Complete genome sequence of Imperialibacter roseus strain P4T.

Imperialibacter roseus strain P4T is a bacterial strain isolated from Permian groundwater. The complete genome of Imperialibacter roseus strain P4T was sequenced to reveal a single circular chromosome of 6,747,663 bp with a GC content of 46.5%.

Morbidity and Mortality of the Transmetatarsal Amputation: A Comparative NSQIP Analysis.

The objective of this investigation was to compare the morbidity and mortality of transmetatarsal amputation to other frequently performed surgical procedures utilizing a large US database. The American College of Surgeons National Surgical Quality Improvement Program (NSQIP) database was interrogated for the purposes of this investigation. We initially extracted data related to the Current Procedural Terminology (CPT) code 28805 (amputation, foot; transmetatarsal) and the variable labels "estimated probability of morbidity" and "estimated probability of mortality." We subsequently performed a CPT code search for those procedures occurring at a frequency greater than 10,000 in the database, and additionally extracted data for estimated probability of morbidity and estimated probability of mortality for these procedures. This resulted in identification of 17 additional procedures. CPT code 28805 was associated with the highest estimated probability of morbidity of the cohort (0.1360 ± 0.0669), and this demonstrated statistical significance higher than all other CPT codes (p < .001). CPT code 28805 was associated with the second-highest estimated probability of mortality of the cohort (0.0327 ± 0.0596). This demonstrated statistical significance less than that of CPT code 27245 (0.0327 ± 0.0596 vs 0.0547 ± 0.0661; p < .0001), but statistical significance higher than all other CPT codes (p<0.001). The results of this investigation indicate that transmetatarsal amputation carries a substantial risk for morbidity and mortality in comparison to other commonly performed surgical procedures.

Open plains are not a level playing field for hominid consonant-like versus vowel-like calls.

Africa's paleo-climate change represents an "ecological black-box" along the evolutionary timeline of spoken language; a vocal hominid went in and, millions of years later, out came a verbal human. It is unknown whether or how a shift from forested, dense habitats towards drier, open ones affected hominid vocal communication, potentially setting stage for speech evolution. To recreate how arboreal proto-vowels and proto-consonants would have interacted with a new ecology at ground level, we assessed how a series of orangutan voiceless consonant-like and voiced vowel-like calls travelled across the savannah. Vowel-like calls performed poorly in comparison to their counterparts. Only consonant-like calls afforded effective perceptibility beyond 100 m distance without requiring repetition, as is characteristic of loud calling behaviour in nonhuman primates, typically composed by vowel-like calls. Results show that proto-consonants in human ancestors may have enhanced reliability of distance vocal communication across a canopy-to-ground ecotone. The ecological settings and soundscapes experienced by human ancestors may have had a more profound impact on the emergence and shape of spoken language than previously recognized.

Micrococcus spp. as a promising source for drug discovery: A review.

Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.

Genomic characterization and molecular dating of the novel bacterium Permianibacter aggregans HW001T, which originated from Permian ground water.

The Permian Basin is a unique ecosystem located in the southwest of the USA. An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater. In our previous study, a novel bacterial strain, Permianibacter aggregans HW001T, was isolated from microalgae cultures incubated with Permian Basin waters, and was shown to originate from the Permian Ocean. In this study, strain HW001T was shown to be the representative strain of a novel family, classified as 'Permianibacteraceae'. The results of molecular dating suggested that the strain HW001T diverged ~ 447 million years ago (mya), which is the early Permian period (~ 250 mya). Genome analysis was used to access its potential energy utilization and biosynthesis capacity. A large number of transporters, carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T. In addition, a series of important metabolic pathways, such as peptidoglycan biosynthesis, osmotic stress response system and multifunctional quorum sensing were annotated, which may confer the ability to adapt to various unfavorable environmental conditions. Finally, the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted, indicating that the adaptation of P. aggregans to a changing marine environment depends on the evolution of their metabolic capabilities, especially in signal transmission. In conclusion, the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00164-3.

Model selection in occupancy models: Inference versus prediction.

