Long-Term Effects of Climate and Litter Chemistry on Rates and Stable Fractions of Decomposing Scots Pine and Norway Spruce Needle Litter—A Synthesis

We have reviewed information on early-, late- and limit-value decomposition stages for litter of Norway spruce (Picea abies) and Scots pine (Pinus silvestris). This synthesis covers c 16 studies/papers made along a climatic gradient; range in mean annual temperature (MAT) from −1 to +7 °C and mean annual precipitation (MAP) from 425 to 1070 mm. Scots pine has an early stage dominated by carbohydrate decomposition and a late stage dominated by decomposition of lignin; Norway spruce has just one stage dominated by lignin decomposition. We used data for annual mass loss to identify rate-regulating factors in both stages; climate data, namely, MAT and MAP, as well as substrate properties, namely, nitrogen (N), acid unhydrolyzable residue (AUR), manganese (Mn). Early-stage decomposition for Scots pine litter was dominated positively by MAT; the late stage was dominated negatively by MAT, N, and AUR, changing with decomposition stage; there was no effect of Mn. Norway spruce litter had no early stage; decomposition in the lignin-dominated stage was mainly negative to MAP, a negative relationship to AUR and non-significant relationships to N and MAT. Mn had a positive relationship. Limit values for decomposition, namely, the accumulated mass loss at which decomposition is calculated to be zero, were related positively to Mn and AUR for Scots pine litter and negatively to AUR for Norway spruce litter. With different sets of rate-regulating factors as well as different compounds/elements related to the limit values, the decomposition patterns or pathways are different

Long-Term Effects of Climate and Litter Chemistry on Rates and Stable Fractions of Decomposing Scots Pine and Norway Spruce Needle Litter—A Synthesis

We have reviewed information on early-, late- and limit-value decomposition stages for litter of Norway spruce (Picea abies) and Scots pine (Pinus silvestris). This synthesis covers c 16 studies/papers made along a climatic gradient; range in mean annual temperature (MAT) from −1 to +7 °C and mean annual precipitation (MAP) from 425 to 1070 mm. Scots pine has an early stage dominated by carbohydrate decomposition and a late stage dominated by decomposition of lignin; Norway spruce has just one stage dominated by lignin decomposition. We used data for annual mass loss to identify rate-regulating factors in both stages; climate data, namely, MAT and MAP, as well as substrate properties, namely, nitrogen (N), acid unhydrolyzable residue (AUR), manganese (Mn). Early-stage decomposition for Scots pine litter was dominated positively by MAT; the late stage was dominated negatively by MAT, N, and AUR, changing with decomposition stage; there was no effect of Mn. Norway spruce litter had no early stage; decomposition in the lignin-dominated stage was mainly negative to MAP, a negative relationship to AUR and non-significant relationships to N and MAT. Mn had a positive relationship. Limit values for decomposition, namely, the accumulated mass loss at which decomposition is calculated to be zero, were related positively to Mn and AUR for Scots pine litter and negatively to AUR for Norway spruce litter. With different sets of rate-regulating factors as well as different compounds/elements related to the limit values, the decomposition patterns or pathways are different

Molecular Diversity of Hard Tick Species from Selected Areas of a Wildlife-Livestock Interface Ecosystem at Mikumi National Park, Morogoro Region, Tanzania

Ticks are one of the most important arthropod vectors and reservoirs as they harbor a wide variety of viruses, bacteria, fungi, protozoa, and nematodes, which can cause diseases in human and livestock. Due to their impact on human, livestock, and wild animal health, increased knowledge of ticks is needed. So far, the published data on the molecular diversity between hard ticks species collected in Tanzania is scarce. The objective of this study was to determine the genetic diversity between hard tick species collected in the wildlife-livestock interface ecosystem at Mikumi National Park, Tanzania using the mitochondrion 16S rRNA gene sequences. Adult ticks were collected from cattle (632 ticks), goats (187 ticks), and environment (28 ticks) in the wards which lie at the border of Mikumi National Park. Morphological identification of ticks was performed to genus level. To identify ticks to species level, molecular analysis based on mitochondrion 16S rRNA gene was performed. Ticks representing the two genera (Hyalomma and Rhipicephalus) were identified using morphological characters. Six species were confirmed based on mitochondrion 16S rRNA gene, including Rhipicephalus microplus, Rhipicephalus evertsi, Hyalomma rufipes, Hyalomma truncatum, Hyalomma marginatum, and Hhyalomma turanicum. The presence of different clusters of tick species reflects the possible biological diversity of the hard ticks present in the study region. Further studies are however required to quantify species of hard ticks present in the study region and the country in general over a larger scale

