High Phylogenetic Diversity Research Articles

Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers

Many multi-regional studies investigating how available habitat area, energy availability, and historical refugia drive freshwater fish diversity have emphasized Northern Hemisphere and tropical areas. Furthermore, while many such studies have examined diversity drivers on basin-scale species richness (i.e., gamma diversity), they typically have not evaluated beta diversity or phylogenetic diversity nor included representative numbers of Southern Hemisphere basins unassociated with tropical rainforests. Here, we examine 784 basins and present the first comprehensive evaluation of the driving effects of gamma diversity and the patterns of beta and phylogenetic diversity across extra-tropical Southern Hemisphere (ETSH) freshwater fish communities. We find that ETSH gamma diversity does not show a strong historical legacy associated with glaciations, and is influenced more by factors related with habitat area and available energy. Additionally, ETSH regions show high beta and phylogenetic diversity and low levels of diadromy, except New Zealand, which shows narrow species diversity and cosmopolitan species dominance. Finally, phylogenetic diversity indicates how the endemism of the three ETSH Mediterranean-climate regions is characteristic of long-term isolation and persistence. These results demonstrate ETSH freshwater fish diversity to be distinct from both the tropics and their Northern Hemisphere latitudinal counterparts.

Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline.

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.

Phylogenetic diversity patterns in forests of a putative refugial area in Greece: A community level analysis

Patterns of phylogenetic diversity and structure of flora in refugial areas may be very complex due to habitat heterogeneity and legacies of various historical processes. Revealing these patterns can help understand the nature of the refugia. Here we study phylogenetic patterns of the flora in one of the main putative Pleistocene refugia of temperate forest biota in Europe through a community-level analysis for the main types of forests. For this purpose, a database of vegetation plots from deciduous and mountain coniferous forests of northern and central Greece was created. The plots were classified into floristically and ecologically interpretable community types. Faith’s phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance, as well as their standardized equivalents, were used to characterize the mean phylogenetic diversity and structure of each community type. All analyses were applied both for all the vascular plant taxa and for angiosperm taxa only. We related the measures of phylogenetic diversity and structure to ecological factors and compared them among community types. The 25 identified community types differed in their phylogenetic diversity and structure. The observed patterns were significantly different when old evolutionary lineages, such as gymnosperms and ferns, were taken into account. A random or overdispersed phylogenetic structure was observed for most of the community types, while only two oak-dominated community types were clustered. The highest phylogenetic diversity and a notably high proportion of plots with an overdispersed phylogenetic structure were observed in two mesic ravine forest community types (one of these transitional to beech forests). Phylogenetic metrics correlated with ecological conditions, in particular, overdispersion was more common in shaded, cool and moist forests. The high phylogenetic diversity and overdispersed structure of the two ravine community types can be related to the putative refugial role of these forest habitats.

Catechol Oxidase versus Tyrosinase Classification Revisited by Site‐Directed Mutagenesis Studies

AbstractCatechol oxidases (COs) and tyrosinases (TYRs) are both polyphenol oxidases (PPOs) that catalyze the oxidation of ortho‐diphenols to the corresponding quinones. By the official classification, only TYRs can also catalyze the hydroxylation of monophenols to ortho‐diphenols. Researchers have been trying to find the molecular reason for the mono‐/diphenolase specificity for decades. However, the hypotheses for the lack of monophenolase activity of plant COs are only based on crystal structures so far. To test these hypotheses, we performed site‐directed mutagenesis studies and phylogenetic analyses with dandelion PPOs offering high phylogenetic diversity, the results of which refute the structure‐based hypotheses. While plant PPOs of phylogenetic group 2 solely exhibit diphenolase activity, plant PPOs of phylogenetic group 1 unexpectedly also show monophenolase activity. This finding sheds new light upon the molecular basis for mono‐/diphenol substrate specificity and challenges the current practice of generally naming plant PPOs as COs.

Catechol Oxidase versus Tyrosinase Classification Revisited by Site-Directed Mutagenesis Studies.

Catechol oxidases (COs) and tyrosinases (TYRs) are both polyphenol oxidases (PPOs) that catalyze the oxidation of ortho-diphenols to the corresponding quinones. By the official classification, only TYRs can also catalyze the hydroxylation of monophenols to ortho-diphenols. Researchers have been trying to find the molecular reason for the mono-/diphenolase specificity for decades. However, the hypotheses for the lack of monophenolase activity of plant COs are only based on crystal structures so far. To test these hypotheses, we performed site-directed mutagenesis studies and phylogenetic analyses with dandelion PPOs offering high phylogenetic diversity, the results of which refute the structure-based hypotheses. While plant PPOs of phylogenetic group 2 solely exhibit diphenolase activity, plant PPOs of phylogenetic group 1 unexpectedly also show monophenolase activity. This finding sheds new light upon the molecular basis for mono-/diphenol substrate specificity and challenges the current practice of generally naming plant PPOs as COs.

