Taxonomic Variation Research Articles

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications

The use of irrigation water sourced from reclamation facilities and untreated surface water bodies may be a practical solution to attenuate the burden on diminishing groundwater aquifers. However, comprehensive microbial characterizations of these water sources are generally lacking, especially with regard to variations through time and across multiple water types. To address this knowledge gap we used a shotgun metagenomic approach to characterize the taxonomic and functional variations of microbial communities within two agricultural ponds, two freshwater creeks, two brackish rivers, and three water reclamation facilities located in the Mid-Atlantic, United States. Water samples (n = 24) were collected from all sites between October and November 2016, and filtered onto 0.2 μm membrane filters. Filters were then subjected to total DNA extraction and shotgun sequencing on the Illumina HiSeq platform. From these data, we found that Betaproteobacteria dominated the majority of freshwater sites, while Alphaproteobacteria were abundant at times in the brackish waters. One of these brackish sites was also host to a greater abundance of the bacterial genera Gimesia and Microcystis. Furthermore, predicted microbial features (e.g. antibiotic resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays) varied based on specific site and sampling date. ARGs were found across samples, with the diversity and abundance highest in those from a reclamation facility and a wastewater-impacted freshwater creek. Additionally, we identified over 600 CRISPR arrays, containing ∼2600 unique spacers, suggestive of a diverse and often site-specific phage community. Overall, these results provide a better understanding of the complex microbial community in untreated surface and reclaimed waters, while highlighting possible environmental and human health impacts associated with their use in agriculture.

Insights into the gastrointestinal tract microbiomes of Indian population

Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.

Assessment of benthic diatoms taxonomic diversity at coastal biotopes with different anthropogenic impact (Crimea, the Black Sea)

An analysis of the taxonomic diversity of benthic diatoms was carried out for near-shore biotopes of Crimea with different content of trace metals and organic pollutants (PCBs, PAHs, DDTs). Taxonomic distinctness indices such as average taxonomic distinctness, AvTD (Δ+) and variation in taxonomic distinctness, VarTD (Λ+) were used for evaluation of the hierarchical structure of diatom taxocenes of two intact sites (Dvuyakornaya Bay and Cape Fiolent) and two heavily polluted water areas (Sevastopol Bay and Balaklava Bay). The highest similarity of species was revealed between healthy biotopes, in spite of their differences in hydrological and hydrochemical conditions. AvTD values for Dvuyakornaya Bay and Cape Fiolent (Δ+ = 79.0 and 76.7, respectively) were lower in comparison with expected average levels (Δ+ = 82.2) evaluated for the flora of benthic Bacillariophyta (1094 species) registered for the Northern part of the Black Sea (NPBS). As established, the taxonomic trees of the diatom taxocenes at pristine water areas are characterized by a moderate degree of vertical evenness and high variability of distances between neighboring clusters of species; they are mainly formed by polyspecific branches close on the genus level. The AvTD values for diatom taxocenes of the heavily polluted Sevastopol Bay (Δ+ = 83.6) and Balaklava Bay (Δ+ = 84.1) were significantly higher than the corresponding indices for undisturbed biotopes and exceeded the expected average level for the entire list of Bacillariophyta for NPBS. The upward trend of AvTD along the increasing technogenic impact can be caused by the disappearance of taxonomically close species with low tolerance from the same genus and prevalence of oligo- and monospecies branches in architectonics of the hierarchical tree. The present study shows that the application of TaxD indices can be considered an additional appropriate indicator tool for quantifying changes in the hierarchical structure of diatom taxocenes under persistent anthropogenic stress.

