bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in
Rhodobacter capsulatus
Authors: Addison Holly , Glatter Timo , K. A. Hochberg Georg , Rebelein Johannes G. 
Published: February 2024

ABSTRACT

Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in
Rhodobacter capsulatus via
proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings,
R. capsulatus
strains with deletions of ferredoxin (
fdx
) and flavodoxin (
fld, nifF
) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase.
R. capsulatus
deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity
in vivo
. Only deletions of
fdxC
or
fdxN
resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both
fdxC
and
fdxN
abolished diazotrophic growth. Differences in the proteomes of ∆
fdxC
and ∆
fdxN
strains, in conjunction with differing plasmid complementation behaviors of
fdxC
and
fdxN,
indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.

IMPORTANCE

Nitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation
via
nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph
Rhodobacter capsulatus
, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
Complete genome sequences of two
Klebsiella pneumoniae
phages from Dakar, Senegal
Authors: Ndiaye Issa , Debarbieux Laurent , Diagne Moussa Moise , Sow Ousmane , Cissé Abdoulaye , Ba Bissoume Sambe , Fall Cheikh , Dieye Yakhya , Dia Ndongo , Seck Abdoulaye , de Magny Guillaume Constantin 
Published: February 2024

ABSTRACT

Two bacteriophages (phages) of
Klebsiella pneumoniae
were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the
Przondovirus
genus within the
Autographiviridae
family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the
Webervirus
genus of the
Drexlerviridae
family.
Draft genome sequence of potentially dikaryotic black fungus
Aureobasidium melanogenum
isolated from aircraft
Authors: Wagner Dominique N. , Varaljay Vanessa A. , Lyon Wanda J. , Crouch Audra L. , Allex-Buckner Clayton , Biffinger Justin C. , Crookes-Goodson Wendy J. , Kelley-Loughnane Nancy , Stamps Blake W. 
Published: February 2024

ABSTRACT

The
Ascomycota
yeast
Aureobasidium melanogenum
strain W12 was isolated from an aircraft polymer-coated surface. The genome size is 53,160,883 bp with a G + C content of 50.13%. The genome contains fatty acid transporters, cutinases, hydroxylases, and lipases potentially used for survival on polymer coatings on aircraft.
Draft genome sequences of
Escherichia
spp. isolates from New Zealand environmental sources
Authors: Biggs Patrick J. , Moinet Marie , Rogers Lynn E. , Devane Megan , Muirhead Richard , Stott Rebecca , Marshall Jonathann C. , Cookson Adrian L. 
Published: February 2024

ABSTRACT

Escherichia coli
is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500
Escherichia
isolates including newly described
Escherichia
species, namely
Escherichia marmotae
,
Escherichia ruysiae,
and
Escherichia whittamii
, obtained from diverse environmental sources to assist with improved public health risk assessments.
Draft genome sequence of
Xylaria bambusicola
isolate GMP-LS, the root and basal stem rot pathogen of sugarcane in Indonesia
Authors: Selvaraj Poonguzhali , Muralishankar Vayutha , Muruganantham Sahanna , Tham Jeremy H. F. , Saeroji Saefudin , Susiyanti Endah , Lau Kenny J. X. , Naqvi Naweed I. 
Published: February 2024

ABSTRACT

The first draft genome of
X. bambusicola
GMP-LS, the causal pathogen of the Root, and Basal Stem Rot disease in Sugarcane is presented based on single-molecule real-time PacBio sequencing. Xylaria genome (72.43 Mb) is predicted to encode 13,430 proteins and will contribute to molecular understanding of fungal pathogenesis.
A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer
Authors: Tomasch Jürgen , Kopejtka Karel , Bílý Tomáš , Gardiner Alastair T. , Gardian Zdenko , Shivaramu Sahana , Koblížek Michal , Kaftan David 
Published: February 2024

ABSTRACT

During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic
Sediminicoccus
sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.

IMPORTANCE

The photoheterotrophic bacterium
Sediminicoccus
sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
Extreme environments simplify reassembly of communities of arbuscular mycorrhizal fungi
Authors: Šibanc Nataša , Clark Dave R. , Helgason Thorunn , Dumbrell Alex J. , Maček Irena 
Published: February 2024

ABSTRACT

The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e., commonness or rarity) and temporal dynamics of species within a community remain largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonize more than two-thirds of terrestrial plant species. Here, we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem—mofettes or natural CO
2
springs caused by geological CO
2
exhalations—are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, “stress tolerant” taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can also reflect the community response to other anthropogenic stressors (e.g., heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.

