Quantifying the difference between phylogenetic diversity and diversity indices

Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection Y of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some specific diversity index, the phylogenetic diversity of Y is not equal to the sum of the diversity indices of the species in Y. In this paper, we investigate the extent of this difference for two commonly-used indices: Fair Proportion and Equal Splits. In particular, we determine the maximum value of this difference under various instances including when the associated rooted phylogenetic tree is allowed to vary across all rooted phylogenetic trees with the same leaf set and whose edge lengths are constrained by either their total sum or their maximum value.

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.

Eutrophication increases the similarity of cyanobacterial community features in lakes and reservoirs

Eutrophication of inland waters is a mostly anthropogenic phenomenon impacting aquatic biodiversity worldwide, and might change biotic community structure and ecosystem functions. However, little is known about the patterns of cyanobacterial community variations and changes both on alpha and beta diversity levels in response to eutrophication. Here, we investigated cyanobacterial communities sampled at 140 sites from 59 lakes and reservoirs along a strong eutrophication gradient in eastern China through using CPC-IGS and 16S rRNA gene amplicon sequencing. We found that taxonomic diversity increased, but phylogenetic diversity decreased significantly along the eutrophication gradient. Both niche width and niche overlap of cyanobacteria significantly decreased from low- to high-nutrient waterbodies. Cyanobacterial community distance-decay relationship became weaker from mesotrophic to hypereutrophic waterbodies, while ecological uniqueness (i.e., local contributions to beta diversity) tended to increase in high-nutrient waterbodies. Latitude and longitude were more important in shaping cyanobacterial community structure than other environmental variables. These findings suggest that eutrophication affects alpha and beta diversity of cyanobacterial communities, leading to increasingly similar community structures in lakes and reservoirs with a higher level of eutrophication. Our work highlights how cyanobacterial communities respond to anthropogenic eutrophication and calls for an urgent need to develop conservation and management strategies to control lake eutrophication and protect freshwater biodiversity.

Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania

Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

BACKGROUND

Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

RESULTS

In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.

CONCLUSION

REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.

Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates

Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.

Phylogenetic diversity and North Andean block conservation

Background

The Northern Andean Block (NAB) harbors high biodiversity; therefore, it is one of the most important areas in the Neotropics. Nevertheless, the settlement of several human populations has triggered the rapid transformation of ecosystems, leading to the extinction or endangerment of many species.

Methods

Because phylogenetic diversity indices quantify the historical distinctness between species, they are adequate tools for evaluating priority conservation areas. We reconstructed 93 phylogenies encompassing 1,252 species and, utilizing their occurrence data sourced from the Global Biodiversity Information Facility, computed the Average Taxonomic Distinctness Index (AvTD) for each grid cell with a spatial resolution of 0.25° within the NAB. The index values for each grid cell were categorized into quantiles, and grid cells displaying values within the upper quantile (Q5) were identified as the most significant in terms of phylogenetic diversity. We also calculated the contribution of endemic species to overall phylogenetic diversity within the NAB, specifically focusing on areas preserved within protected areas.

Results

The NAB Andean region exhibited the highest AvTD, with high AvTD values observed in the middle and southern areas of Cordilleras. Endemic species made a relatively modest contribution to the overall phylogenetic diversity of the NAB, accounting for only 1.2% of the total. Despite their relatively small geographical footprints, protected areas within the NAB have emerged as crucial repositories of biodiversity, encompassing 40% of the total phylogenetic diversity in the region.

Discussion

Although the NAB Andean region has been identified as the most crucial area in terms of AvTD, some regions in the Amazonian Piedemonte and Pacific lowlands have high AvTD levels. Interestingly, some protected areas have been found to harbor higher AvTDs than expected, given their smaller size. Although the delimitation of new PAs and species richness have been the primary factors driving the expansion of PAs, it is also essential to consider the evolutionary information of species to conserve all aspects of biodiversity, or at least cover most of them. Therefore, using phylogenetic diversity measures and the results of this study can contribute to expanding the PA network and improving the connectivity between PAs. This approach will help conserve different aspects of biodiversity and preserve evolutionary relationships between species.

Species tree analyses and speciation-based species delimitation support new species in the relict catfish family Diplomystidae and provide insights on recent glacial history in Patagonia

Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of Diplomystes as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species D. nahuelbutaensis is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: Diplomystes arratiae sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining D. nahuelbutaensis valid only for the Imperial Basin, and Diplomystes habitae sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNA-based taxonomy.

Plant biodiversity offsets negative effects of metals and metalloids soil multi-contamination on ecosystem multifunctionality

Despite increasing metals and metalloids (MM) human-driven soil contamination, how it simultaneously alters biodiversity and ecosystem functioning remains unknown. We used a wide gradient of a 170-year-old MM soil multi-contamination in Mediterranean scrublands to assess the effects of soil multi-contamination on multiple plant biodiversity facets, microbial communities and ecosystem multifunctionality (EMF). We found an overall positive effect of plant biodiversity on EMF mediated by microbial communities, and allowing offsetting the negative impacts of MM soil multi-contamination, especially on soil water holding capacity and nitrogen content. The diversity of distant plant lineages was the key facet promoting EMF by enhancing microbial communities, whereas the subordinate species richness altered EMF. By developing a holistic approach of these complex relationships between soil multi-contamination, plant biodiversity, microbial communities and ecosystem functioning, our results reveal the potential of plant biodiversity, and especially the diversity of evolutionary distant species, to offset the alteration of ecosystem functioning by MM soil multi-contamination. In this worldwide decade of ecosystems restoration, our study helps to identify relevant facets of plant biodiversity promoting contaminated ecosystem functioning, which is crucial to guide and optimize management efforts aiming to restore ecosystems and preserve human health.