Functional diversity among herbivorous sea urchins on a coral reef: grazing rate, dietary preference, and metabolism

Herbivores influence the structure and function of ecosystems, especially in the marine environment where ecosystems can be rapidly transformed due to the presence or absence of a single important grazer or grazing community. Intra-guild variation in the ecological functions of herbivores, however, likely determines their ultimate effects on benthic dynamics. For example, echinoids (sea urchins) can facilitate the growth of stony corals by consuming fleshy algal competitors, yet our understanding of taxonomic variation in their grazing behaviors remains limited. Here, we examined the trophic functions of 5 herbivorous echinoids on a coral reef in Maui, Hawaii. We conducted field-based assays to compare grazing rates and consumption profiles using several key algal functional groups and contrasted the results with reported differences in echinoid metabolism. Grazing rates varied among species by up to 10-fold, with taxonomic differences explaining 77-85% of the variation among individual urchins and metabolic rate explaining 81-98% of the taxonomic variation in mean biomass and energy ingestion rates. Though all species consumed several algae, they also exhibited distinct grazing behaviors. Species with lower metabolic rates exhibited the largest intraspecific variation in diets and showed no clear algal preferences. In contrast, species with higher metabolic rates consistently consumed or avoided specific macroalgae, indicating a positive relationship between metabolic rate and diet specificity. This phylogenetic variation in grazing and metabolism aligns with classic metabolic and foraging theory and suggests that species identity, community structure, and complementarity are likely key to understanding the functional roles of herbivorous echinoid communities on coral reefs.

An approach to determining homogeneity in taxonomic breadth of periphytic ciliate communities in colonization surveys for bioassessment

Abstract Taxonomic distinctness is powerful tool to test the departure of a community from an expected pattern of taxonomic structure in response to environmental change. To determine the homogeneity in taxonomic breadth of periphytic ciliates, a 1-month baseline colonization survey was conducted in Jiaozhou Bay, near Qingdao, northern China, using glass slides as artificial substrates. A total of 240 slides were collected at depths of 1, 2, 3.5 and 5 m after colonization periods of 3, 7, 10, 14, 21 and 28 days. The taxonomic composition and structure of the periphytic ciliate communities differed among the four water depths. The temporal variations in all four taxonomic diversity/distinctness measures had different patterns of variability at each depth. Ellipse test on the pairs of average taxonomic distinctness (Δ+) and variation in taxonomic distinctness (Λ+) demonstrated a spatial variability in homogeneity in taxonomic structure of the ciliate communities from 1 m to 5 m, with high levels at 1 and 2 m compared to those at the other two depths. These results suggest that taxonomic distinctness is a useful indicator to identify the homogeneity in taxonomic breadth of periphytic ciliate communities during the colonization process in marine ecosystems.

Association of dietary patterns with the gut microbiota in older, community-dwelling men

While the gut microbiota is relatively stable through adulthood, its composition is influenced by various host and environmental factors, including changes in health, gastrointestinal processes (e.g., transit time, gastric acidity), medication use, and diet. The association of habitual diet, in the form of a posteriori-derived dietary patterns, and microbiota composition has not been adequately studied, particularly in older men. The objective was to investigate the association of dietary patterns with the composition and diversity of the gut bacterial microbiota in community-dwelling, older men. This cross-sectional study included 517 men who were participants in the Osteoporotic Fractures in Men (MrOS) Study (≥65 y of age at baseline in 2000-2002) and who provided a stool sample and completed an FFQ at MrOS Visit 4 in 2014-2016. Dietary patterns were derived by factor analysis. 16S ribosomal RNA target gene sequencing was performed and taxonomy assignments were derived using the Greengenes database. Linear regression and permutational multivariate analysis of variance (PERMANOVA) considered variations in alpha and beta diversity by dietary pattern, and a model that implements a 0-inflated Gaussian distribution of mean group abundance for each taxa (metagenomeSeq) assessed taxonomic variations by dietary pattern. In multivariable-adjusted models, greater adherence to the Western pattern was positively associated with families Mogibacteriaceae and Veillonellaceae and genera Alistipes, Anaerotruncus, CC-115, Collinsella, Coprobacillus, Desulfovibrio, Dorea, Eubacterium, and Ruminococcus, while greater adherence to the prudent pattern was positively associated with order Streptophyta, family Victivallaceae, and genera Cetobacterium, Clostridium, Faecalibacterium, Lachnospira, Paraprevotella, and Veillonella. The relative abundance of the dominant gut bacterial phyla, Bacteroidetes and Firmicutes, did not differ between participants with greater adherence to the Western pattern, compared with those with greater adherence to the prudent pattern. Dietary patterns were not associated with measures of alpha diversity, but beta diversity measures were significantly associated with both Western and prudent patterns. We observed significant associations between dietary patterns and measures of gut microbial composition in this sample of community-dwelling, older men.