Occupancy models are a vital tool for ecologists studying the patterns and drivers of species occurrence, but their use often involves selecting among models with different sets of occupancy and detection covariates. The information-theoretic approach, which employs information criteria such as Akaike's information criterion (AIC) is arguably the most popular approach for model selection in ecology and is often used for selecting occupancy models. However, the information-theoretic approach risks selecting models that produce inaccurate parameter estimates due to a phenomenon called collider bias, a type of confounding that can arise when adding explanatory variables to a model. Using simulations, we investigated the consequences of collider bias (using an illustrative example called M-bias) in the occupancy and detection processes of an occupancy model, and explored the implications for model selection using AIC and a common alternative, the Schwarz criterion (or Bayesian information criterion, BIC). We found that when M-bias was present in the occupancy process, AIC and BIC selected models that inaccurately estimated the effect of the focal occupancy covariate, while simultaneously producing more accurate predictions of the site-level occupancy probability than other models in the candidate set. In contrast, M-bias in the detection process did not impact the focal estimate; all models made accurate inferences, while the site-level predictions of the AIC/BIC-best model were slightly more accurate. Our results show that information criteria can be used to select occupancy covariates if the sole purpose of the model is prediction, but must be treated with more caution if the purpose is to understand how environmental variables affect occupancy. By contrast, detection covariates can usually be selected using information criteria regardless of the model's purpose. These findings illustrate the importance of distinguishing between the tasks of parameter inference and prediction in ecological modeling. Furthermore, our results underline concerns about the use of information criteria to compare different biological hypotheses in observational studies.

Comparative Radiographic Analysis of the Width of the Lesser Digit Proximal Phalangeal Heads.

BACKGROUND: Digital deformities represent a common presenting abnormality and target for surgical intervention in podiatric medicine and surgery. The objective of this investigation was to compare the radiographic width of the heads of the lesser digit proximal phalanges. METHODS: One hundred fifty consecutive feet with a diagnosis of digital deformity and performance of weightbearing radiographs were analyzed. The maximum width of the heads of the lesser digit proximal phalanges were recorded from the radiographs using computerized digital software. RESULTS: The mean ± standard deviation of the head of the second digit proximal phalanx was 9.74 ± 0.87 mm (range, 7.94-11.78 mm); the head of the third digit proximal phalanx, 9.00 ± 0.91 mm (range,7.27-10.94 mm); the head of the fourth digit proximal phalanx, 8.49 ± 1.01 mm (range, 5.57-10.73 mm); and the head of the fifth digit proximal phalanx, 8.67 ± 0.89 mm (range, 6.50-11.75 mm). The width of the head of the proximal phalanx decreased from the second digit to the third digit (P < .001), decreased from the third digit to the fourth digit (P < .001), and then increased from the fourth digit to the fifth digit (P = .032). CONCLUSIONS: The results of this investigation provide evidence in support of an anatomical and structural contribution to digital deformities. The width of the heads of the lesser digit proximal phalanges decreased from the second to the third to the fourth toes, and then subsequently increased with the fifth proximal phalangeal head.

Uptake of inorganic and organic phosphorus compounds by two marine sponges and their associated bacterial communities in aquaria.

Marine sponges are abundant filter-feeders in benthic ecosystems and many host copious microorganisms. Sponges and their symbionts have emerged as major players within marine biogeochemical cycles, facilitating uptake and release of carbon, nitrogen, and sulfur. Sponge holobionts' role in transforming dissolved carbon and nitrogen is well established; however, the same depth of understanding has not yet been extended to phosphorus. In this aquaria-based study, 32 P-labelled orthophosphate and ATP were used to determine that two sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both take up ambient dissolved inorganic phosphate (DIP) and dissolved organic phosphorus (DOP). Subsequent genetic analyses and chemical extraction showed that sponge symbionts have the potential to synthesise polyphosphate (poly-P) and that this energy-rich form of stored phosphorus is present in both sponges. L. chondrodes, an oligotrophic sponge with a microbiome dominated by cyanobacteria, stores more phosphorus as poly-P (6%-8% of total phosphorus) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. DIP/DOP uptake, as well as poly-P storage, may be driven by two factors: cyanobacterial abundance and nutrient availability. Considering their prevalence in phosphorus-limited ecosystems and their ability to pump large amounts of seawater, sponge holobionts are likely to be key players within benthic phosphorus cycles.