Contrasting latitudinal patterns in phylogenetic diversity between woody and herbaceous communities

Although many studies have shown that species richness decreases from low to high latitudes (the Latitudinal Diversity Gradient), little is known about the relationship between latitude and phylogenetic diversity. Here we examine global latitudinal patterns of phylogenetic diversity using a dataset of 459 woody and 589 herbaceous plant communities. We analysed the relationships between community phylogenetic diversity, latitude, biogeographic realm and vegetation type. Using the most recent global megaphylogeny for seed plants and the standardised effect sizes of the phylogenetic diversity metrics ‘mean pairwise distance’ (SESmpd) and ‘mean nearest taxon distance’ (SESmntd), we found that species were more closely-related at low latitudes in woody communities. In herbaceous communities, species were more closely-related at high latitudes than at intermediate latitudes, and the strength of this effect depended on biogeographic realm and vegetation type. Possible causes of this difference are contrasting patterns of speciation and dispersal. Most woody lineages evolved in the tropics, with many gymnosperms but few angiosperms adapting to high latitudes. In contrast, the recent evolution of herbaceous lineages such as grasses in young habitat types may drive coexistence of closely-related species at high latitudes. Our results show that high species richness commonly observed at low latitudes is not associated with high phylogenetic diversity.

Clonally Diverse Methicillin and Multidrug Resistant Coagulase Negative Staphylococci Are Ubiquitous and Pose Transfer Ability Between Pets and Their Owners.

Sixty-eight owners and 66 pets, from 43 unrelated pet-owning households were screened for methicillin-resistant coagulase negative staphylococci (MRCoNS), potential cases of MRCoNS interspecies transmission (IT), and persistence. MRCoNS isolates were identified by microbiological and molecular tests. MLST-based phylogenetic analysis was performed in Staphylococcus epidermidis isolates. Antimicrobial susceptibility was evaluated using phenotypic and molecular methods. SCCmec type and the presence of biofilm-related ica locus was PCR-tested. Isolates suspected for MRCoNS IT cases were subjected to SmaI-PFGE analysis and individuals from positive households were followed-up for 1 year for carriage dynamics (every 3 months, T0–T4). Nineteen MRCoNS isolates from owners (27.9%) and 12 from pets (16.7%) were detected, coming from 20 households (46.5%). S. epidermidis was predominant (90 and 67% of human and animal strains, respectively), showing high phylogenetic diversity (16 STs among 24 strains). Methicillin-resistant S. epidermidis (MRSE) strains belonged to CC5 (75%), CC11 (12.5%), singleton S556 (8.3%), and S560 (4.17%). Significant host-associated differences were observed for resistance to aminoglycosides, co-trimoxazole, chloramphenicol (higher in animal isolates) and tetracycline (higher among human strains). Multidrug resistance (MDR) was common (68.4%) and associated with human strains. Great diversity of ccr and mec complexes were detected, most strains being non-typeable, followed by SCCmecIV and V. Over one third of isolates (most from owners), carried the ica locus, all MRSE CC5. Two sporadic IT cases (T0) were identified in owners and dogs from two households (4.7%), with diverse interspecies-exchanged clones detected along the sampling year, especially in dogs. A comparative analysis of all MRCoNS, with all nasal coagulase positive staphylococci (CoPS) recovered from the same individuals at T0, revealed that CoPS alone was predominant in owners and pets, followed by co-carriage of CoPS and MRCoNS in owners but single MRCoNS in pets. Statistical analyses revealed that owners are more prone to co-carriage and that co-existence of IT cases and co-carriage are positively interrelated. MRCoNS from healthy owners and their pets are genetically heterogeneous MDR strains that are spread in the community. Therefore, pets also contribute to the dissemination of successful human clones. Owner-pet inhabitancy increases the risk for staphylococcal temporal concomitance with its subsequent risk for bacterial infection and genetic exchange.

