Methodology for fish biodiversity monitoring with environmental DNA metabarcoding:The primers,databases and bioinformatic pipelines

Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.

Environmental barcoding of the ectomycorrhizal fungal genus Cortinarius

Understanding the role of ectomycorrhizal fungi in plant communities is hampered by a lack of knowledge about fungal diversity.DNA barcoding of the ectomycorrhizal fungal genus Cortinarius was used to compare fungal diversity in soil from four plant communities:(i)Nothofagus forest(where Cortinarius is common and diverse),(ii)Kunzea forest(where Cortinarius is present but with low diversity),(iii)a Pinus radiata plantation(Cortinarius is not thought to be present)and(iv)a sub-Antarctic island(where known ectomycorrhizal hosts are absent).PCR primers specific for the ITS region of Cortinarius species were developed.Specificity was tested in vitro and in silico against DNA from basidiocarps of Cortinarius and non-Cortinarius species.The primers were tested for their ability to amplify Cortinarius DNA in soil from forests of the three ectomycorrhizal forest communities and a range of soils from the ectomycorrhiza-free subantarctic Campbell Island.High diversity of Cortinarius was associated with soil of all three ectomycorrhizal communities,despite Cortinarius being previously unrecorded from Pinus.Soil from all three communities share some ectomycorrhizal fungi(including fungi shared between native and exotic hosts),having implications for community succession,introduction of exotic fungi and biodiversity assessment.No Cortinarius was detected from Campbell Island samples.The validated molecular protocol assessed species diversity in a rapid and cost effective way.Baseline biodiversity assessment based on DNA barcoding is more effective at detecting diversity than traditional methods,but requires careful consideration of the difference between ectomycorrhizal fungal diversity in soil versus root-tips.

Stable oligonucleotide-functionalized gold nanosensors for environmental biocontaminant monitoring

The global propagation of environmental biocontaminants such as antibiotic resistant pathogens and their antibiotic resistance genes（ARGs） is a public health concern that highlights the need for improved monitoring strategies. Here, we demonstrate the environmental stability and applicability of an oligonucleotide-functionalized gold nanosensor. The mec A ARG was targeted as model biocontaminant due to its presence in clinically-relevant pathogens and to its emergence as an environmental contaminant.mec A-specific nanosensors were tested for antibiotic resistance gene（ARG） detection in ARG-spiked effluent from four wastewater treatment plants（WWTPs）. The mec A-specific nanosensors showed stability in environmental conditions and in high ionic strength（[MgCl_2] 〈 50 m M）, and high selectivity against mismatched targets. Spectrophotometric detection was reproducible with an LOD of 70 pM（≈ 4 × 10~7 genes/μL）, even in the presence of interferences associated with non-target genomic DNA and complex WWTP effluent. This contribution supports the environmental applicability of a new line of cost-effective, field-deployable tools needed for wide-scale biocontaminant monitoring.

Impact of anthropogenic activities on changes of ichthyofauna in the middle and lower Xiang River

With the population increasing,fish communities,as important components in the river system,were inescapably impacted by human activities.To investigate these impacts,we characterized the fish community’s composition by environmental DNA metabarcoding in the urban and suburban sites along Xiang River in central China.The results showed that 32 species were identified,and most species were from Cypriniform.The analysis indicated no significant differences in fish communities among the three urban areas.However,significant differences were observed between the bank solidified and non-solidified areas,which indicated that the channelization significantly influenced the biodiversity and abundances.An alien species,Clarias gariepinus,was discovered in all examined sites,and it was negatively associated with ten native species.Furthermore,human populations and acidification were also negatively related to diversity.Our findings clearly showed that the consequences of anthropogenic activities shaped ichthyofauna and caused biodiversity loss in the urban river.

Biodiversity of freshwater ciliates(Protista,Ciliophora)in the Lake Weishan Wetland,China:the state of the

Ciliates are core components of the structure of and function of aquatic microbial food webs.They play an essential role in the energy flow and material circulation within aquatic ecosystems.However,studies on the taxonomy and biodiversity of freshwater ciliates,especially those in wetlands in China are limited.To address this issue,a project to investigate the freshwater ciliates of the Lake Weishan Wetland,Shandong Province,commenced in 2019.Here,we summarize our findings to date on the diversity of ciliates.A total of 187 ciliate species have been found,94 of which are identified to species-level,87 to genus-level,and six to family-level.These species show a high morphological diversity and represent five classes,i.e.,Heterotrichea,Litostomatea,Prostomatea,Oligohymenophorea,and Spirotrichea.The largest number of species documented are oligohymenophoreans.A comprehensive database of these ciliates,including morphological data,gene sequences,microscope slide specimens and a DNA bank,has been established.In the present study,we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species.Most of these species are recorded in China for the first time and more than 20%are tentatively identified as new to science.Additionally,an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed.