Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora).

Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.

Disgust in animals and the application of disease avoidance to wildlife management and conservation.

Disgust is an adaptive system hypothesized to have evolved to reduce the risk of becoming sick. It is associated with behavioural, cognitive and physiological responses tuned to allow animals to avoid and/or get rid of parasites, pathogens and toxins. Little is known about the mechanisms and outcomes of disease avoidance in wild animals. Furthermore, given the escalation of negative human-wildlife interactions, the translation of such knowledge into the design of evolutionarily relevant conservation and wildlife management strategies is becoming urgent. Contemporary methods in animal ecology and related fields, using direct (sensory cues) or indirect (remote sensing technologies and machine learning) means, provide a flexible toolbox for testing and applying disgust at individual and collective levels. In this review/perspective paper, we provide an empirical framework for testing the adaptive function of disgust and its associated disease avoidance behaviours across species, from the least to the most social, in different habitats. We predict various trade-offs to be at play depending on the social system and ecology of the species. We propose five contexts in which disgust-related avoidance behaviours could be applied, including endangered species rehabilitation, invasive species, crop-raiding, urban pests and animal tourism. We highlight some of the perspectives and current challenges of testing disgust in the wild. In particular, we recommend future studies to consider together disease, predation and competition risks. We discuss the ethics associated with disgust experiments in the above contexts. Finally, we promote the creation of a database gathering disease avoidance evidence in animals and its applications.

Le dégoût est un système adaptatif supposé avoir évolué afin de réduire le risque de tomber malade. Il est associé à des réponses comportementales, cognitives et physiologiques adaptées pour permettre aux animaux d'éviter et/ou de se débarrasser des parasites, pathogènes et toxines. On sait peu de choses sur les mécanismes et les conséquences de l'évitement des maladies chez les animaux sauvages. Étant donné l'escalade des interactions négatives entre humains et faune, la traduction de ces connaissances dans la conception de stratégies de conservation et de gestion de la faune - prenant en considération l'évolution des espèces - devient urgente. Les méthodes contemporaines en écologie animale et dans les domaines connexes, utilisant des moyens directs (indices sensoriels) ou indirects (technologies de télédétection et apprentissage automatique), fournissent une boîte à outils flexible pour tester et appliquer le dégoût aux niveaux individuel et collectif. Dans cet article de revue/perspective, nous fournissons un cadre empirique pour tester la fonction adaptative du dégoût et les comportements associés d'évitement des maladies chez différentes espèces - des moins sociales aux plus sociales, et dans différents habitats. Nous prédisons divers compromis en fonction du système social et de l'écologie de l'espèce. Nous proposons cinq contextes dans lesquels les comportements d'évitement liés au dégoût pourraient être appliqués: la réhabilitation d'espèces menacées; les espèces envahissantes; les dommages aux cultures; les nuisibles urbains; et le tourisme animalier. Nous mettons en avant certaines perspectives et défis actuels de l'expérimentation sur le dégoût en milieu naturel. En particulier, nous recommandons la considération de plusieurs risques ensemble: maladie, prédation et compétition. Nous discutons également de l'éthique associée aux expériences sur le dégoût dans les contextes ci-dessus. Enfin, nous promouvons la création d'une base de données rassemblant les stratégies d'évitement des maladies chez les animaux et leurs applications.

Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches.

In response to the massive use of biocides for controlling Listeria monocytogenes (hereafter Lm) contaminations along the food chain, strains showing biocide tolerance emerged. Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 Lm strains from different lineages, ecological, geographical and temporal origins. Mobile elements, including prophage-related loci, the Tn6188_qacH transposon and pLMST6_emrC plasmid, were widespread across lineage I and II food strains and associated with tolerance to benzalkonium-chloride (BC), a quaternary ammonium compound (QAC) widely used in food processing. The pLMST6_emrC was also associated with tolerance to another QAC, the didecyldimethylammonium-chloride, displaying a pleiotropic effect. While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with BC or polymeric biguanide tolerance. The latter was restricted to lineage I strains from animal and the environment. In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the Lm adaptation to biocide, especially in food strains but also from animal and the environment. These markers could aid to monitor and predict the spread of biocide tolerant Lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.

