In global biogeochemical networks nitrogen transitions between a number of different oxidation states, from +5 to -3. The two most oxidized states are found in the nitrogen oxyanions nitrate (NO3-, +5) and nitrite (NO2-, +3). These two oxyanions form an electropositive redox couple, with a midpoint redox potential (pH7) of +430 mV, that enables them to serve as both electron acceptor (nitrate) and electron donor (nitrite) in a range of catabolic and anabolic processes. Several enzymatic systems have been identified that can inter-convert the two oxyanions and couple them to a range of electron transport pathways. Recent literature on nitrate reduction and nitrite oxidation by prokaryotes reveals a great number of meta "omics" studies identifying genes, transcripts or peptides functionally related to the nitrate / nitrite redox couple in a wide range of environments. To fully interpret such data in the context of the environment being studied requires a recognition of the different physiological functions the nitrate / nitrite redox couple is able to support. This, in turn, is related to the biochemical diversity of the enzymes that drive this reversible redox couple in nature. This review seeks to define bioenergetically the different enzymes involved in nitrate-nitrite inter-conversion and relate this to the diverse physiological activities that this redox couple supports.

Globally, many species are threatened by population decline because of anthropogenic changes leading to population fragmentation, genetic isolation and inbreeding depression. Genetic rescue, the controlled introduction of genetic variation, is a method used to relieve such effects in small populations. However, without understanding how the characteristics of rescuers impact rescue attempts interventions run the risk of being sub-optimal, or even counterproductive. We use the red flour beetle (Tribolium castaneum) to test the impact of rescuer sex, and sexual selection background, on population productivity. We record the impact of genetic rescue on population productivity in 24 and 36 replicated populations for ten generations following intervention. We find little or no impact of rescuer sex on the efficacy of rescue but show that a background of elevated sexual selection makes individuals more effective rescuers. In both experiments, rescue effects diminish 6-10 generations after the rescue. Our results confirm that the efficacy of genetic rescue can be influenced by characteristics of the rescuers and that the level of sexual selection in the rescuing population is an important factor. We show that any increase in fitness associated with rescue may last for a limited number of generations, suggesting implications for conservation policy and practice.

Stuart Ferguson made important contributions to our understanding of many aspects of bioenergetics, including the operation of the ATP synthase, all of the steps involved in denitification and the mechanism of cytochrome c biogenesis. In this article, we outline his career and describe the development of his research, highlighting his insights into the role of the bacterial periplasm in electron transport reactions and the diversity of covalent attachment mechanisms of heme to apo-cytochrome c.

Nitric oxide (NO) and the greenhouse gas (GHG) nitrous oxide (N2O) contribute significantly to climate change. In rhizobia, the denitrifying enzyme c-type nitric oxide reductase (cNor), encoded by norCBQD genes, is crucial for maintaining a delicate balance of NO and N2O levels. In the soybean endosymbiont Bradyrhizobium diazoefficiens, maximal expression of norCBQD genes in response to NO is controlled by NnrR, which belongs to a distinct clade of the CRP/FNR family of bacterial transcription factors. This protein participates in the FixLJ-FixK2-NnrR regulatory cascade that induces denitrification genes expression in response to oxygen limitation and nitrogen oxides. However, the molecular mechanism underpinning NO sensing by B. diazoefficiens NnrR has remained elusive. Here, we revealed that NnrR induces norCBQD gene expression in response to NO uncoupled from the superimposed FixK2 control. Moreover, NO-mediated induction by NnrR is dependent on haem, as the expression of a norC-lacZ fusion was impaired in a hemN2 mutant defective in haem biosynthesis. In vitro studies showed that NnrR bound haem with a 1:1 stoichiometry (monomer:haem), according to titration experiments of recombinant NnrR protein with hemin performed under anaerobic conditions. Furthermore, the full UV-Visible spectra of haem-reconstituted NnrR showed a peak at 411 nm (ferric form), and at 425 nm (ferrous derivative). This latter complex was able to bind NO under anaerobic conditions. Finally, we performed a functional mutagenesis of specific residues in NnrR predicted as putative ligands for haem binding. While H11 was important for norC expression and Nor activity, a H11A-H56A protein variant showed a reduced affinity for haem binding. Taken together, our results identify haem as the cofactor for NnrR-mediated NO sensing in B. diazoefficiens denitrification, with H11 as a key residue for NnrR function, providing the first insight into the mechanism of an NnrR-type protein. These findings advance our understanding of how bacterial systems orchestrate the denitrification process and respond to environmental cues such as NO.

