Picante: R tools for integrating phylogenies and ecology

The origins and drivers of sexual size dimorphism in sharks

While sexual size dimorphism (SSD) is abundant in nature, there is huge variation in both the intensity and direction of SSD. SSD results from a combination of sexual selection for large male size, fecundity selection for large female size and ecological selection for either. In most vertebrates, it is variation in the intensity of male-male competition that primarily underlies variation in SSD. In this study, we test four hypotheses regarding the adaptive value of SSD in sharks-considering the potential for each of fecundity, sexual, ecological selection and reproductive mode as the primary driver of variation in SSD between species. We also estimate past macroevolutionary shifts in SSD direction/intensity through shark phylogeny. We were unable to find evidence of significant SSD in early sharks and hypothesise that SSD is a derived state in this clade, that has evolved independently of SSD observed in other vertebrates. Moreover, there is no significant relationship between SSD and fecundity, testes mass or oceanic depth in sharks. However, there is evidence to support previous speculation that reproductive mode is an important determinant of interspecific variation in SSD in sharks. This is significant as in most vertebrates sexual selection is thought to be the primary driver of SSD trends, with evidence for the role of fecundity selection in other clades being inconsistent at best. While the phylogenetic distribution of SSD among sharks is superficially similar to that observed in other vertebrate clades, the relative importance of selective pressures underlying its evolution appears to differ.

Invading plants remain undetected in a lag phase while they explore suitable climates

Successful alien species may experience a period of quiescence, known as the lag phase, before becoming invasive and widespread. The existence of lags introduces severe uncertainty in risk analyses of aliens as the present state of species is a poor predictor of future distributions, invasion success and impact. Predicting a species' ability to invade and pose negative impacts requires a quantitative understanding of the commonality and magnitude of lags, environmental factors and mechanisms likely to terminate lag. Using herbarium and climate data, we analysed over 5,700 time series (species × regions) in 3,505 naturalized plant species from nine regions in temperate and tropical climates to quantify lags and test whether there have been shifts in the species' climatic space during the transition from the lag phase to the expansion phase. Lags were identified in 35% of the assessed invasion events. We detected phylogenetic signals for lag phases in temperate climate regions and that annual self-fertilizing species were less likely to experience lags. Where lags existed, they had an average length of 40 years and a maximum of 320 years. Lengthy lags (>100 years) were more likely to occur in perennial plants and less frequent in self-pollinating species. For 98% of the species with a lag phase, the climate spaces sampled during the lag period differed from those in the expansion phase based on the assessment of centroid shifts or degree of climate space overlap. Our results highlight the importance of functional traits for the onset of the expansion phase and suggest that climate discovery may play a role in terminating the lag phase. However, other possibilities, such as sampling issues and climate niche shifts, cannot be ruled out.

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.

Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

Woody species composition, diversity, and ecosystem services of yards along an urban socioeconomic gradient

Woody plants offer a wide range of valuable ecosystem services, but their distribution across socioeconomic gradients in urban landscapes remains poorly understood. Thus, we explored the effect of socioeconomic and legacy factors on plant species richness and phylogenetic diversity, and the motivations for growing and keeping certain species. We sampled a total of 300 households across a socioeconomic gradient in the city of Harare, Zimbabwe, in high-, medium- and low-density areas, representing low to high wealth strata. Trees were mostly grown for ornamental purpose in the rich (low-density) suburbs and utilitarian purposes in the poorer medium to high-density areas. However, trees were also grown with similar proportion for shade across the socioeconomic gradient. Proportion of medicinal and fruit trees increased with household density, while wind break trees were more common in low-density suburbs. Exotic species exhibited greater species richness compared with indigenous species, with both combined and separate assessments of indigenous and exotic species richness revealing a significant positive association with socioeconomic and legacy factors. The composition of species displayed considerable variation along the socioeconomic gradient. Notably, in low-density environments, exotic species maintained elevated phylogenetic diversity in comparison to indigenous species. This distinction was particularly pronounced when analysed independently, revealing a significant positive correlation between exotic species richness and both property value and education level. Our study shows that residents filter specific plant species based on their socioeconomic status and that, relative to low-income households, the rich homeowners have unintentionally incorporated enough exotic species to produce novel phylogenetic diversity of woody plants in their yards. Thus, we confirm the existence of a socioeconomic gradient in terms of species richness, composition, and phylogenetic diversity. However, the imbalance in species richness and phylogenetic diversity across the socioeconomic gradient can be reduced by increased tree planting in open areas, including along streets in medium to high-density areas to improve ecosystem services.