Influence of glyphosate and its metabolite aminomethylphosphonic acid on aquatic plants in different ecological niches.

Glyphosate and its metabolite aminomethylphosphonic acid (AMPA) draw great concern due to their potential threat to aquatic ecosystems. The individual and combined effects of glyphosate and AMPA on aquatic plants in different ecological niches need to be explored. This study aimed to investigate the ecotoxicity of glyphosate and AMPA on the emergent macrophyte Acorus calamus, phytoplankton Chlorella vulgaris, and submerged macrophyte Vallisneria natans after their exposure to glyphosate and AMPA alone and to their mixture. Medium and low concentrations of glyphosate (≤ 0.5 mg L-1) significantly inhibited the growth of V. natans and promoted the growth of C. vulgaris (P < 0.05) but had no significant effect on the growth of A. calamus (P > 0.05). AMPA (≤ 5.0 mg L-1) did not significantly influence the relative growth rate (except C. vulgaris) or malonaldehyde levels but significantly altered the expression levels of chlorophyll-related genes and superoxide dismutase [Cu-Zn] genes in the aquatic plants examined. AMPA mainly affected the oxidative phosphorylation pathway in V. natans and not those in other two plants, indicating that V. natans was more sensitive to AMPA-induced oxidative damage. Moreover, antagonistic effects on plant growth were observed when plants were exposed to low concentrations of glyphosate + AMPA (≤ 0.1 + 0.1 mg L-1). When the concentration of glyphosate + AMPA reached 0.5 + 0.5 and 5.0 + 5.0 mg L-1, the growth of the submerged macrophyte was additively or synergistically inhibited, but the growth of the emergent macrophyte and phytoplankton was antagonistically inhibited. Our results indicated that both the individual and combined effects of glyphosate and AMPA might alter the vertical structure of shallow lakes and accelerate the conversion of shallow lakes from grass-based to algal-based lakes.

Saprophytic to Pathogenic Mycobacteria: Loss of Cytochrome P450s Vis a Vis Their Prominent Involvement in Natural Metabolite Biosynthesis.

Cytochrome P450 monooxygenases (P450s/CYPs) are ubiquitous enzymes with unique regio- and stereo-selective oxidation activities. Due to these properties, P450s play a key role in the biosynthesis of natural metabolites. Mycobacterial species are well-known producers of complex metabolites that help them survive in diverse ecological niches, including in the host. In this study, a comprehensive analysis of P450s and their role in natural metabolite synthesis in 2666 mycobacterial species was carried out. The study revealed the presence of 62,815 P450s that can be grouped into 182 P450 families and 345 subfamilies. Blooming (the presence of more than one copy of the same gene) and expansion (presence of the same gene in many species) were observed at the family and subfamily levels. CYP135 was the dominant family in mycobacterial species. The mycobacterial species have distinct P450 profiles, indicating that lifestyle impacts P450 content in their genome vis a vis P450s, playing a key role in organisms' adaptation. Analysis of the P450 profile revealed a gradual loss of P450s from non-pathogenic to pathogenic mycobacteria. Pathogenic mycobacteria have more P450s in biosynthetic gene clusters that produce natural metabolites. This indicates that P450s are recruited for the biosynthesis of unique metabolites, thus helping these pathogens survive in their niches. This study is the first to analyze P450s and their role in natural metabolite synthesis in many mycobacterial species.

In vitro evidence of root colonization suggests ecological versatility in the genus Mycena.

The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14 C and 32 P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32 P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.

Fungal P450 monooxygenases - the diversity in catalysis and their promising roles in biocontrol activity.

The fungal P450s catalyze vital monooxygenation reactions in primary and secondary metabolism, which may lead to the production of diverse secondary metabolites. Many of these, such as from the family of trichothecenes, involve in biocontrol activities. The diversified nature of fungal P450 monooxygenases makes their host organisms adoptable to various ecological niches. The available genome data analysis provided an insight into the activity and mechanisms of the fungal P450s. However, still more structural and functional studies are needed to elucidate the details of its catalytic mechanism, and the advance studies are also required to decipher further about their dynamic role in various aspects of trichothecene oxygenations. This mini review will provide updated information on different fungal P450 monooxygenases, their genetic diversity, and their role in catalyzing various biochemical reactions leading to the production of plant growth promoting secondary metabolites.

