Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes

The gut microbiota structure reflects both a host phylogenetic history and a signature of adaptation to the host ecological, mainly trophic niches. African cichlid fishes, with their array of closely related species that underwent a rapid dietary niche radiation, offer a particularly interesting system to explore the relative contribution of these two factors in nature. Here we surveyed the host intra- and interspecific natural variation of the gut microbiota of five cichlid species from the monophyletic tribe Perissodini of lake Tanganyika, whose members transitioned from being zooplanktivorous to feeding primarily on fish scales. The outgroup riverine species Astatotilapia burtoni, largely omnivorous, was also included in the study. Fusobacteria, Firmicutes and Proteobacteria represented the dominant components in the gut microbiota of all 30 specimens analysed according to two distinct 16S rRNA markers. All members of the Perissodini tribe showed a homogenous pattern of microbial alpha and beta diversities, with no significant qualitative differences, despite changes in diet. The recent diet shift between zooplantkon- and scale-eaters simply reflects on a significant enrichment of Clostridium taxa in scale-eaters where they might be involved in the scale metabolism. Comparison with the omnivorous species A. burtoni suggests that, with increased host phylogenetic distance and/or increasing herbivory, the gut microbiota begins differentiating also at qualitative level. The cichlids show presence of a large conserved core of taxa and a small set of core OTUs (average 13–15%), remarkably stable also in captivity, and putatively favoured by both restricted microbial transmission among related hosts (putatively enhanced by mouthbrooding behavior) and common host constraints. This study sets the basis for a future large-scale investigation of the gut microbiota of cichlids and its adaptation in the process of the host adaptive radiation.     

Studies on the ferricytochrome a-ferrocytochrome a3-carbon monoxide complex of mammalian cytochrome oxidase. Conditions for preparation and some properties

The conditions for the preparation of the ferricytochrome a-ferrocytochrome a3-carbon monoxide complex (a3+, a3(2)+CO) of cytochrome oxidase [EC 1.9.3.1] by the ferricyanide-reoxidation method and some properties of the prepared complex were studied. The addition of a small volume of concentrated ferricyanide solution to the dithionite-reduced and carbon monoxide-treated cytochrome oxidase preparation was required to obtain the (a3+, a3(2)+CO) spectrum showing absorption maxima at 590, 545, and 429 nm. The addition of larger volumes of ferricyanide solution, thus introducing larger amounts of oxygen into the preparation, caused decomposition of the carbon monoxide complex. A part of the added ferricyanide was immediately reduced by dithionite whereas the remainder was gradually reduced by partial oxidation product(s) of dithionite. The (a3+, a3(2)+CO) complex was stable only when excess ferricyanide remained in the reaction mixture. The formation of the (a3+, a3(2)+CO) spectrum was observed when sodium citrate, phosphate or borate buffer containing either cholate or a non-ionic detergent was employed as the solvent buffer, but not with the buffers containing sodium dodecyl sulfate (SDS) or cetyltrimethyl-ammonium bromide (CETAB). The formation was considerably inhibited by trishydroxymethyl-aminomethane(Tris)-HCl buffer. The (a3+, a3(2)+CO) spectrum appeared with maximal intensity at around pH 7. The pH-dependency of the intensity of the spectrum was not in parallel with the pH-dependent change of the polymerization state of the cytochrome oxidase preparation. On freezing to liquid nitrogen temperature, the (a3+, a3(2)+CO) complex prepared in usual solvent buffers was mostly converted to the oxidized form of cytochrome oxidase (a3+, a3(3)+. However, when prepared in the phosphate buffer, pH 8.0, containing 1.2% (w/v) sodium cholate and with 20% saturation with ammonium sulfate, the complex mostly remained unchanged after the freezing. Based on the results obtained, the stability of the juxta-heme structure of cytochrome a3 was also discussed.     

Long‐read sequence capture of the haemoglobin gene clusters across codfish species

Combining high‐throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short‐read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long‐read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom‐made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage‐specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long‐read capture as a versatile approach for comparative genomic studies by generation of a cross‐species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.     

Intensive local surveys can complement rapid survey techniques to provide insights into the population size and ecology of lichenised fungi

We propose that insights to population ecology of lichenised fungi can be efficiently obtained by combining rapid biodiversity surveys, which representatively sample large areas, with intensive studies in selected populations discovered. To illustrate this approach, we compared results from an Estonian rapid survey scheme with an intensive local population survey of the poorly known epiphytic crustose lichen, Lecanora thysanophora. In contrast to what the data from rapid surveys suggested, the intensive survey revealed that this typically sterile species can occur in remarkably dense populations obviously limited by host tree availability; we also recorded emerging sexual reproduction in the population centre. Our results imply that the detection of even poorly identifiable species may mostly depend on total field effort.