Different sets of traits determine transition of alien species along the invasion continuum

Invasive alien species are currently considered as one of the dominant drivers of global environmental change. Till now, the majority of studies have focused on single or a few traits of alien species that facilitate their invasion. Also inclusion of all the traits which determine the transition of aliens along the different stages of invasion continuum (casual, naturalised and invasive) has remained largely overlooked. In this study, we collected a comprehensive trait dataset on 144 alien plant species of Kashmir Himalaya - a global biodiversity hotspot region. To test which traits of alien species, individually or in combination along with anthropogenic factors, determine their transition along the invasion continuum, we employed chi-square tests, boosted regression trees and phylogenetic methods. We found the perennial life span, longer residence time, greater number of introduced regions, and better seed dispersal mechanism were critical in determining the transition from casual to naturalised. The herbaceous growth form, therophyte Raunkiaer life-form, annual life span, achene fruit, longer residence time and broader introduced range were the species' traits determining transition from naturalised to invasive. Aliens introduced as ornamentals have more propensity to become naturalised; whereas aliens introduced unintentionally show overrepresentation at the invasive stage. Phylogeny alone showed mixed results indicating both clustering and dispersion; however, in combination with other traits, it plays a significant role in determining the stage of invasion. Overall, our study disentangles the individual and interactive roles of multiple traits that determine the transition of alien species' along the invasion continuum. Further, we foresee the potential applicability of our findings in designing robust invasion risk analysis protocols and stage-specific invasion management strategies in this Himalayan region, with learnings for elsewhere in the world.

Global freshwater fish invasion linked to the presence of closely related species

In the Anthropocene, non-native freshwater fish introductions and translocations have occurred extensively worldwide. However, their global distribution patterns and the factors influencing their establishment remain poorly understood. We analyze a comprehensive database of 14953 freshwater fish species across 3119 river basins and identify global hotspots for exotic and translocated non-native fishes. We show that both types of non-native fishes are more likely to occur when closely related to native fishes. This finding is consistent across measures of phylogenetic relatedness, biogeographical realms, and highly invaded countries, even after accounting for the influence of native diversity. This contradicts Darwin's naturalization hypothesis, suggesting that the presence of close relatives more often signifies suitable habitats than intensified competition, predicting the establishment of non-native fish species. Our study provides a comprehensive assessment of global non-native freshwater fish patterns and their phylogenetic correlates, laying the groundwork for understanding and predicting future fish invasions in freshwater ecosystems.

Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River

Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.

The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus

Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues-oviduct, cloaca, and intestine-to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes.

Phylogenetic diversity drives soil multifunctionality in arid montane forest-grassland transition zone

Exploring plant diversity and ecosystem functioning in different dimensions is crucial to preserve ecological balance and advance ecosystem conservation efforts. Ecosystem transition zones serve as vital connectors linking two distinct ecosystems, yet the impact of various aspects of plant diversity (including taxonomic, functional, and phylogenetic diversity) on soil multifunctionality in these zones remains to be clarified. This study focuses on the forest-grassland transition zone in the mountains on the northern slopes of the Tianshan Mountains, and investigates vegetation and soil characteristics from forest ecosystems to grassland ecosystems to characterize plant diversity and soil functioning, as well as the driving role of plant diversity in different dimensions. In the montane forest-grassland transition zone, urease (URE) and total nitrogen (TN) play a major role in regulating plant diversity by affecting the soil nutrient cycle. Phylogenetic diversity was found to be the strongest driver of soil multifunctionality, followed by functional diversity, while taxonomic diversity was the least important driver. Diverse species were shown to play an important role in maintaining soil multifunctionality in the transition zone, especially distantly related species with high phylogeny. The study of multidimensional plant diversity and soil multifunctionality in the montane forest-grassland transition zone can help to balance the relationship between these two elements, which is crucial in areas where the ecosystem overlaps, and the application of the findings can support sustainable development in these regions.

Leaf nitrogen and phosphorus resorption efficiencies are related to drought resistance across woody species in a Chinese savanna

Leaf nutrient resorption and drought resistance are crucial for the growth and survival of plants. However, our understanding of the relationships between leaf nutrient resorption and plant drought resistance is still limited. In this study, we investigated the nitrogen and phosphorus resorption efficiencies (NRE and PRE), leaf structural traits, leaf osmotic potential at full hydration (Ψosm), xylem water potential at 50% loss of xylem-specific hydraulic conductivity (P50) and seasonal minimum water potential (Ψmin) for 18 shrub and tree species in a semiarid savanna ecosystem, in Southwest China. Our results showed that NRE and PRE exhibited trade-off against drought resistance traits (Ψosm and P50) across woody species. Moreover, this relationship was modulated by leaf structural investment. Species with low structural investment (e.g., leaf mass per area, leaf dry mass content and leaf construction cost [LCC]) tend to have high NRE and PRE, while those with high LCCs show high drought resistance, showing more negative Ψosm and P50.These results indicate that species with a lower leaf structural investment may have a greater need to recycle their nutrients, thus exhibiting higher nutrient resorption efficiencies, and vice versa. In conclusion, nutrient resorption efficiency may be a crucial adaptation strategy for coexisting plants in semiarid ecosystems, highlighting the importance of understanding the complex relationships between nutrient cycling and plant survival strategies.