The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota).

Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.

Ecology of Scedosporium Species: Present Knowledge and Future Research.

The genus Scedosporium, which comprises at least five clinically relevant species, i.e. Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum, Scedosporium dehoogii and Scedosporium minutisporum, ranks the second among the filamentous fungi colonizing the airways of patients with cystic fibrosis (CF). This colonization of the airways is thought to contribute to the inflammatory reaction leading to a progressive deterioration of the lung function. Additionally, these colonizing fungi may lead to severe disseminated infections in case of lung transplantation. Therefore, considering the low susceptibility of Scedosporium species to all current antifungal drugs, preventive measures should be defined to reduce the risk of exposure to these fungi for non-colonized CF patients. With this in mind, several studies have been conducted to elucidate the ecology of these fungi and to define possible sources of patient contamination. This review will summarize the major outcomes of those studies, including: the clear demonstration that ecological niches of Scedosporium species are strongly impacted by human activities, and the ability of Scedosporium species to degrade aliphatic and aromatic pollutants which supports the high occurrence of these species in contaminated soils and polluted waters and makes them promising candidates for bioremediation purposes. Finally, prospects for future research in this field are proposed.

Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns.

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics.

Seed dormancy responses to temperature relate to Nothofagus species distribution and determine temporal patterns of germination across altitudes in Patagonia.

Seeds integrate environmental cues that modulate their dormancy and germination. Although many mechanisms have been identified in laboratory experiments, their contribution to germination dynamics in existing communities and their involvement in defining species habitats remain elusive. By coupling mathematical models with ecological data we investigated the contribution of seed temperature responses to the dynamics of germination of three Nothofagus species that are sharply distributed across different altitudes in the Patagonian Andes. Seed responsiveness to temperature of the three Nothofagus species was linked to the thermal characteristics of their preferred ecological niche. In their natural distribution range, there was overlap in the timing of germination of the species, which was restricted to mid-spring. By contrast, outside their species distribution range, germination was temporally uncoupled with altitude. This phenomenon was described mathematically by the interplay between interspecific differences in seed population thermal parameters and the range in soil thermic environments across different altitudes. The observed interspecific variations in seed responsiveness to temperature and its environmental regulation, constitute a major determinant of the dynamics of Nothofagus germination across elevations. This phenomenon likely contributes to the maintenance of patterns of species abundance across altitude by placing germinated seeds in a favorable environment for plant growth.

Brettanomyces bruxellensis, a survivalist prepared for the wine apocalypse and other beverages.

Brettanomyces bruxellensis is a common red wine spoilage yeast. Yet, in addition to wine, it has been isolated from other ecological niches that are just as nutritionally deficient as wine. B. bruxellensis can therefore be regarded as a survivor, well adapted to colonise harsh environments not often inhabited by other yeasts. This review is focused on the nutritional requirements of B. bruxellensis and the relevance thereof for its adaptation to the different matrices within which it occurs. Furthermore, the environmental conditions necessary (e.g. aerobic or anaerobic conditions) for the assimilation of the carbon or nitrogenous sources are discussed in this review. From literature, several confusing inconsistencies, regarding nutritional sources necessary for B. bruxellensis survival, in these specialist ecological niches are evidenced. The main focus of this review is wine but other products and niches that B. bruxellensis inhabits namely beer, cider, fruit juices and bioethanol production plants are also considered. This review highlights the lack of knowledge regarding B. bruxellensis when considering its nutritional requirements in comparison to Saccharomyces cerevisiae. However, there is a large enough body of evidence showing that the nutritional needs of B. bruxellensis are meagre, explaining its ability to colonise harsh environments.

Rupestriomyces and Spissiomyces, two new genera of rock-inhabiting fungi from China.