Defining the indigenous ranges of species to account for geographic and taxonomic variation in the history of human impacts: reply to Sanderson 2019.

Accounting for taxonomic and geographic variation in historic human impacts on indigenous range will facilitate use of IUCN’s Green List of Species.

Diversity and space-time dynamics of fish assemblages in a coastal lagoon, western Atlantic

The knowledge of the temporal and spatial dynamics in the composition of fish fauna makes it possible to identify patterns of occupation of ecosystems, providing a basis for evaluation and preservation of the local biodiversity. Monthly samplings were carried out at seven sites in a coastal lagoon, using a casting net, dip net and beach seine. A total of 4,110 individuals were collected, distributed in 23 families and 49 taxa of fish, with a predominance of Mugilliza, M.curema, Atherinellabrasiliensis, Micropogoniasfurnieri and Eucinostomusargenteus, corresponding to more than 80% total weight of all individuals caught. Regarding seasonality, greater abundances were recorded in fall, influenced by the high abundance of A.brasiliensis in this period. In addition to fall, this species was also abundant in summer. However, this pattern of dominance was different for the families Mugilidae and Gerreidae, with higher abundances in spring and summer, respectively. The highest abundances were found in the southern section of the lagoon, which are related to the high abundance of A.brasiliensis, M.liza and M.curema. In relation to the indices of average taxonomic distinctness and variation in the taxonomic distinctness, no significant differences were detected between the seasons of the year. Thus, the patterns of distribution and occurrence of fish in the lagoon were consistent with the patterns observed in Brazilian coastal lagoons and estuaries, as well as to the coastal shallow areas of the southeastern and southern regions.

Nestling-sized hadrosaurine cranial material from the Hell Creek Formation of northeastern Montana, USA, with an analysis of cranial ontogeny in <em>Edmontosaurus annectens</em>

Author(s): Wosik, Mateusz; Goodwin, Mark B.; Evans, David C. | Abstract: Despite over a century of intense collecting, the Hell Creek Formation has produced exceedingly few specimens of small juveniles and nestling-sized dinosaurs. Here, we report on the first cranial material of nestling-sized hadrosaurid dinosaurs from the formation. The specimens were recovered from the Sandstone Basin locality in Garfield County, northeastern Montana. The material consists of two dentaries, a surangular, and a quadrate from disassociated individuals, which through ontogenetically independent characters allows assignment of the surangular (UCMP 235857) and quadrate (UCMP 235859) to Hadrosaurinae and the dentary (UCMP 235860) to Edmontosaurus. Since Edmontosaurus annectens is the only known hadrosaurid in the formation, we hypothesize that these specimens represent the earliest ontogenetic growth stage of E. annectens providing a significant ontogenetic extension when assessing aspects of cranial ontogeny in this taxon. Using the newly identified nestling cranial material as end members of ontogenetic series for each element in E. annectens, we evaluated ontogenetic variability in phylogenetic characters associated with these elements that are used in assessing phylogenetic relationships among hadrosaurids. Although the quadrate and surangular generally develop isometrically and show minimal ontogenetic variation in morphology, the dentary undergoes significant ontogenetic changes. In particular, the dental battery exhibits a high degree of intraspecific variability through ontogeny. Ontogenetic variability in the dentary should reflect a commensurate degree of variation in the jaws and facial skeleton, suggesting caution should be used when taxonomically identifying small edmontosaur material, such as that known from Alaska. Taxonomic identification of new taxa should be restricted to adult individuals until enough specimens are available to adequately assess taxonomic variation in ontogenetically equivalent semaphorants/ontogimorphs for a large range of complementing taxa.

The distinct response of phenanthrene enriched bacterial consortia to different PAHs and their degradation potential: a mangrove sediment microcosm study.