Extracellular electron transfer is an ancient and ubiquitous process that is used by a range of microorganisms to exchange electrons between the cell and environment. These electron transfer reactions can impact the solubility and speciation of redox-active molecules in the environment, such as metal oxides, while allowing bacteria to survive in areas of limited nutrient availability. Controlled transfer of electrons across the cell envelope requires assembly of electron transport chains that must pass through the outer membrane of Gram-negative bacteria or the S-layer of Gram-positive bacteria, but the mechanisms used by bacteria are still far from understood. Here, we review the literature surrounding characterized extracellular electron transfer pathways and use protein modeling tools to investigate novel electron transfer proteins and protein complexes. While these protein models are hypothetical, they provide new insight into features that may explain how extracellular electron transfer complexes interact with a range of different environmental substrates.

Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot’s pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years, and the prevalence of malaria infection was strongly correlated with pox (Avipoxvirus) prevalence. Evidence of significant association with malaria was found for multiple host loci after controlling for genome-wide divergence due to neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Taken together, our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggests that spatially variable pathogen pressure is an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot’s pipit. Further, our data indicate that spatio-temporal variation in multiple different pathogens (e.g., malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.

Multiheme cytochromes (MHCs) are bacterial electron-transfer proteins. We show from optical spectra and calculations that some of these cytochromes probably contain occupied and unoccupied bands formed from heme π and π* orbitals that span the protein. In the fully oxidised proteins, the unoccupied π*-bands are energetically above the redox-active frontier orbitals, which according to NMR data and calculations, are formed of Fe3+ t2g and porphyrin π-orbitals. These orbitals on different hemes are electronically coupled according to EPR data and calculations, but only weakly so. We suggest a role for the heme bands in the electronic conductivity of single MHCs in bioelectronic junctions that is distinct from the role of the redox-active Fe3+ t2g and porphyrin π-orbitals in physiological electron transfer.

When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.

Bacteria that live at the oxic/anoxic interface have to rapidly adapt to changes in oxygen levels within their environment. The facultative anaerobe Shewanella oneidensis MR-1 can use EET to respire in the absence of oxygen, but on exposure to oxygen, EET could directly reduce extracellular oxygen and generate harmful reactive oxygen species that damage the bacterium.

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.

The soybean endosymbiont Bradyrhizobium diazoefficiens harbours the complete denitrification pathway that is catalysed by a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a nitrous oxide reductase (Nos), encoded by the napEDABC, nirK, norCBQD, and nosRZDFYLX genes, respectively. Induction of denitrification genes requires low oxygen and nitric oxide, both signals integrated into a complex regulatory network comprised by two interconnected cascades, FixLJ-FixK(2)-NnrR and RegSR-NifA. Copper is a cofactor of NirK and Nos, but it has also a role in denitrification gene expression and protein synthesis. In fact, Cu limitation triggers a substantial down-regulation of nirK, norCBQD, and nosRZDFYLX gene expression under denitrifying conditions. Bradyrhizobium diazoefficiens genome possesses a gene predicted to encode a Cu-responsive repressor of the CsoR family, which is located adjacent to copA, a gene encoding a putative Cu+-ATPase transporter. To investigate the role of CsoR in the control of denitrification gene expression in response to Cu, a csoR deletion mutant was constructed in this work. Mutation of csoR did not affect the capacity of B. diazoefficiens to grow under denitrifying conditions. However, by using qRT-PCR analyses, we showed that nirK and norCBQD expression was much lower in the csoR mutant compared to wild-type levels under Cu-limiting denitrifying conditions. On the contrary, copA expression was significantly increased in the csoR mutant. The results obtained suggest that CsoR acts as a repressor of copA. Under Cu limitation, CsoR has also an indirect role in the expression of nirK and norCBQD genes.

Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world's most species-rich order.

Legumes can contribute to emissions of the potent greenhouse gas nitrous oxide (N2O) directly by some rhizobia species that are able to denitrify under free-living conditions and in symbiotic association with the plant. In this study, the capacity of Phaseolus vulgaris-Rhizobium etli symbiosis to emit N2O in response to nitrate (NO3-) has been demonstrated for the first time. We found that bacteroidal assimilatory nitrate reductase (NarB) as well as nitrite reductase (NirK) and nitric oxide reductase (cNor) denitrifying enzymes contribute to nitric oxide (NO) and N2O formation in nodules. We also show that R. etli NarK is involved in NO2- extrusion and links NO3- reduction by NarB in the cytoplasm with NirK and cNor denitrification activities in the periplasm. The knowledge generated in this work will be instrumental for exploring strategies and sustainable practices in agricultural soil management to increase legume crop yield and mitigate greenhouse gas emissions.

