Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon

Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286–37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (∼1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.     

Relationships of reproductive performance indicators in black rhinoceros (Diceros bicornis michaeli) with plant available moisture,plant available nutrients and woody cover

Plant available moisture and plant available nutrients in soils influence forage quality and availability and subsequently affect reproductive performance in herbivores. However, the relationship of soil moisture, soil nutrients and woody forage with reproductive performance indicators is not well understood in mega‐browsers yet these three are important in selecting suitable areas for conservation of mega‐browsers. Here, the eastern black rhinoceros (Diceros bicornis michaeli), a mega‐browser, was studied in seven geographically distinct populations in Kenya to understand the relationships between its reproductive performance indicators and plant available moisture, plant available nutrients and woody cover. Reproductive parameters showed a complex relationship with plant available moisture and plant available nutrients. We found an increase in the predicted yearly percentage of females calving as plant available nutrients decreased in areas of high levels of plant available moisture but no relationship with plant available nutrients in areas of low plant available moisture. Age at first calving was earlier, inter‐calving interval was longer and yearly percentage of females calving was higher at higher woody cover. Woody plant cover contributes positively to black rhino reproduction performance indicators, whereas plant available moisture and plant available nutrients add to the selection of conservation areas, in more subtle ways.     

Scale-dependent bi-trophic interactions in a semi-arid savanna: how herbivores eliminate benefits of nutrient patchiness to plants

The scale of resource heterogeneity may influence how resources are locally partitioned between co-existing large and small organisms such as trees and grasses in savannas. Scale-related plant responses may, in turn, influence herbivore use of the vegetation. To examine these scale-dependent bi-trophic interactions, we varied fertilizer [(nitrogen (N)/phosphorus (P)/potassium (K)] applications to patches to create different scales of nutrient patchiness (patch size 2 × 2 m, 10 × 10 m, or whole-plot 50 × 50 m) in a large field experiment in intact African savanna. Within-patch fertilizer concentration and the total fertilizer load per plot were independently varied. We found that fertilization increased the leaf N and P concentrations of trees and grasses, resulting in elevated utilization by browsers and grazers. Herbivory off-take was particularly considerable at higher nutrient concentrations. Scale-dependent effects were weak. The net effect of fertilization and herbivory was that plants in fertilized areas tended to grow less and develop smaller rather than larger standing biomass compared to plants growing in areas that remained unfertilized. When all of these effects were considered together at the community (plot) level, herbivory completely eliminated the positive effects of fertilization on the plant community. While this was true for all scales of fertilization, grasses tended to profit more from coarse-grained fertilization and trees from fine-grained fertilization. We conclude that in herbivore-dominated communities, such as the African savanna, nutrient patchiness results in the herbivore community profiting rather more than the plant community, irrespective of the scale of patchiness. At the community level, the allometric scaling theory’s prediction of plant—and probably also animal—production does not hold or may even be reversed as a result of complex bi-trophic interactions.     

Non-heritable change of a spirochaete's phenotype by decoration of the cell surface with exogenous lipoproteins

Genetic transformation of Borrelia spp. is limited in development and has found application in only one species. For a non-genetic approach for manipulating the phenotype of these spirochaetes, we determined whether exogenous recombinant lipoproteins would incorporate in the cell's outer membrane. Using unlabelled or 125I-labelled Osp proteins, Osp-specific monoclonal antibodies, proteinase K and formaldehyde as reagents, we found that decoration of spirochaetes had the following characteristics. (i) Purified recombinant OspA or OspD lipoproteins associated with Borrelia burgdorferi and B. hermsii cells that lacked abundant lipoproteins of their own. (ii) This decoration of the cells with exogenous OspA did not affect cell's viability. (iii) The decoration was concentration and temperature dependent and stable for at least 24 h. (iv) Like native OspA, the recombinant OspA decorating the cells was accessible to antibodies and proteases and could be cross-linked to the integral outer membrane protein, P66. (v) Decoration of viable B. burgdorferi and B. hermsii with OspA rendered the cells susceptible to killing by OspA-specific antiserum. Such non-genetic alteration of the surface of a bacterium may be used to study functions and properties of lipoproteins in situ.     