Understanding the microbial community succession to polycyclic aromatic hydrocarbons (PAHs) and identification of important degrading microbial groups are crucial for the designing of appropriate bioremediation strategies. In the present study, two distinct phenanthrene enriched bacterial consortia were treated against high molecular weight (Pyrene, Benzo (a) pyrene and Benzo (a) fluoranthene) and the response was studied in term of taxonomic variations by using High Throughput Illumina sequencing and qPCR analysis. Overall, the type of PAHs significantly affected the composition and the relative abundance of bacterial communities while no obvious difference was detected between bacterial communities of benzo (a) pyrene and benzo (a) fluoranthene treatments. Genera, Novosphingobium, Pseudomonas, Flavobacterium, Mycobacterium, Hoeflae, and Algoriphagus dominated all PAHs treatment groups indicating that they could be the key PAHs degrading phylotypes. Due to the higher abundance of gram-negative PAH-ring hydroxylating dioxygenase gene than that of gram-positive bacteria in all treated groups, we speculated that gram-negative bacteria may contribute more in the PAH degradation. The studied sediments harbored rich PAHs degrading bacterial assemblages involved in both low and high molecular weight PAHs and these findings provided new insight into the perspective of microbial PAHs bioremediation in the mangrove ecosystem.

Diversity of reef associated fishes in hook and line fishery at Mandapam, Gulf of Mannar, south-east coast of India

Reef associated fishes landed by hooks and lines at Mandapam landing centre in Ramanathapuram District, Tamil Nadu for a period of four years from October 2008 to May 2012 were studied based on fortnightly samplings. The hook and line fishing is seasonal in Gulf of Mannar and lasts for six months annually from October - November to April - May, as this area remains rough during the rest of the year. The average annual landing of fish during the study period was 171 t with a peak of 295 t in 2008-09 and showed a decline since then. A total of 32 species of reef associated fishes belonging to 14 families were landed. Among them, Sphyraena barracuda contributed the maximum with a share of 42% followed by Caranx heberi (15%). Family-wise landings indicated the dominance of Sphyraenidae (46%). The diversity index (H’) was the highest during 2008-09 and the evenness of distribution of individuals among different species did not show significant variation in different years. Funnel plots of average taxonomic distinctness (∆+ ) and variation in taxonomic distinctness (λ+ ) indicated that the values in most of the years are within the normal limits.

Pumped Up by the Cold: Elemental Quotas and Stoichiometry of Cold-Water Diatoms

Phytoplankton cellular elemental quotas are important for evaluating the coupling of nutrient cycles and assessing nutrient limitation in the ocean. While cell element quotas have been shown to vary in response to growth conditions (e.g., light, nutrient supply), an overriding trait is cell size and biovolume. Allometric relationships are lacking data for phytoplankton grown under polar temperature conditions (e.g., <5oC); limited field data using single-cell stoichiometry measurements have shown polar diatoms may have significantly different allometry versus low-latitude counterparts. In this study, 11 strains of diatoms isolated from sub/polar waters (both Arctic and Antarctic) were grown in batch growth mode. Cellular carbon (C), nitrogen (N), phosphorus (P), silica (Si), cell number and biovolume were measured during mid-exponential and early stationary growth phases. An allometric log-log relationship was observed between cell element quotas and biovolume, although the strain Odontella aurita was consistently an outlier. Including O. aurita resulted in regression slopes for C, N, P and Si that were lower than values from the reviewed literature of temperate organisms; excluding O. aurita resulted in regression slopes that were more similar to published values for each element. However, the intercepts of the elemental quotas in the allometric relationships ranged from ~5-fold to ~100-fold greater than published values depending upon the element and the growth phase, meaning that the elemental density is significantly higher for diatoms grown at cold temperatures, although the physiological mechanism(s) cannot be resolved in this study. Cellular ratios of C, N, and P were consistent with prior research, but clearly showed the importance of taxonomic variability as all strains of the genus Thalassiosira behaved more similarly to each other than to the other diatom strains tested. Si:C ratios, in contrast, for non-Thalassiosira strains were greater and approached values commonly observed for iron-limited cells. These results show that a different set of allometric scaling equations is needed when considering sub/polar diatoms relative to temperate and tropical diatoms, which will impact regional and global model parameterization. In addition, these results highlight the role of phytoplankton diversity on biogeochemistry, even within the closely aligned families of diatoms.