Dental complexity and diet in amniotes: A meta-analysis

Tooth morphology is among the most well-studied indicators of ecology. For decades, researchers have examined the gross morphology and wear patterns of teeth as indicators of diet, and recent advances in scanning and computer analysis have allowed the development of new and more quantitative measures of tooth morphology. One of the most popular of these new methods is orientation patch count (OPC). OPC, a measure of surface complexity, was originally developed to distinguish the more complex tooth crowns of herbivores from the less complex tooth crowns of faunivores. OPC and a similar method derived from it, orientation patch count rotated (OPCR), have become commonplace in analyses of both modern and fossil amniote dietary ecology. The widespread use of these techniques makes it possible to now re-assess the utility of OPC and OPCR. Here, we undertake a comprehensive review of OPC(R) and diet and perform a meta-analysis to determine the overall difference in complexity between herbivores and faunivores. We find that the relationship between faunivore and herbivore OPC or OPCR values differs substantially across studies, and although some support the initial assessment of greater complexity in herbivores, others do not. Our meta-analysis does not support an overall pattern of greater complexity in herbivores than faunivores across terrestrial amniotes. It appears that the relationship of OPC or OPCR to diet is taxon-specific and dependent on the type of faunivory of the group in question, with insectivores often having values similar to herbivores. We suggest extreme caution in comparing OPC and OPCR values across studies and offer suggestions for how OPCR can constructively be used in future research.

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

Parental cardiorespiratory fitness influences early life energetics and metabolic health

High cardiorespiratory fitness (CRF) is associated with a reduced risk of metabolic disease and is linked to superior mitochondrial respiratory function. This study investigated how intrinsic CRF affects bioenergetics and metabolic health in adulthood and early life. Adult rats selectively bred for low and high running capacity [low capacity runners (LCR) and high capacity runners (HCR), respectively] underwent metabolic phenotyping before mating. Weanlings were evaluated at 4-6 wk of age, and whole body energetics and behavior were assessed using metabolic cages. Mitochondrial respiratory function was assessed in permeabilized tissues through high-resolution respirometry. Proteomic signatures of adult and weanling tissues were determined using mass spectrometry. The adult HCR group exhibited lower body mass, improved glucose tolerance, and greater physical activity compared with the LCR group. The adult HCR group demonstrated higher mitochondrial respiratory capacities in the soleus and heart compared with the adult LCR group, which coincided with a greater abundance of proteins involved in lipid catabolism. HCR and LCR weanlings had similar body mass, but HCR weanlings displayed reduced adiposity. In addition, HCR weanlings exhibited better glucose tolerance and higher physical activity levels than LCR weanlings. Higher respiratory capacities were observed in the soleus, heart, and liver tissues of HCR weanlings compared with LCR weanlings, which were not owed to greater mitochondrial content. Proteomic analyses indicated a greater potential for lipid oxidation in the contractile muscles of HCR weanlings. In conclusion, offspring born to parents with high CRF possess an enhanced capacity for lipid catabolism and oxidative phosphorylation, thereby influencing metabolic health. These findings highlight that intrinsic CRF shapes the bioenergetic phenotype with implications for metabolic resilience in early life.NEW & NOTEWORTHY Inherited cardiorespiratory fitness (CRF) influences early life bioenergetics and metabolic health. Higher intrinsic CRF was associated with reduced adiposity and improved glucose tolerance in early life. This metabolic phenotype was accompanied by greater mitochondrial respiratory capacity in skeletal muscle, heart, and liver tissue. Proteomic profiling of these three tissues further revealed potential mechanisms linking inherited CRF to early life metabolism.

Geographic variations in eco-evolutionary factors governing urban birds: The case of university campuses in China

Urbanization alters natural habitats, restructures biotic communities and serves as a filter for selecting species from regional species pools. However, empirical evidence of the specific traits that allow species to persist in urban areas yields mixed results. More importantly, it remains unclear which traits are widespread for species utilizing urban spaces (urban utilizers) and which are environment-dependent traits. Using 745 bird species from 287 university/institute campuses in 74 cities and their species pools across China, we tested whether species that occur in urban areas are correlated with regards to their biological (body mass, beak shape, flight capacity and clutch size), ecological (diet diversity, niche width and habitat breadth), behavioural (foraging innovation) and evolutionary (diversification rate) attributes. We used Bayesian phylogenetic generalized linear mixed models to disentangle the relative roles of these predictors further, and to determine the extent to which the effects of these predictors varied among different cities. We found that urban birds were more phylogenetically clustered than expected by chance, and were generally characterized by a larger habitat breadth, faster diversification rate, more behavioural innovation and smaller body size. Notably, the relative effects of the attributes in explaining urban bird communities varied with city temperature and elevation, indicating that the filters used to determine urban species were environment dependent. We conclude that, while urban birds are typically small-sized, generalists, innovative and rapidly diversifying, the key traits that allow them to thrive vary spatially, depending on the climatic and topographic conditions of the city. These findings emphasize the importance of studying species communities within specific cities to better understand the contextual dependencies of key traits that are filtered by urban environments.