Cortisol metabolites vary with environmental conditions, predation risk, and human shields in a wild primate, Cercopithecus albogularis.

Environmental challenges are often associated with physiological changes in wildlife that allow animals to maintain homeostasis. Among these, scarcity in resources, and risks from predators, competitors, and humans can all result in psychological and physiological stress. Yet, for habituated species, it is not clear whether this relationship with humans still holds to a lesser degree or is outweighed by the benefits of human presence - such as serving as a buffer from competitors or predators. We investigated how human presence and environmental challenges such as resource availability, weather, predation, and competition may be associated with variation in fecal cortisol metabolite levels (FCMs) in a group of samango monkeys (Cercopithecus albogularis) in the Soutpansberg Mountains, South Africa. FCMs can often broadly track environmental challenges and perturbations. Initially, we employed an exploratory analysis comparing candidate models representing biological hypotheses and found that those incorporating information on human presence had less weight than models for food availability, thermoregulation, and water scarcity. When we examined a subset of the data that included information on intergroup competition and predator alarm calls, we found that FCMs were higher on the day following potential predator encounters but not competitive interactions. As observer numbers increased, responses to predators flattened, indicating that the presence of several humans might deter predators and/or affect samangos' perception of danger - yet we could not distinguish between these possibilities. Together, these results suggest that ecological perturbations track with FCMs in this study population and challenge long-held assumptions that human presence has negligible effects on habituated study animals.

Intolerant baboons avoid observer proximity, creating biased inter-individual association patterns.

Social network analysis is an increasingly popular tool for behavioural ecologists exploring the social organisation of animal populations. Such analyses require data on inter-individual association patterns, which in wild populations are often collected using direct observations of habituated animals. This assumes observers have no influence on animal behaviour; however, our previous work showed that individuals in a habituated group of chacma baboons (Papio ursinus griseipes) displayed consistent and individually distinct responses to observer approaches. We explored the implications of our previous findings by measuring the inter-individual association patterns of the same group of chacma baboons at different observer distances. We found a strong positive association between individual tolerance levels (towards observers) and how often an animal appeared as a neighbour to focal animals when observers were nearer, and a neutral relationship between the same variables when the observer was further away. Additionally, association matrices constructed from different observation distances were not comparable within any proximity buffer, and neither were the individual network metrics generated from these matrices. This appears to be the first empirical evidence that observer presence and behaviour can influence the association patterns of habituated animals and thus have potentially significant impacts on measured social networks.

Camera traps and guard observations as an alternative to researcher observation for studying anthropogenic foraging.

Foraging by wildlife on anthropogenic foods can have negative impacts on both humans and wildlife. Addressing this issue requires reliable data on the patterns of anthropogenic foraging by wild animals, but while direct observation by researchers can be highly accurate, this method is also costly and labor-intensive, making it impractical in the long-term or over large spatial areas. Camera traps and observations by guards employed to deter animals from fields could be efficient alternative methods of data collection for understanding patterns of foraging by wildlife in crop fields. Here, we investigated how data on crop-foraging by chacma baboons and vervet monkeys collected by camera traps and crop guards predicted data collected by researchers, on a commercial farm in South Africa. We found that data from camera traps and field guard observations predicted crop loss and the frequency of crop-foraging events from researcher observations for crop-foraging by baboons and to a lesser extent for vervets. The effectiveness of cameras at capturing crop-foraging events was dependent on their position on the field edge. We believe that these alternatives to direct observation by researchers represent an efficient and low-cost method for long-term and large-scale monitoring of foraging by wildlife on crops.

Microalgal and bacterial auxin biosynthesis: implications for algal biotechnology.

Optimization of microalgal growth and high-value metabolite production are key steps in microalgal mass culture for the algae industry. An emerging technology is the use of phytohormones, like indole-3-acetic acid (IAA), to promote microalgal growth. This requires an understanding of the biosynthesis of IAA in microalgae-bacteria associations and its function in regulating algal physiology and metabolite production. We review the current advances in understanding of microalgal and bacterial auxin biosynthesis and their implications for algal biotechnology.

