Butterfly monitoring using systematically placed transects in contrasting climatic regions - exploring an established spatial design for sampling

Butterfly monitoring schemes are recording programs initiated to monitor nationwide butterfly abundance and distribution patterns, often with help from volunteers. The method generates high-resolution data, but may be associated with a degree of habitat sampling bias if volunteers prefer to survey areas perceived to be high-quality butterfly habitats. This can result in habitats becoming underrepresented in the data set, leading to less information about the butterfly populations there. In the present study, we investigate the possibility of applying a spatial design used by the Swedish Bird Survey for nationwide, grid-based sampling, with a goal to get butterfly monitoring data covering a representative sample of different habitats. We surveyed four 2x2 km sampling squares, split into 100 m segments, in the southernmost region of Sweden (Scania) and four in the northernmost region (Norrbotten). The grid-based transects were compared with volunteer-selected transects in a GIS analysis using a refined Swedish version of CORINE land cover data to see how well these two transect designs represent true habitat coverage. A total of 53 km transect was monitored, resulting in 490 individuals and 29 different species recorded. We found that transect cover correlated significantly with overall land cover using both monitoring methods, though standardised transects outperformed volunteer-selected transects in habitat representation in Scania, but not in Norrbotten. Butterflies were found to aggregate significantly in specific habitats, but with contrasting results for the two geographically different regions. Grasslands in both regions generated a high number of recorded butterflies, although so did clear-cut and residential areas in Norrbotten as well. The highest number of individuals recorded per transect was found in bogs in Scania. This study emphasises the value of complementing free site selection monitoring schemes with spatially representative schemes such as the Swedish Bird Survey, and sheds some light on general habitat preferences for Swedish butterflies in two contrasting climatic regions

Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi.

Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi

Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Leray, M., Wilkins, L. G. E., Apprill, A., Bik, H. M., Clever, F., Connolly, S. R., De Leon, M. E., Duffy, J. E., Ezzat, L., Gignoux-Wolfsohn, S., Herre, E. A., Kaye, J. Z., Kline, D. I., Kueneman, J. G., McCormick, M. K., McMillan, W. O., O’Dea, A., Pereira, T. J., Petersen, J. M., Petticord, D. F., Torchin, M. E., Thurber, R. V., Videvall, E., Wcislo, W. T., Yuen, B., Eisen, J. A. . Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. Plos Biology, 19(8), (2021): e3001322, https://doi.org/10.1371/journal.pbio.3001322.Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.Financial support for the workshop was provided by grant GBMF5603 (https://doi.org/10.37807/GBMF5603) from the Gordon and Betty Moore Foundation (W.T. Wcislo, J.A. Eisen, co-PIs), and additional funding from the Smithsonian Tropical Research Institute and the Office of the Provost of the Smithsonian Institution (W.T. Wcislo, J.P. Meganigal, and R.C. Fleischer, co-PIs). JP was supported by a WWTF VRG Grant and the ERC Starting Grant 'EvoLucin'. LGEW has received funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020) under the Marie Sklodowska-Curie Grant Agreement No. 101025649. AO was supported by the Sistema Nacional de Investigadores (SENACYT, Panamá). A. Apprill was supported by NSF award OCE-1938147. D.I. Kline, M. Leray, S.R. Connolly, and M.E. Torchin were supported by a Rohr Family Foundation grant for the Rohr Reef Resilience Project, for which this is contribution #2. This is contribution #85 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network.

How should we store avian faecal samples for microbiota analyses? Comparing efficacy and cost-effectiveness

