RNA viromes from terrestrial sites across China expand environmental viral diversity.

Environmental RNA viruses are ubiquitous and diverse, and probably have important ecological and biogeochemical impacts. Understanding the global diversity of RNA viruses is limited by sampling biases, dependence on cell culture and PCR for virus discovery, and a focus on viruses pathogenic to humans or economically important animals and plants. To address this knowledge gap, we generated metatranscriptomic sequence data from 32 diverse environments in 16 provinces and regions of China. We identified 6,624 putatively novel virus operational taxonomic units from soil, sediment and faecal samples, greatly expanding known diversity of the RNA virosphere. These newly identified viruses included positive-sense, negative-sense and double-strand RNA viruses from at least 62 families. Sediments and animal faeces were rich sources of viruses. Virome compositions were affected by local environmental factors, including organic content and eukaryote species abundance. Notably, environmental factors had a greater impact on the abundance and diversity of plant, fungal and bacterial viruses than of animal viromes. Our data confirm that RNA viruses are an integral part of both terrestrial and aquatic ecosystems.

Complete mitochondrial genome and the phylogenetic position of a new species, Johnius taiwanensis (Perciformes: Sciaenidae) from Chinese waters.

In this study, the complete mitogenome of a new species, Johnius taiwanensis (Chao et al. 2019) was obtained. Its mitogenome is 18,451 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. taiwanensis. The overall nucleotide composition is: 24.2% A; 18.0% C; 21.1% G, and 36.7% T. Sizes of the 22 tRNA genes range from 66 to 75 bp. Two start codons (ATG and GTG) and three stop codons (TAG, AGA and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 26 species (including J. taiwanensis) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. taiwanensis was placed as sister to the Trewavas croaker J. trewavasae of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.

Complete mitochondrial genome and the phylogenetic position of the blackmouth croaker Atrobucca nibe (Perciformes: Sciaenidae).

In this study, the complete mitogenome of the blackmouth croaker Atrobucca nibe was obtained. Its mitogenome is 16,842 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.2% A; 31.2% C; 16.4% G and 25.2% T. Sizes of the 22 tRNA genes range from 66 to 74 bp. One start codons (ATG) and three stop codons (TAG, AGA, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 20 species (including A. nibe) from the family Sciaenidae, all nodes were strongly supported. The result suggested that A. nibe was subsequent to the group with genera Otolithes, Chrysochir, Megalonibea, Pennahia, Nibea, Dendrophysa, and Johnius.

Complete mitochondrial genome and the phylogenetic position of the Caroun croaker Johnius carouna (perciformes: Sciaenidae).

In this study, the complete mitogenome of the Caroun croaker Johnius carouna was obtained. Its mitogenome is 18,752 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. carouna, same as another two Johnius species available in GenBank, J. distinctus (MF083699) and J. grypotus (KC491206). The overall nucleotide composition is: 24.2% A; 18.0% C; 21.4% G, and 36.4% T. Sizes of the 23 tRNA genes range from 67 to 75 bp. One start codons (ATG) and three stop codons (TAG, AGG, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 21 species (including J. carouna) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. carouna was placed as sister to the silver croaker J. grypotus of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.

[Biological process of phosphorus turnover in surface water body of Xiamen Harbor. II: Grazing pressure of copepod on phytoplankton].

To understand the roles of copepod in the biogeochemical cycling of phosphorus, gut fluorescence method was applied to examine in situ the grazing rate of copepod on the phytoplankton in Xiamen Time Station (XMTS) in May, August and November 2005 and March 2006. In the meanwhile, the abundance and species composition of copepod were investigated, and the grazing pressure of copepod on the phytoplankton was estimated. The results showed that the annual average grazing rate of copepod was 55.53 microg x m(-3) x d(-1), being the highest (108.98 microg x m(-3) x d(-1)) in autumn and the lowest (7.18 microg x m(-3) x d(-1)) in summer. Based on the estimation from our experimental data, the daily grazing rate of copepod populations on the phytoplankton in Xiamen Harbor was, on annual average, about 1.81% of the phytoplankton's standing stock, with the values in spring, summer, autumn, and winter being 3.22%, 0.06%, 3.52% and 0.46%, respectively.