Invasive predators are a major driver of extinctions and continue to threaten native populations worldwide. Island eradications of (mostly mammalian) invasive predators have facilitated the reestablishment of numerous island-endemic populations. Other invasive taxa, such as some predatory birds, could pose a more persistent threat due to their ability to fly and actively re-invade even remote and isolated islands. However, the impact of invasive predatory birds has been largely overlooked. We report on a novel sex-specific impact of an invasive-nest predator, the common myna (Acridotheres tristis), on a reintroduced population of Seychelles warblers (Acrocephalus sechellensis); translocated from Cousin Island to Denis Island in 2004. Regular post-translocation monitoring revealed that female mortality was 20 % higher than males, leading to a 60–70 % male-biased population sex-ratio between 2005 and 2015. This was attributed to common mynas inflicting severe injuries to incubating female Seychelles warblers while attempting to prey upon eggs in their nests. These effects likely contributed to the slower-than-expected population growth observed (relative to previous translocations of Seychelles warblers to other islands) over the same period. An eradication programme beginning in 2011 removed all common mynas from Denis by 2015. Subsequently, we observed a balancing of sex-specific survival and the population sex-ratio of Seychelles warblers and, consequently, accelerated population growth. This study demonstrates the importance of assessing the threat posed by all invasive taxa (not just mammals) to island conservation. Furthermore, we show how extended monitoring is needed to identify problems, and develop solutions, post-translocation.

High-sensitivity charge coupled-device (CCD) cameras, efficient fibre optic bundles, high stable light source and 3D printing technologies now open large possibilities to probe redox species in solution and on confined surface by real-time absorption spectroelectrochemistry. This short review aims at providing an overview of the first work of absorption spectroelectrochemistry on redox-responsive self-assembled monolayers (SAMs). Some practical aspects are emphasized to not underestimate the difficulties involved in set-up such instrumentation.

Telomeres are fascinating stretches of protective DNA that cap the chromosome ends of eukaryotes. Without telomeres, during cell division and DNA replication, DNA repair proteins would misread the ends of chromosomes and attempt to repair or remove this region of the genome, leading to instability. Furthermore, the loss of DNA that inevitably occurs during cell replication due to the “end replication problem” and oxidative damage would erode the coding sequences of chromosomes, eventually causing genome malfunction. Thus functional telomeres protect genome integrity. In the absence of telomere restoration, some reduction in telomere length will occur with each cell division, eventually giving rise to cell replicative senescence often followed by cell death. Short and/or dysfunctional telomeres underly many disease states and are associated with ageing. Consequently, telomere biology is a vibrant area of biomedical research. However, until relatively recently, most of the research on telomeres has been focused on humans or animal models. The basic pattern of progressive telomere loss and little restoration in most somatic tissues, as found in humans, might not apply to all eukaryotes and has received relatively little attention. In fact, any variation in the expected pattern of decline in chromosomal telomere length with progressive rounds of cell replication, as observed in most human tissues, was initially attributed to methodological issues. Importantly, the science of studying telomeres has now expanded to encompass nonmodel organisms. Variation in the pattern of telomere loss and restoration across a range of species promises to reveal great insights into the drivers of lifehistory tradeoffs and evolution, population ecology and consequences of exposure to environmental stress in natural populations. The burgeoning interest in telomere dynamics in nonmodel organisms and increased communication between biomedical researchers and evolutionary ecologists is now enriching our understanding of the diversity of telomere dynamics. While the basics of telomere biology do indeed appear to be conserved across almost all eukaryotes, and the range of species studied is still phylogenetically restricted, differences in detail are increasingly being revealed (Monaghan & Ozanne, 2018). We now have information on how the pattern of telomere change can vary among species and include lengthening as well as shortening across the life course (Brown et al., 2021; Remot et al., 2021). Our understanding of how these patterns relate to environmental factors, species, individual histories and population process is increasing. Furthermore, telomere biology has the potential to be used in conservation biology, providing information about individual and population health (e.g., Eastwood et al., 2022). The molecular ecology of telomeres in nonmodel organisms will have greater impact as new discoveries increase our understanding of the genomics, ecology and evolution underlying telomere diversity. This Special Issue brings together a collection of papers that illustrate the breadth of taxa now being investigated and ways in which emerging hypotheses, formed from the perspectives of ecology, evolution and conservation, are being tested. In this introduction, we highlight how this body of work, including new information and insights, points the way to many research questions that remain to be investigated in this emerging, crossdisciplinary area of biology. Many hypotheses have been put forward about how telomeres function, and how they relate to whole organism outcomes. These hypotheses have their roots in different disciplines and biological levels, and some appear contradictory. The study by Tobler et al. (2021) provides a broad perspective on the literature to date. They spell out the hypotheses most likely to be of interest to ecologists and provide a framework that can be used to clarify and guide further research questions. They group the hypotheses in terms of the biological issues addressed, mainly telomere length and loss in the context of ageing, individual quality and health, life history tradeoffs and physiological processes, identifying underlying assumptions and interrelationships.

