA-ECMO will be pre-emptively initiated. We hypothesise a ‘systematic’ strategy will increase the number of ventilatory-free days at day 28.Methods and analysisWe designed a multicentre randomised controlled trial in parallel groups. Adult patients with obstructive or restrictive lung disease requiring bilateral LTx, without a formal indication for pre-emptive VA-ECMO before LTx, will be included. Patients with preoperative pulmonary hypertension with haemodynamic collapse, ECMO as a bridge to transplantation, severe hypoxaemia or hypercarbia will be secondarily excluded. In the systematic group, VA-ECMO will be systematically implanted before the first pulmonary artery cross-clamp. In the on-demand group, VA-ECMO will be implanted intraoperatively if haemodynamic or respiratory indices meet preplanned criteria. Non-inclusion, secondary exclusion and VA-ECMO initiation criteria were validated by a Delphi process among investigators. Postoperative weaning of ECMO and mechanical ventilation will be managed according to best practice guidelines. The number of ventilator-free days at 28 days (primary endpoint) will be compared between the two groups in the intention-to-treat population. Secondary endpoints encompass organ failure occurrence, day 28, day 90 and year 1 vital status, and adverse events.Ethics and disseminationThe sponsor is the Assistance Publique–Hôpitaux de Paris. The ECMOToP protocol version 2.1 was approved by Comité de Protection des Personnes Ile de France VIII. Results will be published in international peer-reviewed medical journals.Trial registration numberNCT05664204.
ATME—Needs, requirements and cross-sectoral patient journeys of patients with out-of-hospital mechanical ventilation and intensive care in outpatient settings: study protocol for an observational study
Authors: Knizia Nahne-Alina , Hirschler Josefine , Stegbauer Constance , Schwinger Antje , Büscher Andreas , Englert Nathalie , Peters Lara , Bayarassou Hakim A. , Mallmann Leonie , Willms Gerald 
Published: March 2024

IntroductionAn increasing number of tracheotomised and/or ventilated patients with high-cost out-of-hospital intensive care needs and, at the same time, a decreasing number of healthcare professionals inevitably lead to challenges in the care of this patient population. In addition, little is known about this population, their health restrictions, needs, patient journeys, care structures and processes. The project ‘Needs, requirements and cross-sectoral care pathways of out-of-hospital ventilated intensive care patients’ (ATME) aims to analyse these aspects and explore current care structures to inform further development of care in line with patients’ needs and requirements.Methods and analysisQualitative and quantitative methods will be used. In preparation of a semistandardised survey, exploratory interviews will be conducted with tracheotomised and/or ventilated patients with out-of-hospital intensive care needs (TVPOI) (n=15), nursing care providers (n=30), outpatient medical centres, as well as outpatient medical, medical technology and therapeutic care providers (n=35). Three semistandardised survey questionnaires for TVPOI (n=2,000) will be developed and conducted with nursing care facilities (n=250) and outpatient medical centres for mechanical ventilation (n=25). Content analyses will be conducted for qualitative data; survey data will be analysed descriptively. In addition, healthcare claims data will be analysed descriptively to provide information on patient journeys. Three result workshops and one consensus conference will be carried out with representatives of the relevant target groups to analyse the suitability of care structures and to develop recommendations for action to improve TVPOI.Ethics and disseminationThe ATME study received a positive vote from the Ethics Committee of the Osnabrück University of Applied Sciences and is registered in ‘Deutsches Register Klinischer Studien (DRKS)’ (registration number: DRKS00030891). The study results will be presented at national conferences and in relevant peer-reviewed journals. Additionally, study results will be published by the funding institution (the Innovation Committee of the Federal Joint Committee) on their website.