External magnetic field have significant effects on diversity of magnetotactic bacteria in sediments from Yangtze River, Chagan Lake and Zhalong Wetland in China

Magnetotactic bacteria (MTB) can rapidly relocate to optimal habitats by magnetotaxis, and play an important role in iron biogeochemical cycling. This study aimed to evaluate the contribution of the external magnetostatic field to the diversity of MTB in freshwater sediments from Yangtze River (Changjiang River, CJ), Chagan Lake (CGH) and Zhalong Wetland (ZL). The magnetic field intensity was tightly associated with the community richness of MTB in CJ, whereas it was closely related to the diversity of MTB in CGH and ZL (p < 0.05), elucidating a significant variation in the community composition of MTB. Magnetic exposure time appeared more significant correlation with community richness than diversity for MTB in CJ and CGH (p < 0.05), while an opposite relationship existed in ZL (p < 0.01). Herbaspirillum (93.81-96.48 %) dominated in the sediments of these surfacewatesr regardless of waterbody types, while it shifted to Magnetospirillum in ZL under 100 Gs magnetic field. The network connectivity and stability of MTB deteriorate with the increase of magnetic field intensity. Functional analysis showed that the Two-component system and ABC transporter system of MTB obviously responded to magnetic field intensity and exposure time. Our findings will pave the way to understanding the response mechanism of MTB community in freshwater sediments to the external magnetostatic field.

Temperate forest understory vegetation shifts after 40 years of conservation

Understanding how vegetation composition and diversity respond to global changes is crucial for effective ecosystem management and conservation. This study evaluated shifts in understory vegetation after 40 years of conservation within Drawa National Park (NW Poland), to check which plant communities changed the most, and whether vegetation shifts reflect global change symptoms (climate change and pollution) or natural forest dynamics. Using ordination and generalized mixed-effects linear models, we assessed changes in alpha diversity metrics, accounting for taxonomic, functional, and phylogenetic aspects within 170 quasi-permanent plots, surveyed in 1973-85 and resurveyed in 2015-19. We found an overall homogenization of forest vegetation and specific shift patterns in certain forest associations. In coniferous and nutrient-poor broadleaved forests, the overall number of species increased due to the replacement of functionally distinct or specialized species with more ubiquitous species that could exploit increased resource availability. In riparian forests and alder carrs we found either shifts from riparian forest to alder carrs or to mesic broadleaved forests. The most stable communities were fertile broadleaved forests. Our study quantified shifts in taxonomic, functional, and phylogenetic diversity after 40 years of conservation and provides important insights into the shifts in vegetation composition in temperate forest communities. In coniferous and nutrient-poor broadleaved forests we found an increase in species richness and replacement of functionally distinct or specialized species by ubiquitous species, indicating increased resource availability. Shifts between wet broadleaved forests and transition into mesic forests suggest water limitation, which can be related to climate change. The most stable were fertile broadleaved forests fluctuating due to natural stand dynamics. The findings highlight the need for ongoing monitoring and management of ecological systems to preserve their diversity and functionality in the face of global changes.

Influence of phylogenetic diversity of plant communities on tri-trophic interactions

Phylogenetic diversity of plant communities can influence the interaction between plants, herbivores, and their natural enemies. Plant communities with phylogenetically distant species tend to present a wide variety of functional traits and ecological niches, which in turn can influence competitive interactions among plants as well as food and habitat quality for herbivores and their natural enemies. To assess some different mechanisms by which phylogenetic diversity of plant communities can influence herbivores and their natural enemies, we established 12 experimental plots of tropical trees with two treatments: high and low phylogenetic diversity. We measured plant growth and anti-herbivore defenses, herbivore foliar damage, and predator activity in seven species that were present in both treatments. We found significant differences in the expression of plant traits as a function of species identity and their life history, but also depending on the phylogenetic context in which they grew. Pioneer species had higher growth and produced more phenolics in plots with high phylogenetic diversity versus plants in plots with low phylogenetic diversity. Accordingly, herbivore damage in these species was greater in plots with low phylogenetic diversity. Finally, predator activity on caterpillar clay models placed on plants was greater within the low phylogenetic diversity treatment, but only for non-myrmecophytic species. These results suggest that plant phylogenetic diversity can influence the expression of growth and defensive traits and further modify the interaction between plants, herbivores, and their natural enemies. However, such effects depend on plant life history and the presence of mutualistic interaction with ants.

The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present

The current rapid extinction of species leads not only to their loss but also the disappearance of the unique features they harbour, which have evolved along the branches of the underlying evolutionary tree. One proxy for estimating the feature diversity (FD) of a set S of species at the tips of a tree is 'phylogenetic diversity' (PD): the sum of the branch lengths of the subtree connecting the species in S. For a phylogenetic tree that evolves under a standard birth-death process, and which is then subject to a sudden extinction event at the present (the simple 'field of bullets' model with a survival probability of s per species) the proportion of the original PD that is retained after extinction at the present is known to converge quickly to a particular concave function [Formula: see text] as t grows. To investigate how the loss of FD mirrors the loss of PD for a birth-death tree, we model FD by assuming that distinct discrete features arise randomly and independently along the branches of the tree at rate r and are lost at a constant rate [Formula: see text]. We derive an exact mathematical expression for the ratio [Formula: see text] of the two expected feature diversities (prior to and following an extinction event at the present) as t becomes large. We find that although [Formula: see text] has a similar behaviour to [Formula: see text] (and coincides with it for [Formula: see text]), when [Formula: see text], [Formula: see text] is described by a function that is different from [Formula: see text]. We also derive an exact expression for the expected number of features that are present in precisely one extant species. Our paper begins by establishing some generic properties of FD in a more general (non-phylogenetic) setting and applies this to fixed trees, before considering the setting of random (birth-death) trees.

Prevalence and genetic diversity of avian haemosporidian parasites in islands within a mega hydroelectric dam in the Brazilian Amazon

The Brazilian Amazon supports an extremely diverse avifauna and serves as the diversification center for avian malaria parasites in South America. Construction of hydroelectric dams can drive biodiversity loss by creating islands incapable of sustaining the bird communities found in intact forest sites. Besides anthropogenic actions, the presence of parasites can also influence the dynamics and structure of bird communities. Avian malaria (Plasmodium) and related haemosporidian parasites (Haemoproteus and Leucocytozoon) are a globally distributed group of protozoan parasites recovered from all major bird groups. However, no study to date has analyzed the presence of avian haemosporidian parasites in fragmented areas such as land bridge islands formed during artificial flooding following the construction of hydroelectric dams. The aim of this study is to assess the prevalence and molecular diversity of haemosporidians in bird communities inhabiting artificial islands in the area of the Balbina Hydroelectric Dam. The reservoir area covers 443,700 ha with 3546 islands on the left bank of the Uatumã River known to contain more than 400 bird species. We surveyed haemosporidian infections in blood samples collected from 445 understory birds, belonging to 53 species, 24 families, and 8 orders. Passeriformes represented 95.5% of all analyzed samples. We found a low overall Plasmodium prevalence (2.9%), with 13 positive samples (two Plasmodium elongatum and 11 Plasmodium sp.) belonging to eight lineages. Six of these lineages were previously recorded in the Amazon, whereas two of them are new. Hypocnemis cantator, the Guianan Warbling Antbird, represented 38.5% of all infected individuals, even though it represents only 5.6% of the sampled individuals. Since comparison with Plasmodium prevalence data prior to construction of Balbina is not possible, other studies in artificially flooded areas are imperative to test if anthropogenic flooding may disrupt vector-parasite relationships leading to low Plasmodium prevalence.