Tasting of traditional Polish fermented cucumbers: Microbiology, morpho-textural features, and volatilome

In the present study, naturally fermented and unpasteurized cucumbers (Cucumis sativus L.) collected from 4 producers located in different regions of Poland were studied. The fermented cucumbers were characterized by significant nutritional features in terms of polyphenols content and antioxidant activity. Microbiological analyses revealed active bacterial populations of lactococci, thermophilic cocci, lactobacilli, and coagulase-negative cocci. The microbiological characterization of cucumber and brine samples through metataxonomic analysis allowed the dominant species to be detected, being Lactococcus and Streptococcus in cucumbers, and Lactiplantibacillus, Leuconostoc, Pediococcus, Secundilactobacillus, and Lentilactobacillus in brine. The isolation activity offered a clear picture of the main active lactic acid bacteria at the end of fermentation, being Pediococcus parvulus and Lactiplantibacillus plantarum group. All the studied isolates showed a good attitude in fermenting a cucumber-based broth, thus suggesting their potential application as starter or adjunct cultures for guided cucumber fermentation. Moreover, for the same isolates, strong aminopeptidase activity (due to leucine arylamidase and valine arylamidase) was observed, with potential effect on the definition of the final sensory traits of the product. Only a few isolates showed the ability to produce exopolysaccharides in synthetic medium. Of note, the presence of the hdcA gene in some Pediococcus ethanolidurans isolates also confirmed the need for a thorough characterization of starter candidates to avoid undesired adverse effects on consumer's health. No isolate showed the production of bacteriocins against Listeria innocua used as surrogate for Listeria monocytogenes. Based on the results of Headspace Solid-Phase Microextraction-Gas Chromatography/Mass Spectrometry analysis, a rich and complex volatilome, composed by more than 80 VOCs, was recognized and characterized. In more detail, the detected compounds belonged to 9 main classes, being oxygenated terpenes, alcohols, terpenes, ketones, acids, aldehydes, esters, sulfur, and sesquiterpenes.

Geography, phylogeny and host switch drive the coevolution of parasitic Gyrodactylus flatworms and their hosts

BACKGROUND

Gyrodactylus is a lineage of monogenean flatworm ectoparasites exhibiting many features that make them a suitable model to study the host-parasite coevolutionary dynamics. Previous coevolutionary studies of this lineage mainly relied on low-power datasets (a small number of samples and a single molecular marker) and (now) outdated algorithms.

METHODS

To investigate the coevolutionary relationship of gyrodactylids and their fish hosts in high resolution, we used complete mitogenomes (including two newly sequenced Gyrodactylus species), a large number of species in the single-gene dataset, and four different coevolutionary algorithms.

RESULTS

The overall coevolutionary fit between the parasites and hosts was consistently significant. Multiple indicators confirmed that gyrodactylids are generally highly host-specific parasites, but several species could parasitize either multiple (more than 5) or phylogenetically distant fish hosts. The molecular dating results indicated that gyrodactylids tend to evolve towards high host specificity. Speciation by host switch was identified as a more important speciation mode than co-speciation. Assuming that the ancestral host belonged to Cypriniformes, we inferred four major host switch events to non-Cypriniformes hosts (mostly Salmoniformes), all of which occurred deep in the evolutionary history. Despite their relative rarity, these events had strong macroevolutionary consequences for gyrodactylid diversity. For example, in our dataset, 57.28% of all studied gyrodactylids parasitized only non-Cypriniformes hosts, which implies that the evolutionary history of more than half of all included lineages could be traced back to these major host switch events. The geographical co-occurrence of fishes and gyrodactylids determined the host use by these gyrodactylids, and geography accounted for most of the phylogenetic signal in host use.

CONCLUSIONS

Our findings suggest that the coevolution of Gyrodactylus flatworms and their hosts is largely driven by geography, phylogeny, and host switches.

Global mesozooplankton communities show lower connectivity in deep oceanic layers

Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.

Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau

Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes and their responses are still unclear. In this study, we analyzed the diversity, environmental drivers, and assembly process of phytoplankton community in the central QTP lakes. The phytoplankton of these lakes can be primarily distinguished into freshwater and brackish types, with significant differences in species diversity and community dissimilarity. Both shared nearly same key environmental factors that significantly affecting phytoplankton such as EC, and brackish lakes were also positively correlative with TN. Stochastic process was predominant in phytoplankton assembly. Additionally, freshwater and brackish lakes were dominated by dispersal limitation and heterogeneous selection respectively. Alpine lakes had significant EC thresholds, and their diversity and assembly processes changed significantly around the thresholds. The present findings have important implications for understanding and predicting the response of lake phytoplankton communities to climate change and for making decisions to protect the ecological resources of alpine lakes.