IMPORTANCE
Arbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.
(Pan)genomic analysis of two
Rhodococcus
isolates and their role in phenolic compound degradation
Authors: Benning Sarah , Pritsch Karin , Radl Viviane , Siani Roberto , Wang Zhongjie , Schloter Michael 
Published: February 2024

ABSTRACT

The genus
Rhodococcus
is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader
Rhodococcus
pan-genome to study genomic traits of two newly described
Rhodococcus
strains (type-strain
Rhodococcus pseudokoreensis
R79
T
and
Rhodococcus koreensis
R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus
Rhodococcus
based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in
Rhodococcus
was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the
Rhodococcus equi
cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus
Rhodococcus
had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger
Rhodococcus
genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.

IMPORTANCE

Rhodococcus
is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
‘Considering the reality, I am very lucky’: how professional players and staff perceive injury prevention and performance protection in women’s football
Authors: Bolling Caroline , Tomás Rita , Verhagen Evert 
Published: February 2024

ObjectiveTo explore the beliefs and perceptions of professional female footballers and staff regarding injury prevention and performance protection in professional women’s football.MethodsThis qualitative study applied semistructured interviews with 18 participants from 3 top-tier teams from 2 countries (Portugal and England) and 4 nationalities, including 2 physiotherapists, 5 players, 3 team doctors, 2 head coaches, 3 strength and conditioning coaches, 2 managers, and 1 head of performance. Data analysis applied constant comparison analysis, using principles of grounded theory. There were no major differences in the perspectives of players and staff, and the findings are presented together.ResultsIdentifying and reporting injuries and recognising potential injury risk factors were mentioned to influence the prevention of injury. Participants stated that the growth and evolution of women’s football could influence injury risk. Before reaching the professional level, exposure to potential risk factors, such as lack of recovery, limited awareness and opportunities for prevention (eg, preventive exercises and load management strategies), was believed to impact players’ injury risk. Players further described their experiences and the ‘bumpy road’ to becoming a professional player, their current context and potential future improvements for women’s football regarding injury prevention and performance protection.ConclusionProfessional female football players face different injury risks during different moments of their careers. According to elite players and staff, amateur and semiprofessionals have limited resources and lack injury prevention strategies. Professional players and staff perceived the current preventive measures as good and relied on the value of individualised care and a multidisciplinary approach. In the future, more resources and structured injury prevention strategies are needed in youth and non-professional levels of women’s football to reduce injury risk and allow more players to reach their maximal performance.
Understanding the educational inequalities in suicide attempts and their mediators: a Mendelian randomisation study
Authors: Zhu Jiahao , Liu Houpu , Gao Rui , Ding Lilu , Wang Jing , Yang Ye , Zhou Dan , Li Yingjun 
Published: February 2024

BackgroundEducational inequalities in suicide have become increasingly prominent over the past decade. Elucidating modifiable risk factors that serve as intermediaries in the impact of low educational attainment on suicide has the potential to reduce health disparities.AimsTo examine the risk factors that mediate the relationship between educational attainment and suicide attempts and quantify their contributions to the mediation effect.MethodsWe conducted a two-sample Mendelian randomisation (MR) analysis to estimate the causal effect of educational attainment on suicide attempts, utilising genome-wide association study summary statistics from the Integrative Psychiatric Research (iPSYCH; 6024 cases and 44 240 controls) and FinnGen (8978 cases and 368 299 controls). We systematically evaluated 42 putative mediators within the causal pathway connecting reduced educational attainment to suicide attempts and employed two-step and multivariable MR to quantify the proportion of the mediated effect.ResultsIn the combined analysis of iPSYCH and FinnGen, each standard deviation (SD) decrease in genetically predicted educational attainment (equating to 3.4 years of education) was associated with a 105% higher risk of suicide attempts (odds ratio (OR): 2.05; 95% confidence interval (CI): 1.81 to 2.31). Of the 42 risk factors analysed, the two-step MR identified five factors that mediated the association between educational attainment and suicide attempts. The respective proportions of mediation were 47% (95% CI: 29% to 66%) for smoking behaviour, 36% (95% CI: 0% to 84%) for chronic pain, 49% (95% CI: 36% to 61%) for depression, 35% (95% CI: 12% to 59%) for anxiety and 26% (95% CI: 18% to 34%) for insomnia. Multivariable MR implicated these five mediators collectively, accounting for 68% (95% CI: 40% to 96%) of the total effect.ConclusionsThis study identified smoking, chronic pain and mental disorders as primary intervention targets for attenuating suicide risk attributable to lower educational levels in the European population.
Addition of cribriform pattern 4 and intraductal prostatic carcinoma into the CAPRA-S tool improves post-radical prostatectomy patient stratification in a multi-institutional cohort
Authors: Nguyen Ngoc-Nhu Jennifer , Liu Kristen , Lajkosz Katherine , Iczkowski Kenneth A , van der Kwast Theodorus H , Downes Michelle R 
Published: February 2024