Beetle mania: Understanding pond aquatic beetles diversity patterns through a multiple-facet approach

Ecological studies searching for drivers of biodiversity variation have frequently focused on taxonomic richness. However, more aspects of biodiversity, namely diversity facets can be considered to properly assess biotic-environment relationships. Here, we explore the environmental factors that could control the four biodiversity facets of aquatic Coleoptera from 93 regionally sampled Patagonian ponds. We also explore which are the ponds with high diversity values of all facets to prioritize them with a high conservation value. We fitted generalized additive models (GAM) to test relationships among environment (i.e., local and climatic variables) and aquatic beetles diversity facets (i.e., richness (SD), functional diversity (FD), phylogenetic diversity (PD), and local contribution to local beta diversity (LCBD). Climatic drivers were the most important predictors of beetle diversity facets, which exhibited linear and nonlinear responses. Thus, ponds from warmer Patagonia exhibited the highest values of SD and PD, whereas LCBD also peaked on colder sites suggesting that ponds under extreme temperatures sustain unique beetle assemblages. Moreover, ponds located in areas with higher precipitation variability exhibit the highest values of LCBD (i.e., unique assemblages). This result in addition to arid conditions in Patagonia prevailing since 16 m.y.a made us think that Patagonian beetle pond-dwellers are basally adapted to aridity. We calculated an index that summarizes the four facets patterns, to assign high conservation value to those ponds with higher index values. The relative importance of each facet varies from pond to pond. Hence, this multifaceteded approach not only allows us to identify priority areas for biodiversity conservation but also focuses on the importance of including multiple facets to understand biodiversity spatial patterns.

Synthetic phylogenetically diverse communities promote denitrification and stability

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.

Spaces of Phylogenetic Diversity Indices: Combinatorial and Geometric Properties

Biodiversity is a concept most naturally quantified and measured across sets of species. However, for some applications, such as prioritising species for conservation efforts, a species-by-species approach is desirable. Phylogenetic diversity indices are functions that apportion the total biodiversity value of a set of species across its constituent members. As such, they aim to measure each species' individual contribution to, and embodiment of, the diversity present in that set. However, no clear definition exists that encompasses the diversity indices in current use. This paper presents conditions that define diversity indices arising from the phylogenetic diversity measure on rooted phylogenetic trees. In this context, the diversity index 'score' given to a species represents a measure of its unique and shared evolutionary history as displayed in the underlying phylogenetic tree. Our definition generalises the diversity index notion beyond the popular Fair Proportion and Equal-Splits indices. These particular indices may now be seen as two points in a convex space of possible diversity indices, for which the boundary conditions are determined by the underlying shape of each phylogenetic tree. We calculated the dimension of the convex space associated with each tree shape and described the extremal points.

The relative importance of abiotic and biotic environmental conditions for taxonomic, phylogenetic, and functional diversity of spiders across spatial scales

Both abiotic and biotic conditions may be important for biodiversity. However, their relative importance may vary among different diversity dimensions as well as across spatial scales. Spiders (Araneae) offer an ecologically relevant system for evaluating variation in the relative strength abiotic and biotic biodiversity regulation. We quantified the relative importance of abiotic and biotic conditions for three diversity dimensions of spider communities quantified across two spatial scales. Spiders were surveyed along elevation gradients in northern Sweden. We focused our analysis on geomorphological and climatic conditions as well as vegetation characteristics, and quantified the relative importance of these conditions for the taxonomic, phylogenetic, and functional diversity of spider communities sampled across one intermediate (500 m) and one local (25 m) scale. There were stronger relationships among diversity dimensions at the local than the intermediate scale. There were also variation in the relative influence of abiotic and biotic conditions among diversity dimensions, but this variation was not consistent across spatial scales. Across both spatial scales, vegetation was related to all diversity dimensions whereas climate was important for phylogenetic and functional diversity. Our study does not fully support stronger abiotic regulation at coarser scales, and conversely stronger abiotic regulation at more local scales. Instead, our results indicate that community assembly is shaped by interactions between abiotic constrains in species distributions and biotic conditions, and that such interactions may be both scale and context dependent.

Why phylogenetic signal of traits is important in ecosystems: uniformity of a plant trait increases soil fauna, but only in a phylogenetically uniform vegetation

Phylogenetically closely related plant species often share similar trait states (phylogenetic signal), but local assembly may favor dissimilar relatives and thereby decouple the diversity of a trait from the diversity of phylogenetic lineages. Associated fauna might either benefit from plant trait diversity, because it provides them complementary resources, or suffer from it due to dilution of preferred resources. We hence hypothesize that decoupling of trait and phylogenetic diversity weakens the relationship between the plant-trait diversity and the abundance and diversity of associated fauna. Studying permanent meadows, we tested for combined effects of plant phylogenetic diversity and diversity of two functional traits (specific leaf area, leaf dry matter content) on major groups of soil fauna (earthworms, mites, springtails, nematodes). We found that only in phylogenetically uniform plant communities, was uniformity in the functional traits associated with (i) high abundance in springtails, and (ii) high abundance of the sub-group that feeds more directly on plant material (in springtails and mites) or those that are more prone to disturbance (in nematodes), and (iii) high diversity in all three groups tested (springtails, earthworms, nematodes). Our results suggest that soil fauna profits from the resource concentration in local plant communities that are uniform in both functional traits and phylogenetic lineages. Soil fauna would hence benefit from co-occurrence of closely related plants that have conserved the same trait values, rather than of distantly related plants that have converged in traits. This might result in faster decomposition and a positive feedback between trait conservatism and ecosystem functioning.

