Comparison of fish communities using environmental DNA metabarcoding and capture methods in a plateau Erhai Lake,China

Environmental DNA(eDNA)has been used as an important tool for fish diversity analysis,which can greatly solve the problems in traditional survey methodology.However,little work has been done on the actual monitoring accuracy of eDNA.In this study,we analyzed the current status of fish resources in Erhai Lake in Yunnan,SW China,by dividing the lake into three sectors according to habitat differences,and compared the results of eDNA and traditional capture methods to investigate the shortcomings of the current analysis of eDNA results.A total of 27 fish species were detected by eDNA and traditional capture methods,including 20 and 19 fish species,respectively,and additional differences in fish composition between the two methods.The alpha diversity showed higher fish abundance and lower fish diversity by eDNA method compared to the traditional capture method,demonstrating that eDNA was not superior for use in fish diversity analysis.Fish community similarity analysis showed that community differences were generally significant for eDNA(P<0.05).RDA analysis indicated that environmental factors did not significantly affect fish communities monitored by the eDNA method.However,water temperature,aquatic plants,and water depth had significant(P<0.05)effects on fish communities in the traditional capture method,suggesting that eDNA results are insensitive to the effects of environmental factors.Our results illustrate the effectiveness of eDNA in fish identification and the issues in quantification compared to traditional capture methods.Therefore,combining eDNA with traditional methods is a more effective method for analyzing eDNA metabarcoding,following which the protocols of both quantitative methods can be designed to explore the regularity of eDNA quantification.

Assessment of the Characteristics of Demersal Fish Communities Using Species-and Trait-Based Approaches in the Coastal Habitats Along Rongcheng Bay,Shandong Peninsula,China

Biodiversity declines have motivated many studies on the relationship between species diversity and ecosystem functioning.In this study,we described the spatial-temporal characteristics of demersal fish communities along a coastal habitat in Rongcheng Bay,Shandong Peninsula,China with both species-based and biological trait-based approaches.The field survey was carried out monthly using traps from April to October of 2018,and divided into three seasons(spring:April and May;summer:June,July and August;autumn:September,October and November).The study area included five distinct habitats:seagrass bed,natural rocky reef,bare sand,artificial reef together with natural rocky reef,and artificial reef together with bare sand.We analyzed the fish communities with three taxonomic diversity indices,including Shannon-Wiener,Simpson,and Pielou Evenness,as well as four functional diversity indices,including FRic,FEve,FDiv,and FDis,based on 7 functional groups which are categorized into 27 traits.The results showed that there were no significant differences in taxonomic diversity indices among different habitats in the three seasons.However,significant differences were found in the functional richness of fish communities among different habitats in three seasons.Seagrass bed represented the highest functional richness in spring and autumn.This study demonstrates that seagrass bed is very important in enhancing the functional diversity of fish communities in a complex habitat.The study also indicates that the combination of taxonomic diversity and functional diversity will provide a more detailed description of the characteristics of fish communities.

Composition of fish communities in an intertidal salt marsh creek in the Changjiang River estuary,China

Fish communities in a （third-order） intertidal creek in Dongtan marsh in the Changjiang （Yangtze） River estuary were investigated seasonally for one year. A total of 1 996 fish specimens （10 967.8 g） comprising 26 species and 15 families were collected. Abundances of fish communities in the intertidal salt marsh creek were primarily dominated by Boleophthalmus pectinirostris （19.8%）, Collichthys lucidus （18.6%）, Periophthalmus magnuspinnatus （18.2%）, Liza haematocheilus （17.9%）, and secondarily by Mugilogobius abel （8.5%）, L. carinatus （7.2%）, Odontamblyopus lacepedii （4.3%）, and Acanthogobius ommaturus （3.9%）; another 18 species were present only occasionally. Non-MDS ordination and SIMPER analysis indicated that there were two fish communities in the intertidal salt marsh creek. In spring, the communities were dominated by B. pectinirostris, P. magnuspinnatus, C. lucidus and M. abei; in summer, autumn, and winter by L. haematocheilus, L. carinatus, A. ommaturus and O. lacepedii. Some species showed strong habitat selection; L. carinatus and P magnuspinnatus were distributed mainly in the upper and middle creek, while B. pectinirostris, M. abei and O. lacepedii inhabited the middle and lower creek. The study indicated that the salt marshes of the Changjiang River estuary are an important nursery and feeding habitat for many fishes and should be protected.