AimsPre-surgical risk classification tools for prostate cancer have shown better patient stratification with the addition of cribriform pattern 4 (CC) and intraductal prostatic carcinoma (IDC) identified in biopsies. Here, we analyse the additional prognostic impact of CC/IDC observed in prostatectomies using Cancer of Prostate Risk Assessment post-surgical (CAPRA-S) stratification.MethodsA retrospective cohort of treatment-naïve radical prostatectomy specimens from three North American academic institutions (2010–2018) was assessed for the presence of CC/IDC. Patients were classified, after calculating the CAPRA-S scores, into low-risk (0–2), intermediate-risk (3–5) and high-risk (6–12) groups. Kaplan-Meier curves were created to estimate biochemical recurrence (BCR)-free survival. Prognostic performance was examined using Harrell’s concordance index, and the effects of CC/IDC within each risk group were evaluated using the Cox proportional hazards models.ResultsOur cohort included 825 prostatectomies (grade group (GG)1, n=94; GG2, n=475; GG3, n=185; GG4, n=13; GG5, n=58). CC/IDC was present in 341 (41%) prostatectomies. With a median follow-up of 4.2 years (range 2.9–6.4), 166 (20%) patients experienced BCR. The CAPRA-S low-risk, intermediate-risk and high-risk groups comprised 357 (43%), 328 (40%) and 140 (17%) patients, and discriminated for BCR-free survival (p<0.0001). For CAPRA-S scores 3–5, the addition of CC/IDC status improved stratification for BCR (HR 2.27, 95% CI 1.41 to 3.66, p<0.001) and improved the overall c-index (0.689 vs 0.667, analysis of variance p<0.001).ConclusionThe addition of CC/IDC into the CAPRA-S classification significantly improved post-radical prostatectomy patient stratification for BCR among the intermediate-risk group (CAPRA-S scores 3–5). The reporting of CC and IDC should be included in future prostate cancer stratification tools for improved outcome prediction.
Integration of microfluidics in smart acoustic metamaterials
Authors: Nampoothiri Krishnadas Narayanan , Bansal Shubhi , Jha Abhishek , Mittal Prateek 
Published: February 2024

AbstractMicrofluidics has achieved a paradigm-shifting advancement in life sciences, automation, thermal management, and various other engineering streams. In recent years, a considerable amount of research has been conducted on the use of microfluidics in designing novel systems and fabricating next-generation smart materials that are capable of outperforming historical barriers and achieving unprecedented qualities. One such innovative development is the integration of fluidics into building artificially structured smart materials called acoustic metamaterials to achieve active tunability for a real-time controllable manipulation of acoustic waves. Leveraging the capability of microfluidics to automate the manipulation of liquid droplets, fluid streams, or bubbles in a required arrangement has revolutionised the development of actively tunable fluidics-integrated acoustic metamaterials for widescale applications. This review first discusses the prominent microfluidic actuation mechanisms used in the literature to develop fluidics-integrated smart acoustic metamaterials, and then it details integrated metamaterial design and extraordinary applications such as active acoustic wave manipulation or building tunable acoustic holograms etc. The following review concludes by providing the importance and future perspective of integrating microfluidic techniques with novel metamaterial designs, paving the way for innovative futuristic applications.