Metagenomic analysis decodes the fungal diversity of bio-dynamic preparations

Aim: Biodynamic farming system involves use of 8 different biodynamic preparations (BD 500-BD 507). Multi functionality of any ecosystem is due to its microbial diversity and community composition of microbes. So the present study was aimed to determine the total fungal population viz. unculturable ones, metagenomic analysis was done. Methodology: In the present study, 18S rDNA sequencing of V3-V4 amplicon regions was performed to identify and characterize fungal diversity, which existed in these preparations. Results: Alpha diversity was found to be maximum in BD506 with 868 OTU (operational taxanomic units) and minimum in BD507 with 254 OTU. At phylum level, the most abundant phylum was Ascomycota as recorded in 7 BD preparations with exception in the BD 500 (Unassigned). At genus level highest percentage of OTU abundance was observed for unassigned genus in all BD preparations, except Mortierella in BD 500 and BD 502; Microascus in BD 501 and BD504; Gymnoascus in BD503, Scedosporium in BD 505, Mucor in BD 506 and Hyphopichia in BD 507. On the basis of species diversity, BD502, 503 and 506 showed high percentage of OTU abundance for Mucor racemosus, while Mortierella oligospora was abundant in BD500, Dipodascus geotrichum in BD 501, Kernia pachypleura in BD504, Petriella setifera in BD505 and Hyphopichia burtonii in BD 507. Interpretation: This indicated a unqiue class of fungus predominating each type of BD preparation. Furthermore, a large proportion of unassigned fungi at phylum and genus level were detected in metagenome analysis which might have specific roles in contributing for their overall effectiveness of each kind of BD preparations.

Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5’UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3’UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

Comparative analysis of the bacterial community of the Patagonian lichen Peltigera frigida and its soil substrate

<p>The lichen microbiome includes a diverse community of organisms, spanning widely across the bacterial tree of life. Lichens have been proposed to form partially open symbiotic systems, in which some microorganisms may be transmitted along within lichen propagules, while others are acquired from the surrounding environmental community.</p><p>In this survey, we discuss the extent to which the lichen microbiome is connected to that of its immediate substrate. For this we sampled ten specimens of the Patagonian foliose cyanolichen <em>Peltigera frigida</em> and their underlying soil substrates in two forest sites of the Coyhaique National Reserve (Aysén Region, Chile). Using 16S metabarcoding with primers that exclude cyanobacteria, we identified a significant taxonomic divergence between the bacterial communities of lichens and substrates.</p><p>At the Phylum level, Proteobacteria (37% of relative abundance) are most abundant within lichens, while soil substrates are dominated by Acidobacteriota (39%). At the Genus level, some bacteria are significantly more abundant in lichens, such as <em>Sphingomonas</em> (8% in lichens vs 0.2% in substrates) or an unassigned genus of Chitinophagaceae (10% vs 2%). Conversely, genera like the unassigned acidobacterial genus SCN-69-37 (0.9% vs 12%) are more abundant in substrates.</p><p>Overall, our results are consistent with the idea that lichens shape their microbiome obtaining components from various sources, including reproductive propagules and the substrate on which they grow. Further experimental and ecological approaches are needed to assess the contribution of these microorganisms to the fitness of the symbiotic system.</p><p>Funding: FONDECYT 1181510.</p>

Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea mays L. var. DBK 177)

Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.25%, 30 min), resulting in a reduction of the cultivable-dependent fraction of seed-borne bacteria population, but not significantly detected by real-time PCR, microscopy, and biochemical analysis of the roots on germinated seeds. 16S rRNA sequencing revealed that the seed and root bacteriome exhibited similar diversity and did not differ in the structure concerning seed-disinfection. On the other hand, the abundance reduction of the genera f_Enterobacteriaceae_922761 (unassigned genus), Azospirillum, and Acinetobacter in disinfected-seed prior germination seems to display changes in prominence of several new taxa in the roots of germinated seeds. Interestingly, this reduction in the bacteriome negatively affected the germination speed and growth of maize plantlets. Additionally, bacteriome re-shape increased the maize var DKB 177 susceptible to the seed-borne plant pathogen Penicillium sp. Such changes in the natural seed-borne composition removed the natural barrier, increasing susceptibility to pathogens, impairing disinfected seeds to germinate, and develop. We conclude that bacteria borne in seeds modulate the relative abundance of taxa in the root, promote germination, seedling growth, and protect the maize against fungal pathogens.

First Report of a Mesonivirus and Its Derived Small RNAs in an Aphid Species Aphis citricidus (Hemiptera: Aphididae), Implying Viral Infection Activity

We report a new positive-sense single-stranded RNA (ss RNA+) virus from the brown citrus aphid Aphis citricidus. The 20,300 nucleotide (nt)-long viral genome contains five open-reading frames and encodes six conserved domains (TM2, 3CLpro, TM3, RdRp, Zm, and HEL1). Phylogenetic analysis and amino acid sequence analysis revealed this virus might belong to an unassigned genus in the family Mesoniviridae. The presence of the virus was also confirmed in the field population. Importantly, analysis of the virus-derived small RNAs showed a 22-nt peak, implying that viral infection triggers the small interfering RNA pathway as antiviral immunity in aphids. This is the first report of a mesonivirus in invertebrates other than mosquitoes.

Genomic and phylogenetic analysis of two novel bovine papillomaviruses, BPV-9 and BPV-10

Eight bovine papillomavirus (BPV) types, BPV-1–8, have been classified, based on genome nucleotide sequence similarities, in the genera Deltapapillomavirus (BPV-1 and -2), Epsilonpapillomavirus (BPV-5 and -8), Xipapillomavirus (BPV-3, -4 and -6) and an unassigned genus (BPV-7). We report here the complete genome sequence of two new BPV types isolated from separate epithelial squamous papilloma lesions on cattle teats. The genomes are 7303 and 7399 bp in length, respectively, and both have genetic organization and consensus motifs typical of papillomaviruses. A neighbour-joining phylogenetic tree revealed that both viruses cluster with BPV-3, -4 and -6. Nucleotide sequence identities of the BPV L1 major capsid protein of these two new BPVs with BPV-3, their closest relative, are 74.2 and 71.2 %, respectively. These results suggest that both viruses are new BPV types in the genus Xipapillomavirus, and they are designated BPV-9 and BPV-10.

Banana bunchy top virus. [Distribution map].

A new distribution map is provided for Banana bunchy top virus Viruses: Family unassigned: Genus Nanovirus Hosts: Musa spp. Information is given on the geographical distribution in ASIA, China, Fujian, Guangdong, Guangxi, Yunnan, India, Andhra Pradesh, Assam, Karnataka, Kerala, Maharashtra, Orissa, Tamil Nadu, Uttar Pradesh, Indonesia, Java, Kalimantan, Nusa Tenggara, Japan, Bonin Islands, Ryukyu Archipelago, Malaysia, Sarawak, Pakistan, Philippines, Sri Lanka, Taiwan, Vietnam, AFRICA, Burundi, Central African Republic, Congo, Congo Democratic Republic, Egypt, Gabon, Malawi, Rwanda, NORTH AMERICA, USA, Hawaii, OCEANIA, American, Samoa, Australia, New South Wales, Queensland, Fiji, Guam, New Caledonia, Samoa, Tonga, Tuvalu, Wallis and Futuna Islands.

Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant ‘potex-like’ viruses

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus Botrytis cinerea. The mycovirus Botrytis virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3′ terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant ‘tymo-’ and ‘potex-like’ viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in ‘tymo-’ and ‘potex-like’ replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant ‘potex-like’ viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3′-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant ‘potex-like’ virus group.