Consistency in the flight and visual orientation distances of habituated chacma baboons after an observed leopard predation. Do flight initiation distance methods always measure perceived predation risk?

Flight initiation distance (FID) procedures are used to assess the risk perception animals have for threats (e.g., natural predators, hunters), but it is unclear whether these assessments remain meaningful if animals have habituated to certain human stimuli (e.g., researchers, tourists). Our previous work showed that habituated baboons displayed individually distinct and consistent responses to human approaches, a tolerance trait, but it is unknown if the trait is resilient to life-threatening scenarios. If it were consistent, it would imply FIDs might measure specific human threat perception only and not generalize to other threats such as predators when animals have experienced habituation processes. We used FID procedures to compare baseline responses to the visual orientation distance, FID, and individual tolerance estimates assessed after a leopard predation on an adult male baboon (group member). All variables were consistent despite the predation event, suggesting tolerance to observers was largely unaffected by the predation and FID procedures are unlikely to be generalizable to other threats when habituation has occurred. FID approaches could be an important tool for assessing how humans influence animal behavior across a range of contexts, but careful planning is required to understand the type of stimuli presented.

Disappearing Nail Bed: Review of Etiology, Grading System, and Treatment Options.

Disappearing nail bed (DNB) is a condition characterized by irreversible epithelialization of the nail bed following long-standing onycholysis. This phenomenon can occur in fingernails and toenails. Factors implicated in the development of DNB include trauma, manicuring, and onychotillomania and dermatologic conditions like psoriasis and dermatitis. Specifically for the toenail, contributing factors also include increasing age, history of trauma, surgery, onychomycosis, and onychogryphosis. A grading system that stages the progression of onycholysis to DNB has been proposed to aid clinicians in the diagnosis and treatment of these conditions. Several methods have been designated for the treatment of DNB.

Correction: Ou et al. Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas. Microorganisms 2020, 8, 63.

The authors wish to make the following corrections to this paper [...].

Seasonal variation in the behavioural ecology of samango monkeys (Cercopithecus albogularis schwarzi) in a southern latitude montane environment.

Samango monkeys (Cercopithecus albogularis schwarzi) in the Soutpansberg Mountains, South Africa, experience a highly seasonal climate, with relatively cold, dry winters. They must show behavioural flexibility to survive these difficult conditions near the southern limit of the species' distribution and maintain the minimum nutritional intake they require. Through environmental monitoring and behavioural observations of a habituated group of samango monkeys, we explored how they adapted to the highly seasonal climate they experienced in the mountains. Our results indicated that the monkeys varied their foraging behaviours to account for changes in climate and daylight availability. The samangos increased their food intake in colder months, specifically leaves, likely due to an increased need for calories during winter to maintain body temperature. Samango monkeys have anatomical and physiological adaptations for digesting leaves, and these are likely important in explaining their ability to adapt to the broad range of climatic conditions they experience.

Habitat selection of an endangered primate, the samango monkey (Cercopithecus albogularis schwarzi): Integrating scales to prioritize habitat for wildlife management.

AIM: As habitat loss continues to accelerate with global human population growth, identifying landscape characteristics that influence species occurrence is a key conservation priority in order to prevent global biodiversity loss. In South Africa, the arboreal samango monkey (Cercopithecus albogularis sp.) is threatened due to loss and fragmentation of the indigenous forests it inhabits. The aim of this study was to determine the habitat preferences of the samango monkey at different spatial scales, and to identify key conservation areas to inform management plans for this species. LOCATION: This study was carried out in the western Soutpansberg Mountains, which represents the northernmost population of samango monkeys within South Africa, and the only endangered subspecies (C. a. schwarzi). METHODS: We used sequentially collected GPS points from two samango monkey groups followed between 2012 and 2017 to quantify the used and available habitat for this species within the western Soutpansberg Mountains. We developed 2nd-order (selection of ranging area), 3rd-order (selection within range), and 4th-order (feeding site selection) resource selection functions (RSFs) to identify important habitat features at each scale. Through scale integration, we identified three key conservation areas for samango monkeys across Limpopo Province, South Africa. RESULTS: Habitat productivity was the most important landscape variable predicting probability of use at each order of selection, indicating the dependence of these arboreal primates on tall-canopy indigenous forests. Critical habitat across Limpopo was highly fragmented, meaning complete isolation between subpopulations is likely. MAIN CONCLUSIONS: Understanding the habitat characteristics that influence samango monkey distribution across South Africa is crucial for prioritizing critical habitat for this species. Our results indicated that large, contiguous patches of tall-canopy indigenous forest are fundamental to samango monkey persistence. As such, protected area expansion of large forest patches and creation of forest corridors are identified as key conservation interventions for this species.