Zoogeographical regions and geospatial patterns of phylogenetic diversity and endemism of New World bats

The analysis of regional scale patterns of diversity allows insights into the processes that have shaped modern biodiversity at the macro‐scale. Previous analyses studying biogeographic regionalisation across different high‐level taxa have shown similar trends at a global scale. However, incorporating phylogenetic methods when comparing biogeographic regionalisation between subgroups facilitates identification of mechanisms leading to the biogeographic distribution of specific taxa. We analysed the spatial trends of phylogenetic diversity and phylogenetic endemism of 325 species of New World bats, using updated range maps of the modern distributions. These analyses showed phylogeographic signals that reflect the different evolutionary histories of these families. Zoogeographical zones were detected based on range‐weighted phylogenetic turnover. Values of high phylogenetic diversity and endemism were distributed differently across families, suggesting niche conservatism, but a general latitudinal trend of diversity was evident across taxa. Overall, two main bioregions were shared across New World bat taxa (Nearctic and Neotropical), with two additional subregions (Andean and La Platan). We found strong support for an additional transitional zone in the Pacific coast of South America for Emballonuridae and Molossidae. Differences in regionalisation across families indicate that niche conservatism, in situ diversification and dispersal ability are major drivers for the regionalisation of New World bats, within a dual‐centre of diversification scenario. We also found strong inter‐familial support for an independent Caribbean biogeographic region.

Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp

BackgroundDiseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe lack of genomic information of these pathogens. The high phylogenetic diversity observed within strains causing disease on Prunus spp. in nature, raised the question whether other strains or species within the P. syringae species complex were potentially pathogenic on Prunus spp.ResultsTo gain insight into the genomic potential of adaptation and virulence in Prunus spp., a total of twelve de novo whole genome sequences of P. syringae pathovars and species found in association with diseases on cherry (sweet, sour and ornamental-cherry) and peach were sequenced. Strains sequenced in this study covered three phylogroups and four clades. These strains were screened in vitro for pathogenicity on Prunus spp. together with additional genome sequenced strains thus covering nine out of thirteen of the currently defined P. syringae phylogroups. Pathogenicity tests revealed that most of the strains caused symptoms in vitro and no obvious link was found between presence of known virulence factors and the observed pathogenicity pattern based on comparative genomics. Non-pathogenic strains were displaying a two to three times higher generation time when grown in rich medium.ConclusionIn this study, the first set of complete genomes of cherry associated P. syringae strains as well as the draft genome of the quarantine peach pathogen P. syringae pv. persicae were generated. The obtained genomic data were matched with phenotypic data in order to determine factors related to pathogenicity to Prunus spp. Results of this study suggest that the inability to cause disease on Prunus spp. in vitro is not the result of host specialization but rather linked to metabolic impairments of individual strains.

Phylogenetic diversity in freshwater-dwelling Isochrysidales haptophytes with implications for alkenone production.

Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long‐chain ketones that are commonly used for paleotemperature reconstructions. Alkenone‐producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, Group II commonly occurs in brackish and coastal marine environments, and Group III consists of open ocean species. Each group has distinct alkenone distributions; however, only Groups II and III Isochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri‐unsaturated alkenone isomers (C37:3b Me, C38:3b Et, C38:3b Me, C39:3b Et) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small‐subunit (SSU) ribosomal RNA (rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV” clade from the “Greenland” clade. We infer the first partial large‐subunit (LSU) rRNA gene Group I sequence phylogeny, which uncovered additional well‐supported clades embedded within Group I. Relative to Group II, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with Group III. In Group I, the presence of the tri‐unsaturated alkenone isomers appears to be conserved, which is not the case for Group II. This suggests differing environmental influences on Group I and II and perhaps uncovers evolutionary constraints on alkenone biosynthesis.

Testing multiple hypotheses for the high endemic plant diversity of the Tibetan Plateau