Molecular characterization of Brazilian FeLV strains in São Luis, Maranhão Brazil

The feline leukemia virus (FeLV) belongs to the Retroviridae family and Gammaretrovirus genus, and causes a variety of neoplastic and non-neoplastic diseases in domestic cats (Felis catus), such as thymic and multicentric lymphomas, myelodysplastic syndromes, acute myeloid leukemia, aplastic anemia, and immunodeficiency. The aim of the present study was to carry out the molecular characterization of FeLV-positive samples and determine the circulating viral subtype in the city of São Luís, Maranhão, Brazil, as well as identify its phylogenetic relationship and genetic diversity. The FIV Ac/FeLV Ag Test Kit (Alere™) and the commercial immunoenzymatic assay kit (Alere™) were used to detect the positive samples, which were subsequently confirmed by ELISA (ELISA - SNAP® Combo FeLV/FIV). To confirm the presence of proviral DNA, a polymerase chain reaction (PCR) was performed to amplify the target fragments of 450, 235, and 166 bp of the FeLV gag gene. For the detection of FeLV subtypes, nested PCR was performed for FeLV-A, B, and C, with amplification of 2350-, 1072-, 866-, and 1755-bp fragments for the FeLV env gene. The results obtained by nested PCR showed that the four positive samples amplified the A and B subtypes. The C subtype was not amplified. There was an AB combination but no ABC combination. Phylogenetic analysis revealed similarities (78% bootstrap) between the subtype circulating in Brazil and FeLV-AB and with the subtypes of Eastern Asia (Japan) and Southeast Asia (Malaysia), demonstrating that this subtype possesses high genetic variability and a differentiated genotype.

Insight into phylogenomic bias of blaVIM-2 or blaNDM-1 dissemination amongst carbapenem-resistant Pseudomonas aeruginosa

OBJECTIVES

Pseudomonas aeruginosa (P. aeruginosa) are ubiquitous opportunistic pathogens that combine intrinsic and acquired multidrug resistance phenotypes. Due to different types of acquired genes, carbapenem resistance has been expanding in this species. This study hypothesised that the spread of carbapenem resistance among P. aeruginosa is influenced by phylogenomic features, being distinct for different genes.

METHODS

To test this hypothesis, the genomes of P. aeruginosa harbouring blaVIM-2 or blaNDM-1 genes were compared. The blaVIM-2 gene was selected because, although frequent, it is almost restricted to this species and blaNDM-1 gene due to its wide interspecies distribution. A group of genomes harbouring the genes blaVIM-2 (n = 116) or blaNDM-1 (n = 27), available in GenBank, was characterised based on core phylogenomic analysis, functional categories in the accessory genome and mobile genetic elements flanking the selected genes.

RESULTS

Most blaVIM-2 gene hosts belonged to multilocus sequence types (ST) ST111 (n = 32 of 116) and ST233 (n = 27 of 116) and were reported in Europe (n = 75 of 116). The blaNDM-1 gene hosts were distributed by different STs (ST38, ST773, ST235, ST357 and ST654), frequently from Asia (n = 11 of 27). Significant differences in the prevalence of functional protein/enzyme annotations per number of accessory genomes were observed between blaVIM-2+ and blaNDM-1+. The blaVIM-2 gene was frequently inserted in the Tn402-like and Tn21 transposons family and rarely in IS6100, while blaNDM-1 gene was preferentially flanked by ISAba125 and bleMBL genes or associated with IS91 insertion sequence.

CONCLUSION

The hypothesis that carbapenem resistance gene acquisition is not random among phylogenomic lineages was confirmed, suggesting the importance of phylogeny in the dissemination of antibiotic resistance genes.

Global patterns of taxonomic and phylogenetic diversity of flowering plants: Biodiversity hotspots and coldspots

Species diversity of angiosperms (flowering plants) varies greatly among regions. Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes. Here, using a comprehensive data set for regional angiosperm floras across the world, we show geographic patterns of taxonomic (species) diversity, phylogenetic diversity, phylogenetic dispersion, and phylogenetic deviation (i.e., phylogenetic diversity after accounting for taxonomic diversity) across the world. Phylogenetic diversity is strongly and positively correlated with taxonomic diversity; as a result, geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar. Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions, particularly in Eurasia and North America, and in northern Africa. Similarly, phylogenetic dispersion is, in general, higher in tropical regions and lower in temperate regions. However, the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion. As a result, hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations. Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

Plant community phylogeny responses to protections and its main drivers in boreal forests, China: General pattern and implications

Patterns of the phylogenetic structure have been broadly applied to predict community assembly processes. However, the distribution pattern of evolutionary diversity and its drivers under nature conservation are still poorly understood in boreal forests. Here, we investigated 1738 sampling plots and subplots from distinct protection intensities (PIs) zones in five representative National Nature Reserves (NNRs). Multiple comparisons, redundancy analysis, and linear mixed model were performed to identify the changes in community phylogeny across different PIs and NNRs and the drivers for these variations. Our results showed considerable plant community phylogeny variations in different NNRs. As indicated by SesMPD (standardized mean pairwise distance) and SesMNTD (standardized the mean nearest taxon distance), trees, shrubs, and herbs presented overdispersed, clustered, and random distribution patterns, respectively, in different PIs. Protection resulted in the phylogenetic structure between the nearest species of trees showing a more overdispersed pattern (p < 0.05). Protection decreased the phylogenetically clustered degree between the nearest species of shrubs (p > 0.05), while the herbs still maintained a random pattern. Community traits explained the most to phylogeny variation of different communities (24 %-71 %, p < 0.01), followed by geoclimatic factors (2 %-24 %) and conservation processes (1 %-21 %). The higher mean annual precipitation and under branch height at the lower latitude area accompanied the higher SesMPD and SesMNTD. The higher PIs attended with higher tree SesMPD, and the longer protection time resulted in higher shrub PSR (phylogenetic species richness) and PSV (phylogenetic species variability). Including the location of NNRs, community traits, and years of protection, rather than only emphasizing PI itself, could optimize community phylogenetic structure and preserve the evolutionary potential of biodiversity.