Bare rocks in arid and semi-arid climates may harbor a bewildering biodiversity of fungi that are overlooked in China. During a survey of rock-inhibiting fungi in China, more than 1000 were isolated and 14 belonging to Dothideomycetes (Ascomycota) were selected for detailed study. Phylogenetic trees based on combined sequence datasets of mt 16S rDNA, partial nuc rDNA 18S and 28S indicated that these strains clustered in two distinct, well supported and previously unknown lineages within the class Dothideomycetes. Therefore two new genera were established corresponding to those two clades. Spissiomyces gen. nov. is characterized by thick-walled, yellowish brown hyphae and globose or subglobose conidia, if present. Rupestriomyces gen. nov. is characterized by globose, barrel-shaped, ampulliform or ovoidal conidia formed from acropetal, catenate hyphae. Further phylogenetic analyses using combined sequence datasets of the rDNA internal transcribed spacer (ITS) region and 16S rDNA, part of genes of RPB2, TUB2, nuc rDNA 18S and 28S revealed that those strains represented five new species (i.e. Spissiomyces aggregatus, S. ramosus, Rupestriomyces sinensis, R. ampulliformis, R. torulosus). They were described, illustrated and compared with similar taxa based on morphological characteristics and phylogenetic relationships. The results of this paper provides insight into the richness and diversity of rock-inhibiting fungi in nature.

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator.

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.

The effect of El Niño and La Niña episodes on the existing niche and potential distribution of vector and host species of American Cutaneous Leishmaniasis.

Leishmaniasis is a zoonotic disease transmitted to humans by a protozoan parasite through sandfly vectors and multiple vertebrate hosts. The Pan American Health Organization reported a declining trend in cases, with Brazil, Colombia, Peru, Nicaragua, and Bolivia having the most cases in 2020. There are still knowledge gaps in transmission and the parasite-host relationship. Ecological niche modeling has been used to study host-vector relationships, disease dynamics, and the impact of climate change. Understanding these aspects can aid in early surveillance and vector control strategies. The potential distribution of five host species associated with the transmission of cutaneous leishmaniasis (CL) was modeled. Occurrence data were collected for each host species, and environmental variables were used to build the models. Climatic data from El Niño, La Niña, and Neutral episodes were used to compare the predicted distributions. Additionally, the potential distributions of four vector species were compared to identify overlaps with host species. Niche analysis was conducted to evaluate changes in vector niches across episodes and to identify host-vector pairs based on niche overlap in geographic and environmental spaces. After spatial thinning, 467 records were obtained, and 1,190 candidate models were evaluated for each species. Results showed the distribution of occurrences in the environmental space, highlighting a high risk of extrapolation beyond the calibration areas. Movement-Oriented Parity analysis revealed distinct distribution patterns under different climate conditions, with areas of environmental similarity identified. Bradypus variegatus exhibited a broad potential distribution, while Dasypus novemcinctus and Didelphis marsupialis had more restricted ranges. Sylvilagus braziliensis covered most of the Neotropics. Our study provides valuable insights into ecological niches and geographic ranges of these species, contributing to the understanding of cutaneous leishmaniasis transmission dynamics.

The Diverse Mycorrizal Morphology of Rhododendron dauricum, the Fungal Communities Structure and Dynamics from the Mycorrhizosphere.