Woody species with higher hydraulic efficiency or lower photosynthetic capacity discriminate more against 13C at the global scale

Leaf carbon isotope composition (δ13C) provides an integrative record on the carbon and water balance of plants over long periods. Photosynthetic ability and hydraulic traits which are highly associated with stomatal behavior could affect leaf δ13C. Association between photosynthetic ability and leaf δ13C has been examined, however, how hydraulic traits influence leaf δ13C has not been fully understood. To fill this gap, we investigated the variations in leaf δ13C among 2591 woody species (547 shrub and 2044 tree species), and analyzed the link of leaf δ13C with leaf photosynthetic and xylem hydraulic traits. Our result showed that leaf δ13C was positively correlated to leaf photosynthetic ability and capacity. For hydraulic traits, leaf δ13C was negatively related to hydraulic conductivity (Ks), xylem pressure inducing 50 % loss of hydraulic conductivity (P50) and vessel diameter (Vdia). Associations of leaf δ13C with xylem hydraulic traits indicate woody species with stronger hydraulic safety discriminated less against 13C, while woody species with higher hydraulic efficiency had more negative leaf δ13C. Shrub species, which showed a lower Vdia and P50, had a significant less negative leaf δ13C than tree species. Furthermore, woody species inhabiting in dry regions discriminated less against 13C than those growing in humid regions. Moreover, leaf δ13C displayed a low phylogenetic signal based on Blomberg's K statistic. Overall, woody species with a higher leaf photosynthetic ability or stronger hydraulic safety system discriminated less against 13C and adopt the provident water use strategy.

Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench

Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.

Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows

Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.

Phylogenetic diversity and community wide-trait means offer different insights into mechanisms regulating aboveground carbon storage

Both attributes of functional traits and phylogenetic diversity influence ecosystem functions, but which of these factors is most important is still poorly understood in natural systems. Using data from West African forests and tree savannas, we analyse how (i) phylogenetic diversity complements attributes of functional traits in explaining aboveground carbon (AGC); (ii) phylogenetic diversity relates with attributes of functional traits along gradients of phylogenetic signal; and (iii) pathways between phylogenetic diversity and attributes of functional traits relate AGC to soil and climate. Phylogenetic diversity was measured as standardised effect size of Mean Pairwise Distance (sesMPD) and Mean Nearest Taxon Distance (sesMNTD). Functional dispersion (FDis) and community weighted mean (CWM) were calculated for four traits related to leaf economics spectrum and plant life-history. Functional traits-based models explained 11 % of AGC variability. With two out of the four traits being phylogenetically conserved, incorporating phylogenetic diversity in the models increased the explained variance in AGC by 15 %. The slope of phylogenetic diversity-trait relationship was more responsive to trait conservatism for FDis than CWM. AGC was positively influenced by sesMPD and CWM of plant maximum height. In turn, CWM of plant maximum height increased with higher soil nitrogen and climate moisture, whereas sesMPD was negatively related with climate moisture. Although FDis was positively associated with sesMPD, it was not as important as sesMPD and CWM of plant maximum height in influencing and relating AGC to soil nitrogen and climate moisture. Our results suggest that phylogenetic diversity is important for AGC but does not fully reflect the functional mechanisms pertaining to community-wide trait means. The study also demonstrates the role of environment in regulating AGC, which operates through differences in community fitness driven by tall plant stature, and evolutionary processes whereby closely related species are maintained in less arid environments.

Wetland soil organic carbon balance is reversed by old carbon and iron oxide additions

Iron (Fe) oxides can stabilize organic carbon (OC) through adsorption and co-precipitation, while microbial Fe reduction can disrupt Fe-bound OC (Fe-OC) and further increase OC mineralization. The net effects of OC preservation and mineralization mediated by Fe oxides are still unclear, especially for old carbon (formed from plant litters over millions of years) and crystalline Fe oxides. Accelerating the recovery of wetland carbon sinks is critical for mitigating climate change and achieving carbon neutrality. Quantifying the net effect of Fe-mediated OC mineralization and preservation is vital for understanding the role of crystalline Fe oxides in carbon cycling and promoting the recovery of soil carbon sinks. Here, we explored the OC balances mediated by hematite (Hem) and lignite addition (Lig) to freshwater wetland (FW, rich in C and Fe) and saline-alkaline wetland (SW, poor in C and Fe) soil slurries, incubated under anaerobic conditions. Results showed that Lig caused net OC accumulation (FW: 5.9 ± 3.6 mg g-1; SW: 8.3 ± 3.2 mg g-1), while Hem caused dramatic OC loss, particularly in the FW soils. Hem inhibited microbial Fe(III) reduction by decreasing the relative abundance of Fe respiration reducers, while substantially enhancing OC mineralization through the shift in the microbial community structure of FW soils. Lig resulted in carbon emission, but its contribution to preservation by the formation of Fe-OC was far higher than that which caused OC loss. We concluded that crystalline Fe oxide addition solely favored the increase of OC mineralization by adjusting the microbial community structure, while old carbon enriched with an aromatic and alkyl promoted Fe-OC formation and further increased OC persistence. Our findings could be employed for wetland restoration, particularly for the recovery of soil carbon sinks.