Lower diversity of recruits in coastal reef assemblages are associated with higher sea temperatures in the tropical South Atlantic

Climate change will lead to community shifts and increase the vulnerability of coastal marine ecosystems, but there is yet insufficient detail of how early life stages of marine populations are linked to oceanic-climate dynamics. This study aimed to investigate how ocean-climate variability is associated with spatial and temporal changes in benthic larval recruitment of tropical reef assemblages. Recruitment (abundance, richness, and diversity) of benthic invertebrates was monitored for one year on macroalgal beds in four rocky reefs in a marine protected region in the Eastern coast of Brazil, and compared to fluctuations in meteo-oceanographic conditions at multiple temporal scales (days, weeks, and months). Our results revealed that recruitment of benthic invertebrates varies widely (up to 15 orders of magnitude) among sampled reefs and in time, with wave height, wind speed, and sea temperature being significantly related to recruitment variability. We detected strong taxonomic variability in recruitment success and ocean-climate variables, which highlights the complexity of estimating community vulnerability to climate change in benthic communities. Given that macroalgal beds are key to recruitment of some species regionally (4–30 km), the protection of coastal nursery habitats may be critical for marine conservation and species adaptation in a climate change scenario. Considering the projected ocean-climate change in IPCC scenarios, our study suggests that recruitment of marine populations in coastal reefs could be highly sensitive to climate change in the tropical South Atlantic Ocean.

Do functional traits of chironomid assemblages respond more readily to eutrophication than taxonomic composition in Chinese floodplain lakes?

Abstract Functional trait-based measures can reflect local environmental conditions and are claimed as promising approaches for environmental monitoring and assessment programs. The chironomid larvae are a diverse and ecologically important group of benthic macroinvertebrates and have a set of functional traits that can be used to assess environmental quality of freshwater ecosystems. However, little is known regarding the relationships between chironomid functional structure and human disturbances, especially at a fine taxonomic resolution. Here, we compared the responses of functional traits and traditional taxonomic measures of chironomid assemblages to eutrophication in the Yangtze floodplain lakes. We found that functional composition showed higher sensitivity and robustness in discriminating the extents of eutrophication than taxonomic composition. Specifically, about half of functional categories examined significantly differed among the lake groups, while only two taxonomical measures (the abundance of Tanytarsini and Polypedilum) are suitable for assessing environmental quality of floodplain lakes. The macrophytic lakes showed higher abundance of scrapers, the small body size and oligotrphic individuals. Whereas the algal lakes were associated with high abundance of eutrophic/hypertrophic chironomids and those with haemoglobin. Chironomid assemblages showed significant differences among four lake groups for both trait-based and taxonomy-based variations, but with larger differences for trait-based groups. The distance-based redundancy analysis (dbRDA) indicated that taxonomic and functional assemblage structures were explained primarily by similar water quality variables (chlorophyll a, transparency and TN), but more functional variation (24.6%) was explained by environmental factors than taxonomic variation (10.9%) in chironomid assemblages. Our results indicated that chironomid trait-based approaches were more sensitive and robust to water quality gradients than taxonomy-based approaches. Therefore, we argued that the chironomid functional traits deserve considerations for biomonitoring programs in the lakes we studied and other freshwater lakes and aquatic ecosystems.

The Macromolecular Basis of Phytoplankton C:N:P Under Nitrogen Starvation.

Biogeochemical cycles in the ocean are strongly affected by the elemental stoichiometry (C:N:P) of phytoplankton, which largely reflects their macromolecular content. A greater understanding of how this macromolecular content varies among phytoplankton taxa and with resource limitation may strengthen physiological and biogeochemical modeling efforts. We determined the macromolecular basis (protein, carbohydrate, lipid, nucleic acids, pigments) of C:N:P in diatoms and prasinophytes, two globally important phytoplankton taxa, in response to N starvation. Despite their differing cell sizes and evolutionary histories, the relative decline in protein during N starvation was similar in all four species studied and largely determined variations in N content. The accumulation of carbohydrate and lipid dominated the increase in C content and C:N in all species during N starvation, but these processes differed greatly between diatoms and prasinophytes. Diatoms displayed far greater accumulation of carbohydrate with N starvation, possibly due to their greater cell size and storage capacity, resulting in larger increases in C content and C:N. In contrast, the prasinophytes had smaller increases in C and C:N that were largely driven by lipid accumulation. Variation in C:P and N:P was species-specific and mainly determined by residual P pools, which likely represent intracellular storage of inorganic P and accounted for the majority of cellular P in all species throughout N starvation. Our findings indicate that carbohydrate and lipid accumulation may play a key role in determining the environmental and taxonomic variability in phytoplankton C:N. This quantitative assessment of macromolecular and elemental content spanning several marine phytoplankton species can be used to develop physiological models for ecological and biogeochemical applications.