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot’s pipit ( Anthus berthelotii ) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses provide evidence that pathogen-mediated selection has shaped genomic variation among relatively recently colonised island bird populations, and highlights the utility of genotype-environment associations for identifying candidate genes involved in adaption to local pathogen pressures.

Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic analysis of a Paracoccus denitrificans NtrY mutant grown under denitrifying conditions revealed the induction of different TonB-dependent siderophore transporters and proteins related to iron homeostasis. This mutant showed lower intracellular iron content than the wild-type strain, and a reduced growth under denitrifying conditions in iron-limited media. Under iron-rich conditions, it releases higher concentrations of siderophores and displayes lower nitrous oxide reductase (NosZ) activity than the wild-type, thus leading to nitrous oxide emission. Bioinformatic and qRT-PCR analyses revealed that NtrYX is a global transcriptional regulatory system that responds to iron starvation and, in turn, controls expression of the iron-responsive regulators fur, rirA, and iscR, the denitrification regulators fnrP and narR, the nitric oxide-responsive regulator nnrS, and a wide set of genes, including the cd1-nitrite reductase NirS, nitrate/nitrite transporters and energy electron transport proteins.

Here, we explore a mechanism of quantum dots related photoreduction of two redox-active proteins, cytochrome c and ferredoxin, by detailed analysis of fluorescence decay and reconstruction of time-resolved emission spectra (TRES). We used two types of cadmium telluride quantum dots, with diameters of 2.6 nm and 3.9 nm and maximum emissions at 550 nm and at 650 nm, respectively, which are known to be able to reduce proteins with different efficiencies. First, we observed that for a pure quantum dots solution, the fluorescence decay can be well fitted by three components. The average fluorescence lifetimes, as well as separate time constants, depend on the nanocrystal diameter. In the presence of proteins, fluorescence decay is faster and cytochrome c has a greater impact than ferredoxin. The TRES experiment showed that a fraction of the medium τ decay component is dominant in a pure quantum dot solution, with the maximum corresponding to the steady-state spectrum. The addition of ferredoxin does not change this pattern, while the presence of cytochrome c strongly promotes the shortest τ. Additionally, potassium iodide titration experiments were used to verify the origin of individual decay components. We propose that reduction occurs by electron transfer from both conductive band and surface trap states.

In socially monogamous species, extra-pair paternity (EPP) is predicted to increase variance in male reproductive success (RS) beyond that resulting from genetic monogamy, thus, increasing the "opportunity for selection" (maximum strength of selection that can act on traits).This prediction is challenging to investigate in wild populations because lifetime reproduction data are often incomplete.Moreover, age-specific variances in reproduction have been rarely quantified.We analyzed 21 years of near-complete social and genetic reproduction data from an insular population of Seychelles warblers (Acrocephalus sechellensis).We quantified EPP's contribution to lifetime and age-specific opportunities for selection in males.We compared the variance in male genetic RS vs social ("apparent") RS (RS ap ) to assess if EPP increased the opportunity for selection over that resulting from genetic monogamy. Despite not causinga statistically significant excess (19%) of the former over the latter, EPP contributed substantially (27%) to the variance in lifetime RS, similarly to within-pair paternity (WPP, 39%) and to the positive WPP-EPP covariance (34%).Partitioning the opportunity for selection into age-specific (co)variance components, showed that EPP also provided a substantial contribution at most ages, varying with age.Therefore, despite possibly not playing the main role in shaping sexual selection in Seychelles warblers, EPP provided a substantial contribution to the lifetime and age-specific opportunity for selection, which can influence evolutionary processes in age-structured populations.