AbstractAimThe Tibetan Plateau harbours the highest alpine and endemic plant diversity in the world, attributed to rapid diversification during the plateau uplift and Quaternary climate fluctuations. However, there is little understanding of which hypotheses associated with these geological and climatic processes garner strong support as explanations for the observed diversity patterns. Here, we test support for hypotheses related to uplift and climate changes that could account for the high endemicity and phylogenetic diversity of the world’s highest plateau.LocationTibetan Plateau (TP).Time periodNeogene, Quaternary and current period.Major taxa studiedTibetan endemic seed plants.MethodsWe collated data on endemic seed‐plant distribution based on county‐level mapping from published monographs and online databases. We calculated species richness (SR) and phylogenetic diversity for endemic herbs, shrubs, trees, and all plants for 0.5‐degree × 0.5‐degree grid cells covering the TP. We derived environmental and evolutionary predictors to evaluate eight biogeographical hypotheses associated with plateau uplift and climate fluctuations, and used partial regression analysis and mixed conditional autoregressive (CAR) models to assess the relative contribution of each predictor to the extant diversity of the TP.ResultsWe found plateau uplift independently explained more variance in diversity than climate fluctuations, but there were also strong interaction effects. The full CAR models including all predictors explained 37%–75% of the total variation across diversity measures and life forms. The predictor representing the montane museum hypothesis explained the most variation (c. 25%), but each predictor explained at least 6%.Main conclusionsThese results demonstrate that both the plateau uplift and Quaternary climate fluctuations had large impacts on current patterns of species diversity, but the influence of plateau uplift was more pronounced than that of climate changes. Our study suggests that plateau uplift and climate changes are the original drivers of complex biogeographical processes accounting for the biodiversity of the TP.

High specialization and limited structural change in plant‐herbivore networks along a successional chronosequence in tropical montane forest

Secondary succession is well‐understood, to the point of being predictable for plant communities, but the successional changes in plant‐herbivore interactions remains poorly explored. This is particularly true for tropical forests despite the increasing importance of early successional stages in tropical landscapes. Deriving expectations from successional theory, we examine properties of plant‐herbivore interaction networks while accounting for host phylogenetic structure along a succession chronosequence in montane rainforest in Papua New Guinea. We present one of the most comprehensive successional investigations of interaction networks, equating to &gt; 40 person years of field sampling, and one of the few focused on montane tropical forests. We use a series of nine 0.2 ha forest plots across young secondary, mature secondary and primary montane forest, sampled almost completely for woody plants and larval leaf chewers (Lepidoptera) using forest felling. These networks comprised of 12 357 plant‐herbivore interactions and were analysed using quantitative network metrics, a phylogenetically controlled host‐use index and a qualitative network beta diversity measure. Network structural changes were low and specialisation metrics surprisingly similar throughout succession, despite high network beta diversity. Herbivore abundance was greatest in the earliest stages, and hosts here had more species‐rich herbivore assemblages, presumably reflecting higher palatability due to lower defensive investment. All herbivore communities were highly specialised, using a phylogenetically narrow set of hosts, while host phylogenetic diversity itself decreased throughout the chronosequence. Relatively high phylogenetic diversity, and thus high diversity of plant defenses, in early succession forest may result in herbivores feeding on fewer hosts than expected. Successional theory, derived primarily from temperate systems, is limited in predicting tropical host‐herbivore interactions. All succession stages harbour diverse and unique interaction networks, which together with largely similar network structures and consistent host use patterns, suggests general rules of assembly may apply to these systems.

Disentangling direct and indirect effects of water availability, vegetation, and topography on avian diversity

Climate is a major driver of species diversity. However, its effect can be either direct due to species physiological tolerances or indirect, whereby wetter climates facilitate more complex vegetation and consequently higher diversity due to greater resource availability. Yet, studies quantifying both direct and indirect effects of climate on multiple dimensions of diversity are rare. We used extensive data on species distributions, morphological and ecological traits, and vegetation across Australia to quantify both direct (water availability) and indirect (habitat diversity and canopy height) effects of climate on the species richness (SR), phylogenetic diversity (PD), and functional diversity (FD) of 536 species of birds. Path analyses revealed that SR increased with wetter climates through both direct and indirect effects, lending support for the influence of both physiological tolerance and vegetation complexity. However, residual PD and residual FD (adjusted for SR by null models) were poorly predicted by environmental conditions. Thus, the FD and PD of Australian birds mostly evolved in concert with SR, with the possible exception of the higher-than-expected accumulation of avian lineages in wetter and more productive areas in northern and eastern Australia (with high residual PD), permitted probably by older biome age.

Integrating trait and evolutionary differences untangles how biodiversity affects ecosystem functioning.