Characterization of Pipistrellus pygmaeus Bat Virome from Sweden

Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species

House crickets (Othroptera: Gryllidae: Acheta domesticus) reared in small-scale laboratory conditions harbour limited viral flora

Insects, such as crickets, are being used as a viable food source in many regions of the world, given their nutritional value for human and animal consumption. This study investigated the viral communities present in European house crickets and whether feed influences the composition of the crickets’ virome. The crickets were reared under environmentally controlled conditions and fed fresh red clover (fresh), red clover haylage (haylage), red clover hay (hay) or control feed. The viral metagenomic analysis of six replicates from each feed treatment showed that only a few reads were classified as viruses, mainly assigned to phages and insect-related viruses. A significant difference (PXinmoviridae, Polydnaviridae, Metaviridae, unclassified and ‘other’ viruses were also found in all the feed treatments. The results from this study may indicate that the feed for the crickets determines the richness of the viral flora of crickets, but overall, very few viral reads were identified, making it hard to draw any conclusion regarding the impact of the feed on viral richness

Development of an in situ assay for simultaneous detection of the genomic and replicative form of PCV2 using padlock probes and rolling circle amplification

<p>Abstract</p> <p>Background</p> <p>In this study we utilized padlock probes and rolling circle amplification as a mean to detect and study the replication of porcine circovirus type 2 (PCV2) in cultured cells and in infected tissue. Porcine circovirus type 2 is a single-stranded circular DNA virus associated with several severe diseases, porcine circovirus diseases (PCVD) in pigs, such as postweaning multisystemic wasting syndrome. The exact reason and mechanisms behind the trigger of PCV2 replication that is associated with these diseases is not well-known. The virus replicates with rolling circle replication and thus also exists as a double-stranded replicative form.</p> <p>Results</p> <p>By applying padlock probes and rolling circle amplification we could not only visualise the viral genome but also discriminate between the genomic and the replicative strand in situ. The genomic strand existed in higher numbers than the replicative strand. The virus accumulated in certain nuclei but also spread into the cytoplasm of cells in the surrounding tissue. In cultured cells the average number of signals increased with time after infection.</p> <p>Conclusions</p> <p>We have developed a method for detection of both strands of PCV2 in situ that can be useful for studies of replication and in situ detection of PCV2 as well as of DNA viruses in general.</p

Bornaviruses in naturally infected Psittacus erithacus in Portugal: insights of molecular epidemiology and ecology

Background: The genus Orthobornavirus comprises non-segmented, negative-stranded RNA viruses able to infect humans, mammals, reptiles and various birds. Parrot bornavirus 1 to 8(PaBV-1 to 8) causes neurological and/or gastrointestinal syndromes and death on psittacines. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a death of two female Psittacus erithacus(grey parrot). Methods and Results: Both parrots were submitted for a complete standardised necropsy. Tissue samples were analysed by PCR. The findings in necropsy were compatible with bornavirus infection. Analysis revealed PaBV-4 related with genotypes detected in captive and in wild birds. The N and X proteins of PaBV-4 were more related to avian bornaviruses, while phosphoprotein was more related to variegated squirrel bornavirus 1 (VSBV-1). Within the P gene/phosphoprotein a highly conserved region between and within bornavirus species was found. Conclusions: Portugal is on the routes of the intensive world trade of psittacines. Broad screening studies are required to help understanding the role of wild birds in the emergence and spread of pathogenic bornaviruses. PaBV-4 phosphoprotein is closer to VSBV-1 associated with lethalencephalitis in humans than with some of the avian bornaviruses. The highly conserved P gene/phosphoprotein region is a good target for molecular diagnostics screenings

Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing

Peste-des-petits-ruminants virus (PPRV) is currently the focus of a control and eradication program. Full genome sequencing has the opportunity to become a powerful tool in the eradication program by improving molecular epidemiology and the study of viral evolution. PPRV is prevalent in many resource-constrained areas, with long distances to laboratory facilities, which can lack the correct equipment for high-throughput sequencing. Here we present a protocol for near full or full genome sequencing of PPRV. The use of a portable miniPCR and MinION brings the laboratory to the field and in addition makes the production of a full genome possible within 24 h of sampling. The protocol has been successfully used on virus isolates from cell cultures and field isolates from tissue samples of naturally infected goats