Key pollen host plants provide balanced diets for wild bee larvae: A lesson for planting flower strips and hedgerows

Abstract Bee‐friendly plants are defined by the quantity of food they produce and the visitation rates of adult insects foraging for nectar. However, it is pollen nutritional quality that enables proper larval development of bees, affecting their populations. Not all plants produce pollen that satisfies the nutritional requirements of bee larvae, and we lack an understanding of how different plant pollens impact bee nutritional demands. This study examined whether nutritionally desirable key plant species may promote wild bee larval development, which is essential if the population is to thrive. The generalist solitary mason bee Osmia bicornis L. was used as a model species to examine differences between bee larva nutritional demand and host plant nutrient supply; an ecological stoichiometry framework was applied. The stoichiometric ratios of 12 elements were investigated in bee bodies and cocoons (reflecting nutritional demand) and in the pollen supplied by the mother (nutritional supply; N = 15 × 2 sexes). Similarly, the stoichiometry of 62 pollen taxa, including native, alien, and garden plants and crops, was compared with the bee demand based on the literature. Compared to males, females had higher demands for P, Cu and Zn and were supplied with pollen richer in these elements. Therefore, when collecting pollen for their progeny, Osmia provides daughters and sons with different pollen mixtures, reflecting sex‐specific nutritional demand. Bees may be limited by the availability of P, Na, Mn, Mg, K, Fe, Ca, Zn and Cu, with high taxonomic variability in their concentrations in pollen. Female fitness may be particularly related to a high proportion of P in the diet. Synthesis and applications. Access to key plant species that allow nutritionally balanced larval diets may be essential for bee development, whether food is gathered intentionally or randomly. Such plant species—and not only those rich in nectar and pollen—should be promoted in wild bee conservation efforts, including planting flower strips and hedgerows. Bee‐friendly plants should not be defined and planted solely based on the quantities of food they produce and on the visitation rates of adult insects foraging for energy.

Inter-regional beta-diversity patterns of the woody flora of Greece

This study aimed to estimate and explain the compositional differentiation and observed beta-diversity (partitioned as turnover and nestedness) patterns of woody species in Greece. Specifically, the 13 phytogeographical regions of Greece were compared at three taxonomic levels: family, genus, and (sub-) species. In Greece, 565 woody taxa have been identified, which are classified into 224 genera and 85 families. Phytogeographical regions were grouped according to their similarity in floristic composition using cluster analysis. Dominant beta diversity gradients were detected using Mantel directional correlation tests applied at the three taxonomic levels. The 13 phytogeographical regions formed three groups; namely, the northern, central, and southern (Aegean Islands) regions. The taxonomic variation among the phytogeographical regions at the species level was related to a gradient of richness of widespread taxa and Balkan endemic taxa. Analysis at the taxonomic levels of species and genus produced similar results, yet, at the family level, floristic differences were less pronounced, with phytogeographical regions being aggregated in two groups: the southernmost island regions versus all other regions. Beta diversity was higher along a northwestern to southeastern gradient, which was related to a dominant climatic gradient throughout Greece. The partitioning of beta diversity between neighboring phytogeographical regions showed that species turnover was the dominant component; yet, some phytogeographical regions (e.g., Kiklades) were characterized by high nestedness. In conclusion, analysis of woody taxa provides different insights regarding the floristic variation of phytogeographical regions.

Blood Microbiome Profile in CKD : A Pilot Study.