Cycloartane glycosides from leaves of Oxyanthus pallidus

From the MeOH extract of leaves of Oxyanthus pallidus, three cycloartane glycosides, named pallidiosides A-C, were isolated together with two known compounds, oleanolic acid and 3-O-β-D-glucopyranosyl-β-sitosterol. The structures of pallidiosides A-C were assigned on the basis of spectral studies and comparison with published literature data. The known compounds were identified by means of Co TLC and confirmed by their physical constants.     

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (d_XY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.     

Herbaceous production in South India—limiting factors and implications for large herbivores

This study’s goal was to better understand the growth pattern and limitations of the herbaceous production that supports South India’s rich large herbivore grazer assemblage. We conducted a fully factorial nitrogen and water (three levels each) treatment field experiment in the herbivore rich South Indian Western Ghats region to determine the seasonal pattern and the extent to which nitrogen and water availability limit herbaceous production. Graminoid production was found to be nitrogen limited. Despite low rainfall, additional water did not significantly increase overall biomass production nor extend growth in the dry season. Accumulated standing biomass was highest in the late wet season (November) and lowest in the dry season (May). Leaf nitrogen was highest in the early wet season (June) and lowest in the late dry season (March). Grazing had a positive effect on grass production by extending the growing season. Biomass production and graminoid leaf nitrogen concentration levels in the study area were similar to other tropical areas in the world. Also similar to other tropical large herbivore areas, the dry season poses an annual challenge for large herbivores in the study area —particularly the smaller bodied species—to satisfy their nutrient requirements.     

Foraging behaviour of wild impala (Aepyceros melampus) and Burchell's zebra (Equus burchelli) in relation to sward height

Foraging behaviour plays a key role in the interaction between herbivores and vegetation, their predominant food source. Understanding this interaction is crucial to providing information that is useful for conservation of herbivores. The objective of this study was to determine how sward height influences functional response and movement patterns of free ranging wild impala and zebra at the Kenya Wildlife Service Training Institute. The study was conducted for 3 months. Sward height is an important parameter that indicates how intensive a sward has been grazed and it influences intake rate through its effect on bite size. Bite size, instantaneous intake rate, specific mass intake rate and feeding station interval for impala and zebra increased with sward height. Sward height in combination with an animal's sex was found to have a profound effect on specific mass intake rate in impala. Zebra had a longer feeding station interval and lower stepping rate in tall swards compared to impala. Despite differences in their specific body mass and digestive strategies, impala and zebra maximized their intake rates in tall swards as a trade‐off among the swards. Tall swards are therefore critical in the study area and should be protected from bush encroachment which is a persistent problem.     

Front Cover

In most animals, competition for mating opportunities is higher among males, whereas females are more likely to provide parental care. In few species, though, these "conventional" sex roles are reversed such that females compete more strongly for matings and males provide most or all parental care. This "reversal" in sex roles is often combined with classical polyandry—a mating system in which a female forms a harem with several males. Here, we review the major hypotheses relating such role reversals to evolutionary and behavioural traits (anisogamy, phylogenetic history, sexy males, parental care, genetic paternity, trade‐off between mating and parenting, adult sex ratio) and to ecological factors (food supply, offspring predation). We evaluate each hypothesis in relation to coucals (Centropodinae), a group of nesting cuckoos of great interest for mating system and parental care theory. The black coucal (Centropus grillii) is the only known bird combining classical polyandry with altricial development of young, a costly trait with regard to parental care. Our long‐term study offers a unique possibility to compare the strongly polyandrous black coucal with a monogamous close relative breeding in the same area and habitat, the white‐browed coucal (C. superciliosus). We show that the evolution of sex roles in coucals and other animals has many different facets. Whereas phylogenetic constraints are important, confidence in genetic paternity is not. In combination with facilitating ecological conditions, adult sex ratios are key to understanding sex roles in coucals, shorebirds, and most likely also other animals. We plead for more studies including experimental tests to understand how biased adult sex ratios emerge and whether they drive sexual selection or vice versa. How do sex ratios and sexual selection interact and feedback on each other? Answers to these questions will be fundamental for understanding the evolution of sex roles in mating and parenting in coucals and other species.