Contrasting relationships between plant-soil microbial diversity are driven by geographic and experimental precipitation changes

Soil microbe diversity plays a key role in dryland ecosystem function under global climate change, yet little is known about how plant-soil microbe relationships respond to climate change. Altered precipitation patterns strongly shape plant community composition in deserts and steppes, but little research has demonstrated whether plant biodiversity attributes mediate the response of soil microbial diversity to long- and short-term precipitation changes. Here we used a comparative study to explore how altered precipitation along the natural and experimental gradients affected associations of soil bacterial and fungal diversity with plant biodiversity attributes (species, functional and phylogenetic diversity) and soil properties in desert-shrub and steppe-grass communities. We found that along both gradients, increasing precipitation increased soil bacterial and fungal richness in the desert and soil fungal richness in the steppe. Soil bacterial richness in the steppe was also increased by increasing precipitation in the experiment but was decreased along the natural gradient. Plant biodiversity and soil properties explained the variations in soil bacterial and fungal richness from 43 % to 96 % along the natural gradient and from 19 to 46 % in the experiment. Overall, precipitation effects on soil bacterial or fungal richness were mediated by plant biodiversity attributes (species richness and plant height) or soil properties (soil water content) along the natural gradient but were mediated by plant biodiversity attributes (functional or phylogenetic diversity) in the experiment. These results suggest that different mechanisms are responsible for the responses of soil bacterial and fungal diversity to long- and short-term precipitation changes. Long- and short-term precipitation changes may modify plant biodiversity attribute effects on soil microbial diversity in deserts and steppes, highlighting the importance of precipitation changes in shaping relationships between plant and soil microbial diversity in water-limited areas.

Riparian areas as a conservation priority under climate change

Identifying climatic refugia is important for long-term conservation planning under climate change. Riparian areas have the potential to provide climatic refugia for wildlife, but literature remains limited, especially for plants. This study was conducted with the purpose of identifying climatic refugia of plant biodiversity in the portion of the Mekong River Basin located in Xishuangbanna, China. We first predicted the current and future (2050s and 2070s) potential distribution of 50 threatened woody species in Xishuangbanna by using an ensemble of small models, then stacked the predictions for individual species to derive spatial biodiversity patterns within each 10 × 10 km grid cell. We then identified the top 17 % of the areas for spatial biodiversity patterns as biodiversity hotspots, with climatic refugia defined as areas that remained as biodiversity hotspots over time. Stepwise regression and linear correlation were applied to analyze the environmental correlations with spatial biodiversity patterns and the relationships between climatic refugia and river distribution, respectively. Our results showed potential upward and northward shifts in threatened woody species, with range contractions and expansions predicted. The spatial biodiversity patterns shift from southeast to northwest, and were influenced by temperature, precipitation, and elevation heterogeneity. Climatic refugia under climate change were related closely to river distribution in Xishuangbanna, with riparian areas identified that could provide climatic refugia. These refugial zones are recommended as priority conservation areas for mitigating the impacts of climate change on biodiversity. Our study confirmed that riparian areas could act as climatic refugia for plants and emphasizes the conservation prioritization of riparian areas within river basins for protecting biodiversity under climate change.

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families

CRISPR-Cas is a widespread anti-viral adaptive immune system in the microorganisms. Viruses living in bacteria or some phages carry anti-CRISPR proteins to evade immunity by CRISPR-Cas. The anti-CRISPR proteins are prevalent in phages capable of lying dormant in a CRISPR-carrying host, while their orthologs frequently found in virulent phages. Here, we propose a probabilistic strategy of ancestral sequence reconstruction (ASR) and Hidden Markov Model (HMM) profile search to fish out sequences of anti-CRISPR proteins from environmental metagenomic, human microbiome metagenomic, human microbiome reference genome, and NCBI's non-redundant databases. Our results revealed that the metagenome database dark matter might contain anti-CRISPR encoding genes.

The relative roles of multiple drivers on benthic ciliate communities in an intertidal zone

Intertidal biodiversity is being severely disrupted as a result of increased anthropogenic activity. However, our knowledge about how natural gradients, human induced disturbance and biotic interactions affect biodiversity is limited. So, we investigated how three facets of alpha diversity and community composition of benthic ciliates responded to environmental and biological gradients in the intertidal zone of Zhejiang, China. The key determinants and their relative effects on ciliate communities were identified using structural equation modeling, distance-based redundancy analysis and variation partitioning analysis. Our results revealed that sediment grain size was the most important factor affecting alpha diversity and community composition. Human induced eutrophication had significant effects on phylogenetic alpha diversity and community composition. However, the effects of biotic interactions on ciliate communities were relatively small. Moreover, we found community composition was more sensitive to human disturbance than alpha diversity, thus, more suitable for indicating human-induced eutrophication.

Effects of multi-resource addition on grassland plant productivity and biodiversity along a resource gradient

The change of plant biodiversity caused by resource-enhancing global changes has greatly affected grassland productivity. However, it remains unclear how multi-resource enrichment induces the effects of multifaceted biodiversity on grassland productivity under different site resource constraints. We conducted a multiple resource addition (MRA) experiment of water and nutrients at three sites located along a resource gradient in northern China. This allowed us to assess the response of aboveground net primary productivity (ANPP), species (species richness and plant density), functional (functional richness and community-weighted mean of traits) and phylogenetic (phylogenetic richness) diversity to increasing number of MRA. We used structural equation model (SEM) to examine the direct and indirect effects of MRA and multifaceted biodiversity on ANPP. The combined addition of the four resources increased ANPP at all three sites. But with increasing number of MRA, biodiversity varied at the three sites. At the high resource constraint site, species richness, plant density and leaf nitrogen concentration (LNC) increased. At the medium resource constraint site, plant height and LNC increased, leaf dry matter content (LDMC) decreased. At the low resource constraint site, species, functional and phylogenetic richness decreased, and height increased. The SEM showed that MRA increased ANPP directly at all three sites, and indirectly by increasing plant density at the high constraint site and height at the medium constraint site. Independent of MRA, ANPP was affected by height at the high resource constraint site and LNC at the low resource constraint site. Our results illustrate that multi-resource addition positively affects productivity, while affects biodiversity depending on site resource constraint. The study highlights that site resource constraint conditions need to be taken into consideration to better predict grassland structure and function, particularly under the future multifaceted global change scenarios.

Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.

Effect of sampling design on estimation of phylogenetic diversity metrics of fish community

Phylogenetic diversity has been widely used to explore diversity patterns and assess processes governing the species composition in community. The estimates of many metrics depend on high-quality data collected from well-designed sampling surveys. However, knowledge of impacts of sampling design on estimation of phylogenetic diversity metrics remains unclear. This study is aim to evaluate the influence of sampling design on phylogenetic diversity metrics estimation of fish community. Simple random sampling (SRS), systematic sampling (SS) and stratified random sampling (StRS) with different sampling intensities were chosen and mean pairwise distances (MPD), mean nearest taxon distance (MNTD), phylogenetic diversity (PD), phylogenetic species variability (PSV), phylogenetic species evenness (PSE) and phylogenetic species richness (PSR) were selected. SRS and StRS showed similar impact on phylogenetic diversity indices estimation and performed relatively well for collecting data to estimate phylogenetic diversity. The accuracy and precision of the estimation increased with sampling intensity under SRS and StRS except SS. MNTD was the only metric not underestimated in four seasons. Metrics strongly influenced by species richness were underestimated when sampling intensity was insufficient. MPD, PSV and PSE showed an obvious seasonal change, which was due to the seasonal differences in fish species composition. In cases where under-sampling is suspected or logistically unavoidable, phylogenetic diversity metrics that are relatively insensitive to sampling design (e.g., MPD and PSV) should be prioritized, especially for exploring the temporal variation in fish community. This study reveals it is indispensable to evaluate sampling design when estimating phylogenetic diversity metrics, especially those indices susceptible to species richness.

Vertical characterisation of phylogenetic divergence of microbial community structures, interaction, and sustainability in estuary and marine ecosystems

The changes in the aquatic environmental conditions often influence the microbial community assemblages and genome repertoire. Studies investigating the aquatic diversity and ecosystem services were primarily conducted in horizontal environments while neglecting the microbial phylogenetic divergences, biotrophic interactions, and eco-sustainability at water vertical layers. We investigated the mechanisms of microbial transitions, and the ecological significance of water depth layers in the estuary and marine ecosystems. The results demonstrated that the salinity and turbidity increased with increasing water depth (0-50 m), while temperature and pH decreased significantly. The bacterial and eukaryotic diversity and composition significantly increased with an elevating water depth. Bacterial phyla such as Desulfobacterota, Acidobacteriota, Myxococcota, Gemmatimonadota, Campilobacterota, and Latescibacterota were increased significantly. However, niche preference occurred, and some microbes showed differential nestedness at water vertical layers. In the eukaryotic community, Eustigmatales group were the only clades predominantly phylogenetically nested at the surface water depth. c_Conoidasida, o_Gregarinasina, f_Eugregarinorida, and g_Lankesteria were the most predominant at the middle depth. While Mediophyceae clades, p_SAR, and the Animalia clades were the most predominant groups nested at the bottom depths. The microbial interaction, structure, and stability were increased with increasing depth. The vertical phylogenetic turnover of the microbial community was related to the feeding mechanisms. Phototrophic organisms were particularly adapted at the surface, and middle depth by parasitic and pathogenic organisms, while the bottom was inhabited by diatoms, decomposers, and detritus protists. This study demonstrated that the bottom depth was the most ecologically stable area with more profound ecosystem services.

Effects of discordance between species and gene trees on phylogenetic diversity conservation

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying phylogenetic tree. Traditionally, phylogenetic trees were inferred from single genes and the resulting gene trees were assumed to be a valid estimate for the species tree, i.e., the "true" evolutionary history of the species under consideration. However, nowadays it is common to sequence whole genomes of hundreds or thousands of genes, and it is often the case that conflicting genealogical histories exist in different genes throughout the genome, resulting in discordance between individual gene trees and the species tree. Here, we analyze the effects of gene and species tree discordance on prioritization decisions based on the FP index. In particular, we consider the ranking order of taxa induced by (i) The FP index on a species tree, and (ii) The expected FP index across all gene tree histories associated with the species tree. On the one hand, we show that for particular tree shapes, the two rankings always coincide. On the other hand, we show that for all leaf numbers greater than or equal to five, there exist species trees for which the two rankings differ. Finally, we illustrate the variability in the rankings obtained from the FP index across different gene tree and species tree estimates for an empirical multilocus mammal data set.

A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements

Background

Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids.

Methods

To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters.

Results

A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters.

Conclusions

We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.

Dominant species control effects of nitrogen addition on ecosystem stability

Increased nitrogen (N) deposition is known to reduce the ecosystem stability, while the underlying mechanisms are still controversial. We conducted an 8-year multi-level N addition experiment in a temperate semi-arid grassland to identify the mechanisms (biodiversity, species asynchrony, population stability and dominant species stability) driving the N-induced loss of temporal stability of aboveground net primary productivity (ANPP). We found that N addition decreased ecosystem, population, and dominant species stability; decreased species richness and phylogenetic diversity; increased species dominance; but had nonsignificant effects on community-wide species asynchrony. Structural equation model revealed that N-induced loss of ecosystem stability was mainly driven by the loss of dominant species stability and the reduction in population stability. Moreover, species relative instability was negatively related with species relative production and the slopes increase with N addition, indicating that N addition weakened the stabilizing effect of dominant species on ecosystem function. Overall, our results highlight that the dominant species control the temporal stability of ANPP in grassland ecosystem under N addition, and support 'dominance management' as an effective strategy for conserving ecosystem functioning in grassland under N deposition.

