Soil microbial communities are sensitive to differences in fertilization intensity in organic and conventional farming systems

Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic and integrated farming, can provide numerous benefits for soil quality but also compromise the environment by polluting soils and producing greenhouse gases through animal husbandry. The need for reduced stocking density is inevitably accompanied by lower FYM inputs, but little research is available on the impact of these effects on the soil microbiome. We collected soil samples from winter wheat plots of a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities and measured soil quality parameters and microbial community diversity through DNA metabarcoding. High-input fertilization, corresponding to 1.4 livestock units (LU) improved the soil's nutritional status and increased soil microbial biomass and respiration when compared to low-input at 0.7 LU. Bacterial and fungal α-diversity was largely unaffected by fertilization intensity, whereas their community structure changed consistently, accompanied by an increase in the bacterial copiotroph-to-oligotroph ratio in high-input systems and by more copiotrophic indicator OTUs associated with high than low-input. This study shows that reduced nutrient availability under low-input selects oligotrophic microbes efficiently obtaining nutrients from various carbon sources; a potentially beneficial trait considering future agroecosystems.

The swan genome and transcriptome, it is not all black and white

BACKGROUND

The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.

RESULTS

Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.

CONCLUSION

Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

Reference genomes for conservation

High-quality reference genomes for non-model species can benefit conservation.

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

BACKGROUND

The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.

FINDINGS

This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.

CONCLUSIONS

This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

BACKGROUND

Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of genes. In this article, we present and describe the Avian Immunome DB (AVIMM) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K ("Bird 10,000 Genomes") consortium's whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for AVIMM.

CONSTRUCTION AND CONTENT

A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the "seed" for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. AVIMM is supplemented by a command-line interface and a web front-end to query the database.

UTILITY AND DISCUSSION

The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. AVIMM is publicly accessible at https://avimm.ab.mpg.de .

Integrin alpha E(CD103)beta 7 mediates adhesion to intestinal microvascular endothelial cell lines via an E-cadherin-independent interaction

Integrins are important for T cell interactions with endothelial cells. Because the integrin alpha(E)beta(7) is expressed on some circulating gut-homing T cells and as T cell numbers are reduced in the intestinal lamina propria of alpha(E)-deficient mice, we evaluated whether alpha(E)beta(7) mediates binding to intestinal endothelial cells. We found that anti-alpha(E)beta(7) mAbs partially blocked the binding of cultured intraepithelial T cells to human intestinal microvascular endothelial cells (HIMEC). Furthermore, alpha(E)beta(7)-transfected K562 cells bound more efficiently than vector-transfected K562 cells to HIMEC. Finally, HIMEC bound directly to an alpha(E)beta(7)-Fc fusion protein. These interactions were partially blocked by anti-alpha(E)beta(7) mAbs, and endothelial cell binding to the alpha(E)beta(7)-Fc was dependent upon the metal ion-dependent adhesion site within the alpha(E) A domain. Of note, the HIMEC lacked expression of E-cadherin, the only known alpha(E)beta(7) counterreceptor as assessed by functional studies, flow cytometry, and RT-PCR. Thus, HIMEC/alpha(E)beta(7) binding was independent of E-cadherin. In addition, this interaction appeared to be tissue selective, as HIMEC bound to the alpha(E)beta(7)-Fc, whereas microvascular endothelial cells from the skin did not. Finally, there was evidence for an alpha(E)beta(7) ligand on intestinal endothelial cells in vivo, as alpha(E)beta(7) expression enhanced lymphocyte binding around vessels in the lamina propria in tissue sections. Thus, we have defined a novel interaction for alpha(E)beta(7) at a nonepithelial location. These studies suggest a role for alpha(E)beta(7) in interactions with the intestinal endothelium that may have implications for intestinal T cell homing or functional responses.

Do nifedipine and verapamil potentiate the cardiac toxicity of magnesium sulfate?

We hypothesized that verapamil and nifedipine would potentiate the cardiac toxicity of magnesium in a dose-dependent manner. The hypothesis was tested in the isolated perfused rat heart model (Langendorff's apparatus) with Sprague-Dawley rats. After excision of hearts, each heart was exposed to increasing doses of verapamil and nifedipine followed by magnesium sulfate. Heart rate, contractility, and left ventricular systolic pressure were measured. Nifedipine and verapamil infusion in this model caused dose-dependent decreases in all three parameters measured (p values 0.05 to 0.01). The addition of magnesium sulfate potentiated these dose-dependent decreases (p values 0.01 to 0.0002). Nifedipine and verapamil caused similar depression at equivalent doses. Nifedipine and verapamil cause dose-dependent cardiac depression that is potentiated by the addition of magnesium sulfate in the isolated perfused rat heart. Caution is called for when magnesium sulfate and calcium channel blockers are administered in combination.