Biodiversity and ecosystem functioning (BEF) research advocates that biodiversity loss has a drastic alteration on ecosystem functioning. However, studies have barely investigated how the evolutionary dependence of species traits affects EF. Here, we developed an integrated approach combining functional (FD) and phylogenetic diversity (PD) into a single space to disentangle the effects of diversity on leaf decomposition. We conducted an experiment manipulating plant leaves into litterbags containing four species (from a pool of 27) combined in four different treatments represented by low or high FD and PD; these treatments present different scenarios of trait evolution and, therefore, a treatment with high FD and low PD, for instance, mimics a community assembled by divergent trait evolution of close relatives. We found that leaf decomposition was 30% slower in pools with high FD and PD. We show species pool with higher FD and PD have non-additive effects on decomposition, which means there is a negative effect of mixtures combining species with great functional and evolutionary differences. In addition, interactive effects of PD and FD were more important to leaf decomposition than their isolated effects. Our results suggest that PD and FD have interactive effects on decomposition and represent different axes of ecosystem variation, indicating we should avoid using phylogenies as a proxy for functional diversity. We argue that future BEF experiments may alter their design by considering a multifaceted scenario investigating community effects on ecosystem functioning, and idiosyncratic effects of key traits which may determine community assembly and ecosystem processes.

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities.

Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.

Multiple facets of biodiversity drive the diversity-stability relationship.

A substantial body of evidence has demonstrated that biodiversity stabilizes ecosystem functioning over time in grassland ecosystems. However, the relative importance of different facets of biodiversity underlying the diversity-stability relationship remains unclear. Here we use data from 39 grassland biodiversity experiments and structural equation modelling to investigate the roles of species richness, phylogenetic diversity and both the diversity and community-weighted mean of functional traits representing the 'fast-slow' leaf economics spectrum in driving the diversity-stability relationship. We found that high species richness and phylogenetic diversity stabilize biomass production via enhanced asynchrony in the performance of co-occurring species. Contrary to expectations, low phylogenetic diversity enhances ecosystem stability directly, albeit weakly. While the diversity of fast-slow functional traits has a weak effect on ecosystem stability, communities dominated by slow species enhance ecosystem stability by increasing mean biomass production relative to the standard deviation of biomass over time. Our in-depth, integrative assessment of factors influencing the diversity-stability relationship demonstrates a more multicausal relationship than has been previously acknowledged.

High phylogenetic diversity and abundance pattern of Labyrinthulomycete protists in the coastal waters of the Bohai Sea

The unicellular Labyrinthulomycete protists have long been considered to play a significant role in ocean carbon cycling. However, their distribution and biogeochemical function remain poorly understood. We present a large-scale study of their spatiotemporal abundance and diversity in the coastal waters of Bohai Sea using flow cytometry and high-throughput sequencing. These protists display niche preferences and episodic higher biomass than that of bacterioplankton with much phylogenetic diversity (> 4000 OTUs) ever reported. They were ubiquitous with a typical abundance range of 100-1000 cells ml-1 and biomass range of 0.06-574.59 μg C L-1 . The observed spatiotemporal abundance variations support the current 'left-over scavengers' nutritional model and highlight these protists as a significant component of the marine microbial loop. The higher average abundance and phylogenetic diversity in the nearshore compared with those in the offshore reveal their predominant role in the terrigenous matter decomposition. Furthermore, the differential relationship of the protist genera to environmental conditions together with their co-occurrence network suggests their unique substrate preferences and niche partitioning. With few subnetworks and possible keystone species, their network topology indicates community resilience and high connectance level of few operational taxonomic units (OTUs). We demonstrate the significant contribution of these protists to the secondary production and nutrient cycling in the coastal waters. As secondary producers, their role will become more important with increasingly coastal eutrophication.

Integrating phylogenetic and functional biodiversity facets to guide conservation: a case study using anurans in a global biodiversity hotspot

The Cerrado is one of the most threatened biomes in Brazil, with little spatial representation within the Protected Area network. Recently, proposed conservation plans worldwide have advocated for the use of multiple biodiversity facets to protect unique evolutionary and functional processes. Our aim was to identify areas with high biodiversity representativeness applying this multifaceted perspective, and propose conservation plans based on the joint analysis of taxonomic, functional and phylogenetic diversity. We used a database of the Brazilian National Program for Research in Biodiversity, which employs a standard protocol for sampling tadpoles. The Cerrado database includes samples from 165 water bodies spread over 15 localities, covering most of the Central Brazilian Cerrado. We selected four morphological traits to calculate functional diversity and used a dated phylogeny available in the literature to compute phylogenetic diversity. Our approach selected five priority areas for conservation, one of which is already protected. Our results highlighted the importance of four new areas which show high values of diversity, including original lineages and traits, and urgently need conservation prioritization. Furthermore, unlike the current protected network, our approach performs significantly better than random at protecting sites with high phylogenetic and functional diversity. We therefore discuss how the multifaceted indices considered can help protect key ecosystem functions and evolutionary legacy in anuran communities of the Brazilian Cerrado.

High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems.

We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.