Structure and assembly process of fungal communities in the Yangtze River Estuary

Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders

Phylosymbiosis is an association between host-associated microbiome composition and host phylogeny. This pattern can arise via the evolution of host traits, habitat preferences, diets, and the co-diversification of hosts and microbes. Understanding the drivers of phylosymbiosis is vital for modelling disease-microbiome interactions and manipulating microbiomes in multi-host systems. This study quantifies phylosymbiosis in Appalachian salamander skin in the context of infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd), while accounting for environmental microbiome exposure. We sampled ten salamander species representing >150M years of divergence, assessed their Bd infection status, and analysed their skin and environmental microbiomes. Our results reveal a significant signal of phylosymbiosis, whereas the local environmental pool of microbes, climate, geography, and Bd infection load had a smaller impact. Host-microbe co-speciation was not evident, indicating that the effect stems from the evolution of host traits influencing microbiome assembly. Bd infection is correlated with host phylogeny and the abundance of Bd-inhibitory bacterial strains, suggesting that the long-term evolutionary dynamics between salamander hosts and their skin microbiomes affect the present-day distribution of the pathogen, along with habitat-linked exposure risk. Five Bd-inhibitory bacterial strains showed unusual generalism: occurring in most host species and habitats. These generalist strains may enhance the likelihood of probiotic manipulations colonising and persisting on hosts. Our results underscore the substantial influence of host-microbiome eco-evolutionary dynamics on environmental health and disease outcomes.

Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat

The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.

Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion

Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.

Different Microeukaryotic Trophic Groups Show Different Latitudinal Spatial Scale Dependences in Assembly Processes across the Continental Shelves of China

The relative role of stochasticity versus determinism is critically dependent on the spatial scale over which communities are studied. However, only a few studies have attempted to reveal how spatial scales influence the balance of different assembly processes. In this study, we investigated the latitudinal spatial scale dependences in assembly processes of microeukaryotic communities in surface water and sediment along the continental shelves of China. It was hypothesized that different microeukaryotic trophic groups (i.e., autotroph, heterotroph, mixotroph, and parasite) showed different latitudinal scale dependences in their assembly processes. Our results disclosed that the relative importance of different assembly processes depended on a latitudinal space scale for planktonic microeukaryotes. In surface water, as latitudinal difference increased, the relative contributions of homogenous selection and homogenizing dispersal decreased for the entire community, while those of heterogeneous selection and drift increased. The planktonic autotrophic and heterotrophic groups shifted from stochasticity-dominated processes to heterogeneous selection as latitudinal differences surpassed thresholds of 8° and 16°, respectively. For mixotrophic and parasitic groups, however, the assembly processes were always dominated by drift across different spatial scales. The balance of different assembly processes for the autotrophic group was mainly driven by temperature, whereas that of the heterotrophic group was driven by salinity and geographical distance. In sediment, neither the entire microeukaryotic community nor the four trophic groups showed remarkable spatial scale dependences in assembly processes; they were always overwhelmingly dominated by the drift. This work provides a deeper understanding of the distribution mechanisms of microeukaryotes along the continental shelves of China from the perspective of trophic groups.

Functional host-specific adaptation of the intestinal microbiome in hominids

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

Effects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen

Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90 of these strains to inoculate tomato plants with different degrees of physical permeability to invasion (intact roots, wounded roots and xylem inoculation) and quantify the phytopathogen population dynamics during invasion. Our results reveal that the permeability of plant roots impacts the degree of population bottleneck, genetic diversity, and composition of Ralstonia populations. We also find that selection is the main driver structuring pathogen populations when barriers to infection are less permeable, i.e., intact roots, the removal of root physical and immune barriers results in the predominance of stochasticity in population assembly. Taken together, our study suggests that plant root permeability constitutes a bottleneck for phytopathogen invasion and genetic diversity.

Niche types and community assembly

Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.

Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.

Disease- and stage-specific alterations of the oral and fecal microbiota in Alzheimer's disease

Microbial communities in the intestinal tract are suggested to impact the ethiopathogenesis of Alzheimer's disease (AD). The human microbiome might modulate neuroinflammatory processes and contribute to neurodegeneration in AD. However, the microbial compositions in patients with AD at different stages of the disease are still not fully characterized. We used 16S rRNA analyses to investigate the oral and fecal microbiota in patients with AD and mild cognitive impairment (MCI; n = 84), at-risk individuals (APOE4 carriers; n = 17), and healthy controls (n = 50) and investigated the relationship of microbial communities and disease-specific markers via multivariate- and network-based approaches. We found a slightly decreased diversity in the fecal microbiota of patients with AD (average Chao1 diversity for AD = 212 [SD = 66]; for controls = 215 [SD = 55]) and identified differences in bacterial abundances including Bacteroidetes, Ruminococcus, Sutterella, and Porphyromonadaceae. The diversity in the oral microbiota was increased in patients with AD and at-risk individuals (average Chao1 diversity for AD = 174 [SD = 60], for at-risk group = 195 [SD = 49]). Gram-negative proinflammatory bacteria including Haemophilus, Neisseria, Actinobacillus, and Porphyromonas were dominant oral bacteria in patients with AD and MCI and the abundance correlated with the cerebrospinal fluid biomarker. Taken together, we observed a strong shift in the fecal and the oral communities of patients with AD already prominent in prodromal and, in case of the oral microbiota, in at-risk stages. This indicates stage-dependent alterations in oral and fecal microbiota in AD which may contribute to the pathogenesis via a facilitated intestinal and systemic inflammation leading to neuroinflammation and neurodegeneration.