Insights into short- and long-term crop-foraging strategies in a chacma baboon (Papio ursinus) from GPS and accelerometer data.

Crop-foraging by animals is a leading cause of human-wildlife "conflict" globally, affecting farmers and resulting in the death of many animals in retaliation, including primates. Despite significant research into crop-foraging by primates, relatively little is understood about the behavior and movements of primates in and around crop fields, largely due to the limitations of traditional observational methods. Crop-foraging by primates in large-scale agriculture has also received little attention. We used GPS and accelerometer bio-loggers, along with environmental data, to gain an understanding of the spatial and temporal patterns of activity for a female in a crop-foraging baboon group in and around commercial farms in South Africa over one year. Crop fields were avoided for most of the year, suggesting that fields are perceived as a high-risk habitat. When field visits did occur, this was generally when plant primary productivity was low, suggesting that crops were a "fallback food". All recorded field visits were at or before 15:00. Activity was significantly higher in crop fields than in the landscape in general, evidence that crop-foraging is an energetically costly strategy and that fields are perceived as a risky habitat. In contrast, activity was significantly lower within 100 m of the field edge than in the rest of the landscape, suggesting that baboons wait near the field edge to assess risks before crop-foraging. Together, this understanding of the spatiotemporal dynamics of crop-foraging can help to inform crop protection strategies and reduce conflict between humans and baboons in South Africa.

Impacts of invasive plants on animal behaviour.

The spread of invasive species is a threat to ecosystems worldwide. However, we know relatively little about how invasive species affect the behaviour of native animals, even though behaviour plays a vital role in the biotic interactions which are key to understanding the causes and impacts of biological invasions. Here, we explore how invasive plants - one of the most pervasive invasive taxa - impact the behaviour of native animals. To promote a mechanistic understanding of these behavioural impacts, we begin by introducing a mechanistic framework which explicitly considers the drivers and ecological consequences of behavioural change, as well as the moderating role of environmental context. We then synthesise the existing literature within this framework. We find that while some behavioural impacts of invasive plants are relatively well-covered in the literature, others are supported by only a handful of studies and should be explored further in the future. We conclude by identifying priority topics for future research, which will benefit from an interdisciplinary approach uniting invasion ecology with the study of animal behaviour and cognition.

Assumptions about fence permeability influence density estimates for brown hyaenas across South Africa.

Wildlife population density estimates provide information on the number of individuals in an area and influence conservation management decisions. Thus, accuracy is vital. A dominant feature in many landscapes globally is fencing, yet the implications of fence permeability on density estimation using spatial capture-recapture modelling are seldom considered. We used camera trap data from 15 fenced reserves across South Africa to examine the density of brown hyaenas (Parahyaena brunnea). We estimated density and modelled its relationship with a suite of covariates when fenced reserve boundaries were assumed to be permeable or impermeable to hyaena movements. The best performing models were those that included only the influence of study site on both hyaena density and detection probability, regardless of assumptions of fence permeability. When fences were considered impermeable, densities ranged from 2.55 to 15.06 animals per 100 km2, but when fences were considered permeable, density estimates were on average 9.52 times lower (from 0.17 to 1.59 animals per 100 km2). Fence permeability should therefore be an essential consideration when estimating density, especially since density results can considerably influence wildlife management decisions. In the absence of strong evidence to the contrary, future studies in fenced areas should assume some degree of permeability in order to avoid overestimating population density.