The association between gut dysbiosis, high intestinal permeability, and endotoxemia-mediated inflammation is well established in CKD. However, changes in the circulating microbiome in patients with CKD have not been studied. In this pilot study, we compare the blood microbiome profile between patients with CKD and healthy controls using 16S ribosomal DNA sequencing. Blood bacterial DNA was studied in buffy coat samples quantitatively by 16S PCR and qualitatively by 16S targeted metagenomic sequencing using a molecular pipeline specifically optimized for blood samples in a cross-sectional study comparing 20 nondiabetic patients with CKD and 20 healthy controls. There were 22 operational taxonomic units significantly different between the two groups. 16S metagenomic sequencing revealed a significant reduction in α diversity (Chao1 index) in the CKD group compared with healthy controls (127±18 versus 145±31; P=0.04). Proteobacteria phylum, Gammaproteobacteria class, and Enterobacteriaceae and Pseudomonadaceae families were more abundant in the CKD group compared with healthy controls. Median 16S ribosomal DNA levels did not significantly differ between CKD and healthy groups (117 versus 122 copies/ng DNA; P=0.38). GFR correlated inversely with the proportion of Proteobacteria (r=-0.54; P≤0.01). Our pilot study demonstrates qualitative differences in the circulating microbiome profile with lower α diversity and significant taxonomic variations in the blood microbiome in patients with CKD compared with healthy controls.

Taxonomic variation in levels of endemism: a case study of Italian tenebrionid beetles

Abstract Levels of endemism are usually expressed as percentage of endemics among all species recorded in a given area. Endemism levels also vary among taxa, yet inter‐taxon variation in endemism levels has received much less attention. We used the Italian tenebrionids to investigate how endemism levels vary among different but related lineages. We evaluated endemism variations among taxonomic levels both as a percentage of endemics to the number of species included in a given taxon (i.e. the tendency of a taxon to produce endemics) and as a percentage to the total number of species (i.e. the importance of that taxon to the overall endemic component). We also considered the residuals of regression lines of endemics against non‐endemics. We tested the influence of phylogenetic position, lifestyle, and body size on the percentage of endemics within genera. Use of percentages and residuals gave similar outcomes. Pimeliinae were the subfamily with the highest level of endemism. Erodiini, Pimeliini, Tentyriini, Asidini, Opatrini, and Pedinini were among the tribes with the highest endemism levels. Asida, Pimelia, Tentyria, and Opatrum were the genera with the highest levels of endemism. Phylogenetic position and body size affected significantly endemism levels, with genera including larger species being also those with higher endemism, whereas lifestyle was not significant. This suggests that endemism in the Italian tenebrionid beetles is phylogenetically constrained and that lines including larger species (which are possibly less subject to passive dispersal) tend to be richer in endemics, independently from their lifestyle.

Evaluation of the taxonomic and functional variation of freshwater plankton communities induced by trace amounts of the antibiotic ciprofloxacin

Ciprofloxacin (CIP), one of the most frequently detected antibiotics in water systems, has become an aquatic contaminant because of improper disposal and excretion by humans and animals. It is still unknown how trace amounts of CIP affect the aquatic microbial community diversity and function. We therefore investigated the effects of CIP on the structure and function of freshwater microbial communities via 16S/18S rRNA gene sequencing and metatranscriptomic analyses. CIP treatment (7 μg/L) did not significantly alter the physical and chemical condition of the water body as well as the composition of the main species in the community, but slightly increased the relative abundance of cyanobacteria and decreased the relative abundance of eukaryotes. Metatranscriptomic results showed that bacteria enhanced their phosphorus transport and photosynthesis after CIP exposure. The replication, transcription, translation and cell proliferation were all suppressed in eukaryotes, while the bacteria were not affected in any of these aspects. This interesting phenomenon was the exact opposite to both the antibacterial property of CIP and its safety for eukaryotes. We hypothesize that reciprocal and antagonistic interactions in the microcosm both contribute to this result: cyanobacteria may enhance their tolerance to CIP through benefiting from cross-feeding and some secreted substances that withstand bacterial CIP stress would also affect eukaryotic growth. The present study thus indicates that a detailed assessment of the aquatic ecotoxicity of CIP is essential, as the effects of CIP are much more complicated in microbial communities than in monocultures. CIP will continue to be an environmental contaminant due to its wide usage and production and more attention should be given to the negative effects of antibiotics as well as other bioactive pollutants on aquatic environments.