Establishment of plastic-associated microbial community from superworm gut microbiome

Gut microbial communities of plastic-munching worms provide novel insights for the development of plastic-processing biotechnologies. Considering the complexity of worm maintenance and the gut microbial communities, it is challenging to apply the worms directly in plastic processing. Harnessing the power of microbial communities derived from the worm gut microbiomes in vitro may enable a promising bioprocess for plastic degradation. Here, we established stable and reproducible plastic-associated biofilm communities derived from the gut microbiome of a superworm, Zophobas atratus, through a two-stage enrichment process: feeding with plastics (HDPE, PP, and PS) and in vitro incubation of gut microbiomes obtained from the plastic-fed worms. Plastic feeding exhibited marginal influence on bacterial diversity but substantially changed the relative abundance of different bacterial groups, and intriguingly, enriched potential plastic degraders. More prominent shifts of microbial communities were observed during the in vitro incubation of the gut microbiomes. Taxa containing plastic-degrading strains were further enriched, while other taxa represented by lactic acid bacteria were depleted. Additionally, the plastic characterization confirmed the degradation of the incubated plastics by the plastic-associated microbial communities. Community functional inference for both gene abundance and community phenotype suggested that the in vitro incubation enhanced plastic-degrading potential. Deterministic ecological effects, in particular, selection processes, were identified as the main driving force of the observed community shifts. Our findings provide novel insights into plastic-munching-worm-inspired bioprocessing of plastic wastes.

Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions

Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.

Revised New World bioregions and environmental correlates for vectors of Chagas disease (Hemiptera, Triatominae)

The subfamily Triatominae includes a group of hematophagous insects, vectors of the parasite Trypanosoma cruzi, which is the etiological agent of Chagas disease, also known as American trypanosomiasis. Triatomines occur in the Old and New World and occupy diverse habitats including tropical and temperate areas. Some studies suggest the distributions of triatomines group into three or four regions. This study objectively determined bioregions focused specifically on New World Triatominae, using clustering and ordination analysis. We also identified indicator species by bioregion and investigated relationships among bioregions and environmental variables using redundancy analysis and multivariate regression trees. We delineated seven bioregions specific to Triatominae and linked each with indicator species. This result suggests more biogeographical structure exists than was revealed in earlier studies that were more general, subjective, and based on older taxonomic and distributional information. Precipitation, elevation, and vegetation were important variables in the delimitating bioregions. This implies that more detailed study of how these factors influence triatomine distributions could benefit understanding of how Chagas disease is spread.

A systematic evaluation on the relationship between hypo-osmoregulation and hyper-osmoregulation in decapods of different habitats

Decapods occupy all aquatic, and terrestrial and semi-terrestrial environments. According to their osmoregulatory capacity, they can be osmoconformers or osmoregulators (hypo or hyperegulators). The goal of this study is to gather data available in the literature for aquatic decapods and verify if the rare hyporegulatory capacity of decapods is associated with hyper-regulatory capacity. The metric used to quantify osmoregulation was the osmotic capacity (OC), the gradient between external and internal (hemolymph) osmolalities. We employ phylogenetic comparative methods using 83 species of decapods to test the correlation between hyper OC and hypo OC, beyond the ancestral state for osmolality habitat, which was used to reconstruct the colonization route. Our analysis showed a phylogenetic signal for habitat osmolality, hyper OC and hypo OC, suggesting that hyper-hyporegulators decapods occupy similar habitats and show similar hyper and hyporegulatory capacities. Our findings reveal that all hyper-hyporegulators decapods (mainly shrimps and crabs) originated in estuarine waters. Hyper OC and hypo OC are correlated in decapods, suggesting correlated evolution. The analysis showed that species which inhabit environments with intense salinity variation such as estuaries, supratidal and mangrove habitats, all undergo selective pressure to acquire efficient hyper-hyporegulatory mechanisms, aided by low permeabilities. Therefore, hyporegulation can be observed in any colonization route that passes through environments with extreme variations in salinity, such as estuaries or brackish water.

Rich diversity and active spatial-temporal dynamics of Thalassiosira species revealed by time-series metabarcoding analysis

Thalassiosira is a species-rich genus in Bacillariophyta that not only contributes positively as primary producer, but also poses negative impacts on ecosystems by causing harmful algal blooms. Although taxonomical studies have identified a large number of Thalassiosira species, however, the composition of Thalassiosira species and their geographical distribution in marine ecosystems were not well understood due primarily to the lack of resolution of morphology-based approaches used previously in ecological expeditions. In this study, we systematically analyzed the composition and spatial-temporal dynamic distributions of Thalassiosira in the model marine ecosystem Jiaozhou Bay by applying metabarcoding analysis. Through analyzing samples collected monthly from 12 sampling sites, 14 Thalassiosira species were identified, including five species that were not previously reported in Jiaozhou Bay, demonstrating the resolution and effectiveness of metabarcoding analysis in ecological research. Many Thalassiosira species showed prominent temporal preferences in Jiaozhou Bay, with some displaying spring-winter preference represented by Thalassiosira tenera, while others displaying summer-autumn preference represented by Thalassiosira lundiana and Thalassiosira minuscula, indicating that the temperature is an important driving factor in the temporal dynamics. The application of metabarcoding analysis, equipped with appropriate molecular markers with high resolution and high specificity and databases of reference molecular marker sequences for potential all Thalassiosira species, will revolutionize ecological research of Thalassiosira species in Jiaozhou Bay and other marine ecosystems.