It is generally believed that mycorrhiza is a microecosystem composed of mycorrhizal fungi, host plants and other microscopic organisms. The mycorrhiza of Rhododendron dauricum is more complex and the diverse morphology of our investigated results displays both typical ericoid mycorrhizal characteristics and ectomycorrhizal traits. The characteristics of ectendoomycorrhiza, where mycelial invade from the outside into the root cells, have also been observed. In order to further clarify the mycorrhizal fungi members and other fungal communities of R. dauricum mycorrhiza, and explore the effects of vegetation and soil biological factors on their community structure, we selected two woodlands in the northeast of China as samples-one is a mixed forest of R. dauricum and Quercus mongolica, and the other a mixed forest of R. dauricum, Q. mongolica, and Pinus densiflor. The sampling time was during the local growing season, from June to September. High-throughput sequencing yielded a total of 3020 fungal amplicon sequence variants (ASVs), which were based on sequencing of the internal transcribed spacer ribosomal RNA (ITS rRNA) via the Illumina NovaSeq platform. In the different habitats of R. dauricum, there are differences in the diversity of fungi obtained from mycorrhizal niches, and specifically the mycorrhizal fungal community structure in the complex vegetation of mixed forests, where R. dauricum is found, exhibits greater stability, with relatively minor changes over time. Soil fungi are identified as the primary source of fungi within the mycorrhizal niche, and the abundance of mycorrhizal fungi from mycorrhizal niches in R. dauricum is significantly influenced by soil pH, organic matter, and available nitrogen. The relationship between soil fungi and mycorrhizal fungi from mycorrhizal niches is simultaneously found to be intricate, while the genus Hydnellum emerges as a central genus among mycorrhizal fungi from mycorrhizal niches. However, there is currently a substantial gap in the foundational research of this genus, including the fact that mycorrhizal fungi from mycorrhizal niches have, compared to fungi present in the soil, proven to be more sensitive to changes in soil moisture.

Revealing microbial community assembly patterns and succession process in the blackening process of black-odor water.

Human-imported pollutants could induce water black, changing microbial community structure and function. Employed 16S rRNA high-throughput sequencing, field-scale investigations and laboratory-scale experiments were successively conducted to reveal mechanistic insights into microbial community assembly and succession of black-odor waters (BOWs). In the field-scale investigation, livestock breeding wastewater (56.7 ± 3.2%) was the most critical microbial source. Moreover, fermentation (27.1 ± 4.4%) was found to be the dominant function. Combined with laboratory experiments, the critical environmental factors, such as total organic carbon (30-100 mg/L), ammonia nitrogen (2.5-9 mg/L), initial dissolved oxygen (2-8 mg/L) and chlorophyll a (0-90 mg/L), impacted the intensity of blackening. The differentiation of ecological niches within the microbial community played a significant role in driving the blackening speed. In laboratory-scale experiments, the microbial ecological niche determined the blackening timing and dominations of the stochastic processes in the microbial assembly process (88 - 51%). The three stages, including the anaerobic degradation stage, blackening stage and slow recovery stage, were proposed to understand the assembly of the microbial communities. These findings enhance our understanding of microorganisms in BOWs and provide valuable insights for detecting and managing heavily organic polluted waters.

Shifts in the microbial community and metabolome in rumen ecological niches during antler growth.

Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.

Evaluation of Human Settlement Environment and Identification of Development Barriers Based on the Ecological Niche Theory: A Case Study of Northern Shaanxi, China.

The quality of human settlement environment (HSE) is related to people's well-being. Since the implementation of the Western Development Strategy and the Grain to Green Program, the HSE in northern Shaanxi has undergone a major transformation. In order to explore the evolution pattern and seek a coordinated development strategy for all systems in the whole region, this paper, from the perspective of "production-living-ecological", evaluates the HSE niche breadth of northern Shaanxi based on the ecological niche theory, analyzes its spatial differentiation characteristics, and identifies the development barrier factors, with the help of ArcGIS spatial analysis tools and the barrier degree model. It is found that: from 2000 to 2020, (1) the niche breadth of HSE in northern Shaanxi is high in the north and low in the south, showing obvious spatial unevenness; (2) the development of transportation promotes the improvement of HSE, but also intensifies the spatial unevenness, and the uncoordinated development rate of transportation and production and living systems has seriously restricted the further development of HSE; (3) the niche breadth of the ecosystem for each county is much lower than that of the production and living systems, and the ecological environment becomes the short board of the improvement of HSE in northern Shaanxi. Based on the patterns and problems found in the study, this paper proposes a strategy to improve the HSE of northern Shaanxi by prioritizing the balanced development of production, living systems, and transportation, strictly implementing the concept of ecological priority, dynamically adjusting the hierarchy of policies, vigorously optimizing the industrial layout, and focusing on the joint improvement of the human settlement environment in the whole region. This study expands the theories and evaluation methods of HSE to a certain extent, and the results have guiding values for promoting the sustainable development of HSE in northern Shaanxi and even the whole Loess Plateau region.