Analyses of bacterial DNA in faecal samples are becoming ever more common, yet we still do not know much about bird microbiomes. These challenges partly lie in the unique chemical nature of their faeces, and in the choice of sample storage method, which affects DNA preservation and the resulting microbiome composition. However, there is little information available on how best to preserve avian faeces for microbial analyses. This study evaluates five widely used methods for preserving nucleic acids and inferring microbiota profiles, for their relative efficacy, cost, and practicality. We tested the five methods (in-situ bead-beating with a TerraLyzer instrument, silica-bead desiccation, ethanol, refrigeration and RNAlater buffer) on 50 fresh faecal samples collected from captive House sparrows (Passer domesticus). In line with other studies, we find that different storage methods lead to distinct bacterial profiles. Storage method had a large effect on community composition and the relative abundance of dominant phyla such as Firmicutes and Proteobacteria, with the most significant changes observed for refrigerated samples. Furthermore, differences in the abundance of aerobic or facultatively aerobic taxa, particularly in refrigerated samples and those stored in ethanol, puts limits on comparisons of bacterial communities across different storage methods. Finally, the methods that did not include in-situ bead-beating did not recover comparable levels of microbiota to the samples that were immediately processed and preserved using a TerraLyzer device. However, this method is also less practical and more expensive under field work circumstances. Our study is the most comprehensive analysis to date on how storage conditions affect subsequent molecular assays applied to avian faeces and provides guidance on cost and practicality of methods under field conditions

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene. Conclusions: We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vulturesopen

Early-life gut dysbiosis linked to juvenile mortality in ostriches

Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health

Evolutionary genomics of host-microbe interactions

The microbes living inside hosts have highly important consequences for host health and fitness. From the host’s perspective, some microbes exhibit mutualistic tendencies, others parasitic, and some commensal, but this is context-dependent and opportunistic lifestyles are widespread in nature. Our knowledge of how hosts interact molecularly with different microbes is, however, poor, and little research has been done on non-model organisms from a genomic and community-wide perspective. In this PhD thesis, I investigate host-microbe interactions from multiple angles, and utilize high-throughput sequencing techniques to paint a broad, overarching picture of the relationship between hosts and microbes. My PhD comprised two related projects, 1) host-microbiome interactions and 2) host-parasite interactions. In the former, I have evaluated how to best sample and measure the gut microbiomes of avian hosts (Paper I and II). Different sections of the ostrich gastrointestinal tract were characterized and shown to harbour divergent microbial communities (Paper I, II, and IV). I have further demonstrated that the gut microbiome of juvenile ostriches is colonized in a successional manner and gradually develops over time (Paper III), and is strongly linked to growth and mortality (Paper III and IV). In the second project I described the avian transcriptome response to malaria infection over time and to parasites with different virulence (Paper V and VI). Birds with malaria infection experience a range of transcriptional changes that involves for example the immune system, stress response, cell death regulation, and regulatory genes. To evaluate the molecular response of the malaria parasite, I assembled the blood transcriptome of Plasmodium ashfordi and showed that parasite gene expression is host-specific (Paper VII). This transcriptome was subsequently used, together with a genome assembly of Haemoproteus tartakovskyi, to construct a phylogeny of haemosporidian parasites which showed strong support for a monophyletic clade of mammalian malaria parasites (Paper VIII). Finally, the assembled transcriptome and genome were utilized to identify thiamine biosynthesis enzymes in avian Plasmodium (Paper IX), and to demonstrate that the avian Plasmodium parasites exhibit the most AT-rich genes of eukaryotes (Paper X). In summary, this work offers new insights into host-microbiome and host-parasite interactions, and enables a greater understanding of the multifaceted relationship between hosts and their microbes

Plasmodium parasites of birds have the most AT-rich genes of eukaryotes

The genomic architecture of organisms, including nucleotide composition, can be highly variable, even among closely-related species. To better understand the causes leading to structural variation in genomes, information on distinct and diverse genomic features is needed. Malaria parasites are known for encompassing a wide range of genomic GC-content and it has long been thought that Plasmodium falciparum, the virulent malaria parasite of humans, has the most AT-biased eukaryotic genome. Here, I perform comparative genomic analyses of the most AT-rich eukaryotes sequenced to date, and show that the avian malaria parasites Plasmodium gallinaceum, P. ashfordi, and P. relictum have the most extreme coding sequences in terms of AT-bias. Their mean GC-content is 21.21, 21.22 and 21.60 %, respectively, which is considerably lower than the transcriptome of P. falciparum (23.79 %) and other eukaryotes. This information enables a better understanding of genome evolution and raises the question of how certain organisms are able to prosper despite severe compositional constraints