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest

Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.

A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus

BACKGROUND

Although it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau.

RESULTS

Our results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus.

CONCLUSIONS

Our findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.

Biodiversity communication in the digital era through the Emoji tree of life

Emojis enable direct expressions of ideas and emotions in digital communication, also contributing to discussions on biodiversity conservation. Nevertheless, the ability of emojis to represent the Earth's tree of life remains unexplored. Here, we quantified the taxonomic comprehensiveness of currently available nature-related emojis and tested whether the expanding availability of emojis enables a better coverage of extant biodiversity. Currently available emojis encompass a broad range of animal species, while plants, fungi, and microorganisms are underrepresented. Within animals, vertebrates are significantly overrepresented compared to their actual richness, while arthropods are underrepresented. Notwithstanding these taxonomic disparities, animal taxa represented by emojis more than doubled from 2015 to 2022, allowing an improved representation of both taxonomic and phylogenetic diversity, driven by the recent addition of cnidarians and annelids. Creating an inclusive emoji set is essential to ensure a fair representation of biodiversity in digital communication and showcase its importance for biosphere functioning.

Forest swamp succession alters organic carbon composition and survival strategies of soil microbial communities

Forest swamp ecosystems plays crucial role in the global carbon cycle. However, the effects of forest swamp succession on soil organic matter (SOM) and microbial community structure remain unclear. To determine the drivers of SOM change and soil microbial communities in forest swamp succession, a 'space instead of time' approach was used. Soil samples from 0 to 40 cm were collected along forest swamp (early stage), dried-up forest swamp (middle stage), and forest (late stage) ecosystems. Our findings reveal that as succession progresses, the relative content of aromatics decreases and SOM undergoes a transition towards a more readily degradable form. These changes affect soil carbon sequestration and nutrient availability. Bacterial diversity was significantly influenced by succession and changes in soil depth, with fungi exhibiting higher resilience. Soil properties and environmental conditions exert influence over the structure and function of microorganisms. As succession occurred, microbial interactions shifted from cooperation to competition, with bacteria displaying a deterministic distribution pattern and fungi exhibiting a random distribution pattern. SOM quality plays a key role in shaping microbial communities and influencing their growth strategies. Microorganisms are the major drivers of soil respiration, with K-strategist dominated communities in early succession exhibiting slower degradation rates, whereas r-strategists dominated in later stages, leading to faster decomposition.

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Completing a molecular timetree of apes and monkeys

The primate infraorder Simiiformes, comprising Old and New World monkeys and apes, includes the most well-studied species on earth. Their most comprehensive molecular timetree, assembled from thousands of published studies, is found in the TimeTree database and contains 268 simiiform species. It is, however, missing 38 out of 306 named species in the NCBI taxonomy for which at least one molecular sequence exists in the NCBI GenBank. We developed a three-pronged approach to expanding the timetree of Simiiformes to contain 306 species. First, molecular divergence times were searched and found for 21 missing species in timetrees published across 15 studies. Second, untimed molecular phylogenies were searched and scaled to time using relaxed clocks to add four more species. Third, we reconstructed ten new timetrees from genetic data in GenBank, allowing us to incorporate 13 more species. Finally, we assembled the most comprehensive molecular timetree of Simiiformes containing all 306 species for which any molecular data exists. We compared the species divergence times with those previously imputed using statistical approaches in the absence of molecular data. The latter data-less imputed times were not significantly correlated with those derived from the molecular data. Also, using phylogenies containing imputed times produced different trends of evolutionary distinctiveness and speciation rates over time than those produced using the molecular timetree. These results demonstrate that more complete clade-specific timetrees can be produced by analyzing existing information, which we hope will encourage future efforts to fill in the missing taxa in the global timetree of life.

Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome

In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.

Plant Secondary Compounds Promote White Adipose Tissue Browning via Modulation of the Gut Microbiota in Small Mammals

The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.

Bee wisdom: exploring bee control strategies for food microflora by comparing the physicochemical characteristics and microbial composition of beebread

IMPORTANCE

Bees are a valuable model for investigating the relationship between environmental factors, gut microbiota, and organismal health. Beebread, produced from collected pollen, is a natural food source and a primary reservoir of gut microorganisms. Although pollen typically has diverse bacterial species, beebread has low species richness and bacterial abundance. Consequently, considerable attention has been paid to the adaptive strategies employed by honey bees to cope with the microorganisms within their food environment during co-evolution with plants. This study identified the distribution patterns of beebread's physicochemical characteristics, showing how bees use fermentation to enrich specific microbes. These findings help understand the relationship between environmental and food-associated microbes and bee intestinal microbiota. They also bridge gaps in the literature and provide a valuable reference for studying the complex interplay between these factors.

Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research

BACKGROUND

Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction.

RESULTS

Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities.

CONCLUSIONS

This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.