Early impacts of the largest Amazonian hydropower project on fish communities

Hydropower is a threat to freshwater fishes. Despite a recent boom in dam construction, few studies have assessed their impact on mega-diverse tropical rivers. Using a before-after study design, we investigated the early impacts of the Belo Monte hydroelectric complex, the third-largest hydropower project in the world, on fishes of the Xingu River, a major clear-water tributary of the lower Amazon. We explored impacts across different river sectors (upstream, reservoir, reduced flow sector, and downstream) and spatial scales (individual sectors vs. all sectors combined) using joint species distribution models and different facets of diversity (taxonomic, functional, and phylogenetic). After 5 years of the Belo Monte operation, species richness declined ~12% in lentic and ~16% in lotic environments. Changes in abundance were of less magnitude (<4%). Effects were particularly negative for species of the families Serrasalmidae (mainly pacus), Anostomidae (headstanders), Auchenipteridae, and Pimelodidae (catfishes), whereas no taxonomic group consistently increased in richness or abundance. The reservoir and downstream sectors were the most impacted, with declines of ~24-29% in fish species richness, overall reductions in fish body size and trophic level, and a change in average body shape. Richness and abundance also declined in the reduced river flow, and changes in size, shape, and position of fins were observed. Relatively minor changes were found in the upstream sector. Variation in functional and phylogenetic diversity following river impoundment was subtle; however, across sectors, we found a reduction in functional divergence, indicating a decline in the abundance of species located near the extremities of community functional space. This may be the first sign of an environmental filtering process reducing functional diversity in the region. Greater changes in flow and habitats are expected as hydropower operations ramp up, and continued monitoring is warranted to understand the full scope and magnitude of ecological impacts.

Phylogenetic, functional and taxonomic responses of wild bee communities along urbanisation gradients

Increasing urbanisation is one of the primary drivers of land-use change that threaten biodiversity. Wild bee communities have been reported with contrasting responses to urbanisation, with varying effects on abundance and taxonomical diversity. The suite of functional traits exhibited by wild bee species might determine their persistence in urban areas. Urbanisation thus can impose an environmental filter with potential consequences on the functional and phylogenetical diversity of wild bee communities. Here, we sampled 2944 wild bee specimens from 156 species in 29 sites located along an urbanisation gradient using a replicated design in three mid-sized cities in the Loire valley (France). We show that urban landscape cover has a negative effect on overall species richness and taxonomical diversity indices, while total abundance remains constant. Species loss was taxon dependent, mainly driven by Andrenidae and Halictidae. Only a few species, especially of the genus Lasioglossum, were positively affected by the urban landscape cover. Urban and peri-urban areas differed in their composition of bee assemblages. Species turnover was the main component of beta diversity, driving community dissimilarities through the urban gradient. Urbanisation favours bees with small body sizes, social structure and extended flight periods but did not affect the phylogenetic or the functional diversity of communities. Our findings have implications for understanding the factors involved in the environmental filter exerted through the urban gradient on bee communities helping to implement conservation measures and managing urban spaces for bees.

Counting and optimising maximum phylogenetic diversity sets

In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary ‘Tree of Life’. This approach recognises that extinction not only removes species but also the branches of the tree on which unique features shared by the extinct species arose. In this paper, we investigate three questions that are relevant to PD. The first asks how many sets of species of given size k preserve the maximum possible amount of PD in a given tree. The number of such maximum PD sets can be very large, even for moderate-sized phylogenies. We provide a combinatorial characterisation of maximum PD sets, focusing on the setting where the branch lengths are ultrametric (e.g. proportional to time). This leads to a polynomial-time algorithm for calculating the number of maximum PD sets of size k by applying a generating function; we also investigate the types of tree shapes that harbour the most (or fewest) maximum PD sets of size k. Our second question concerns optimising a linear function on the species (regarded as leaves of the phylogenetic tree) across all the maximum PD sets of a given size. Using the characterisation result from the first question, we show how this optimisation problem can be solved in polynomial time, even though the number of maximum PD sets can grow exponentially. Our third question considers a dual problem: If k species were to become extinct, then what is the largest possible loss of PD in the resulting tree? For this question, we describe a polynomial-time solution based on dynamical programming.

A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest

Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.

Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith's Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function

Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.

Diversity patterns of cushion plants on the Qinghai-Tibet Plateau: A basic study for future conservation efforts on alpine ecosystems

The Qinghai-Tibet Plateau (QTP) is an important cushion plant hotspot. However, the distribution of cushion plants on the QTP is unknown, as are the factors that drive cushion plant distribution, limiting our understanding of the evolution of cushion species in the region. In this study, we assessed spatial patterns of total cushion plant diversity (including taxonomic and phylogenetic) over the entire QTP and compared patterns of diversity of cushion plants with different typologies (i.e., compact vs. loose). We also examined how these patterns were related to climatic features. Our results indicate that the southern QTP hosts the highest total cushion plant richness, especially in the south-central Hengduan Mountains subregion. The total number of cushion species declines from south to north and from southeast to northwest. Compact cushion plants exhibit similar patterns as the total cushion plant richness, whereas loose cushion plants show random distribution. Cushion plant phylogenetic diversity showed a similar pattern as that of the total cushion plant richness. In addition, cushion plant phylogenetic community structure was clustered in the eastern and southwestern QTP, whereas random or overdispersed in other areas. Climatic features represented by annual energy and water trends, seasonality and extreme environmental factors, had significant effects on cushion plant diversity patterns but limited effects on the phylogenetic community structure, suggesting that climatic features indeed promote the formation of cushion plants. Because cushion plants play vital roles in alpine ecosystems, our findings not only promote our understanding of the evolution and formation of alpine cushion plant diversity but also provide an indispensable foundation for future studies on cushion plant functions and thus alpine ecosystem sustainability in the entire QTP region.

Biochar reduced extractable dieldrin concentrations and promoted oligotrophic growth including microbial degraders of chlorinated pollutants

The role of organic amendments for natural degradation of aged persistent organic pollutants (POPs) in agricultural soils remains controversial. We hypothesised that organic amendments enhance bacterial activity and function at the community level, facilitating the degradation of aged POPs. An incubation study was conducted in a closed chamber over 12 months to assess the effects of selected organic amendments on extractable residues of aged dieldrin. The role of bacterial diversity and changes in community function was explored through sequenced marker genes. Linear mixed effect models indicated that, independent of amendment type, cumulative CO₂ release was negatively associated with decreases in dieldrin concentration, by up to 7% per µmol CO₂-C respired by microorganisms. The addition of poultry litter led to the highest daily carbon mineralisation, which was associated with low dieldrin dissipation after 9 months. In comparison, biochar resulted in significant decreases in extractable dieldrin residues over time, which coincided with shifts towards aerobic, oligotrophic, gram-negative bacteria, some with dehalogenation metabolism, and with increased potentials for biosynthesis of membrane components such as fatty acids and high redox quinones. The results supported an alternative theory that labile carbon promoted blooms of copiotrophic growth, which suppressed the required community-level traits and oligotrophic diversity to degrade chlorinated pollutants.

Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt

Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data's functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.

COVID-index: A texture-based approach to classifying lung lesions based on CT images

COVID-19 is an infectious disease caused by a newly discovered type of coronavirus called SARS-CoV-2. Since the discovery of this disease in late 2019, COVID-19 has become a worldwide concern, mainly due to its high degree of contagion. As of April 2021, the number of confirmed cases of COVID-19 reported to the World Health Organization has already exceeded 135 million worldwide, while the number of deaths exceeds 2.9 million. Due to the impacts of the disease, efforts in the literature have intensified in terms of studying approaches aiming to detect COVID-19, with a focus on supporting and facilitating the process of disease diagnosis. This work proposes the application of texture descriptors based on phylogenetic relationships between species to characterize segmented CT volumes, and the subsequent classification of regions into COVID-19, solid lesion or healthy tissue. To evaluate our method, we use images from three different datasets. The results are promising, with an accuracy of 99.93%, a recall of 99.93%, a precision of 99.93%, an F1-score of 99.93%, and an AUC of 0.997. We present a robust, simple, and efficient method that can be easily applied to 2D and/or 3D images without limitations on their dimensionality.

Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

BACKGROUND

Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled.

RESULTS

Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans.

CONCLUSIONS

Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.

Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China

Fe(III) reducing bacteria (FeRB) play a vital role in the biogeochemical cycle of Fe, C and N in nature. The volcanic lake can be considered as an ideal habitat for FeRB. Here, we investigated the diversity and spatial distribution of FeRB in sediments of Wenbo lake in Wudalianchi volcano based on culture-dependent and independent methods. A total of 28 isolates affiliated with the genera of Enterobacter, Bacillus, Pseudomonas and Clostridium were obtained from 18 sediment samples. We detected 783 operational taxonomic units (OTUs) belonged to FeRB using high high-throughput sequencing, and the dominant phyla were Proteobacteria (3.65%), Acidobacteria (0.29%), Firmicutes (10.78%). The representative FeRB genera such as Geobacter, Pseudomonas, Thiobacillus and Acinetobacter distributed widely in Wenbo lake. Results showed that the diversity and abundance of FeRB declined along the water-flow direction from Libo to Jingbo. In contrast, the FeRB diversity decreased and the FeRB abundance increased along with depth transect of sediments. It was found that the dominant phylum changed from Firmicutes to Proteobacteria along the water-flow direction, while changed from Proteobacteria to Firmicutes along with the depth of sediments. RDA indicated that the FeRB distribution were driven by soluble total iron, total organic carbon, Fe(II) and Fe(III). These will provide information for understanding the role of FeRB in the elements geochemical cycles in the volcanic environment.

Soil abiotic properties and plant functional diversity co-regulate the impacts of nitrogen addition on ecosystem multifunctionality in an alpine meadow

Soil abiotic properties and plant diversity have been shown to affect ecosystem functions in alpine meadow ecosystems. However, we know little about the relative importance of these factors in driving the responses of multiple ecosystem functions simultaneously (multifunctionality) to nitrogen (N) enrichment. Here, we measured soil abiotic properties (soil pH; available nitrogen, AN; available phosphorous, AP; and dissolved organic carbon, DOC) and multiple plant diversity metrics (species diversity, SD; functional diversity, FD; and phylogenetic diversity, PD) after a 5-year N fertilization experiment (0, 5, 10, and 15 g N m^-2 yr^-1) to evaluate their roles in mediating the impacts of N addition on aboveground plant functions (APF), soil microbial functions (SMF), and ecosystem multifunctionality (EMF) in a N-limited Tibetan alpine meadow. We found that N addition decreased APF but increased SMF and EMF. Structural equation models (SEMs) showed that APF was co-driven by soil DOC and the community weighted mean for plant traits (CWMs), and SMF was driven by soil DOC, soil AN, CWMs and functional dispersion (FD_is). The effects of N addition on EMF were driven by soil AN and FD_is. Our results suggest that the effects of N enrichment on APF, SMF, and EMF are driven by differential mechanisms. Furthermore, the findings suggest that FD is superior to SD and PD in mediating the responses of ecosystem functions to N enrichment.

Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads

Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages?

Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages. Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants, researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera. However, whether the result of a study using species-level phylogenies generated in these ways is robust, compared to that based on phylogenies fully resolved at the species level, has not been assessed. Here, we use 1093 angiosperm tree assemblages (each in a 110 × 110 km quadrat) in North America as a model system to address this question, by examining six commonly used metrics of phylogenetic structure (phylogenetic diversity and phylogenetic relatedness) and six climate variables commonly used in ecology. Our results showed that (1) the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level (the mean of correlation coefficients is 0.973), and (2) the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny. Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.

Novel Paju Apodemus paramyxovirus 1 and 2, harbored by Apodemus agrarius in the Republic of Korea

Paramyxoviruses harbored by multiple natural reservoirs pose a potential threat to public health. Jeilongvirus has been proposed as a novel paramyxovirus genus found in rodents, bats, and cats. Paramyxovirus RNA was detected in 108/824 (13.1%) Apodemus agrarius captured at 14 trapping sites in the Republic of Korea. We first present two genetically distinct novel paramyxoviruses, Paju Apodemus paramyxovirus 1 (PAPV-1) and 2 (PAPV-2). The disparity between PAPV-1 (19,716 nucleotides) and -2 (17,475 nucleotides) revealed the presence of the SH gene and length of the G gene in the genome organization. The phylogeny of PAPV-1 and -2 belonged to distinct genetic lineages of Jeilongvirus, respectively, even though these viruses were originated from A. agrarius. PAPV-1 infected human epithelial and endothelial cells, facilitating the induction of type I/III interferons, interferon-stimulated genes, and pro-inflammatory cytokines. Therefore, this study provides insights into the molecular epidemiology, genetic diversity, and virus-host interactions of novel rodent-borne paramyxoviruses.