Status and historical changes in the fish community in Erhai Lake

Erhai Lake is the second largest freshwater lake on the Yunnan Plateau, Southwest China. In recent decades, a number of exotic fish species have been introduced into the lake and the fish community has changed considerably. We evaluated the status of the fish community based on surveys with multimesh gillnet, trap net, and benthic fyke-net between May 2009 and April 2012. In addition, we evaluated the change in the community using historical data （1952-2010） describing the fish community and fishery harvest. The current fish community is dominated by small-sized fishes, including Pseudorasbora parva, Rhinogobius giurinus, Micropercops swinhonis, Hemiculter leucisculus, and Rhinogobius cliffordpopei. These accounted for 87.7% of the 22 546 total specimens collected. Omnivorous and carnivorous species dominated the community. A canonical correspondence analysis （CCA） plot revealed that the distribution of fishes in the lake is influenced by aquatic plants, water temperature, pH, and season. The abundance of indigenous species has declined sharply, and a majority of endemic species have been extirpated from the lake （a decrease from seven to two species）. In contrast, the number of exotic species has increased since the 1960s to a total of 22 at present. The fishery harvest decreased initially following the 1960s, but has since increased due to the introduction of non-native fish and stocking of native fish. The fishery harvest was significantly correlated with total nitrogen, not total phosphorus, during the past 20 years. Based on our results, we discuss recommendations for the restoration and conservation of the fish resources in Erhai Lake.

Fish community diversity in the middle continental shelf of the East China Sea

The status of fishery stocks in the coastal waters of China is far from ideal, mainly due to climate change and the impacts of human activities （e.g., pollution and overfishing）. Thus, the restoration and protection of fishery resources have become critical and complex. The stability and balanced structure of the fish community is a basic foundation for the protection of fishery resources. Based on data collected from bottom trawls by the R/V Beidou in continental shelf of the East China Sea in November 2006 and February 2007, changes in the composition and diversity of fish species and functional groups were analyzed. The research area was divided into offshore waters and inshore waters by the two-way indicator species analysis （TWIA）. The results showed that the dominant species were different between offshore waters and inshore waters and also varied with the survey time. The most abundant family was Sciaenidae and Teraponidae in November 2006, Sciaenidae, Engraulidae and Triglidae were most abundant in February 2007. The species belonged mainly to mobile piscivores （G6）, benthivores/piscivores （G4）, benthivores （G3） and planktivores （G1）, and the dominant species in November 2006 were commercial species （e.g. Larimichthys polyactis and Trichiurusjaponicus）, but small-sized species were dominant in February 2007 （e.g., Harpadon nehereus, Benthosema pterotum, Champsodon capensis, and Acropoma japonieum）. The species diversity showed a similar trend as the functional group diversity. Stations with higher diversity were mainly distributed in inshore waters in February 2007, whereas higher diversity was found in offshore waters in November 2006. The highest biomass and species number were found in G6 group, followed by the G4, G5 and GI groups. The distribution of the number of individuals of each functional group showed the opposite trend as that of the biomass distribution. In addition, the size spectra were mainly concentrated around 3-29 cm, and the individual number of fish species gradually decreased with the increase in body size, but the relative biomass showed a moderate fluctuation in each size class. These changes showed that species with faster growth rate and earlier maturity age became dominant in continental shelf of the East China Sea. So the variations in biological characteristics of fish should be fully considered in maintaining sustainable utilization of fishery resource.

Temporal and spatial variation of fish assemblages in Dianshan Lake, Shanghai, China

Using multi-mesh gillnets and trawls, the fish communities in Dianshan Lake at 6 stations from Oct. 2009 to Jul. 2010 were investigated seasonally to reveal the biodiversity and its spatial and temporal distribution patterns. The long-term changes in their structural characteristics were then analyzed to identify the main infl uencing factors and several measures for lake restoration were put forward. Thirty six species, belonging to 9 family and 30 genera, were collected, amongst which, the order Cypriniformes accounted for 61.1% of the total species number. In terms of importance value, Cypriniformes was the predominant group, Coilia nasus the dominant species, while Cyprinus carpio and Rhinogobius giurinus were the subdominant taxa. The community types did not differ among stations, but between seasons. There were no significant differences between seasons and among stations in species diversity, but richness differed both spatially and seasonally. Along with the process of eutrophication and the drastic reduction of the area colonized by macrophytes from 1959 to 2009–2010, the fish diversity declined markedly, and species numbers of herbivores and piscivores declined proportionately more than those of invertivores, omnivores, and planktivores. The decline of potamophilus and river-lake migratory fish was more marked than those of sedentary, river-sea migratory, and estuarine fishes. Eutrophication concomitant with sharp reduction of macrophyte area and overfishing may be the main reasons for the decline in fish diversity in Dianshan Lake.

Study on fish community structure in the Zhujiang Estuaryand its adjacent waters

Based on data of demersal trawl Samples from 1987 to 1988 in the Zhujiang Estuary and its adjacent waters, relationships between fish community and environmental factors are studied by using clssification , MDS ordina-tion and several community parameters. The results shaw that the distribution of fish shoes is zoned by salinty anddivided into three types. The freshwater community which is restricted in the Lianhua Hill - Humen waterway is sim-ple and stable, the coastal community which lives in the shallow waters is complex, and the estuary community whichis idenhfied in the Lingdingyang area and affected by Physical and ecological pinemore greatly greatly has obvious seasonalvariations.

Determination of the Fish Community Structure of an Intertidal Rocky Zone of the Pacific Coast of Baja California Sur

The intertidal zone (also known as seashore) are transition areas between land and sea, that are greatly influenced by the tide cycle, therefore, environmental parameters, such as temperature and salinity, oscillate according to the periods in which these areas are exposed to air. Intertidal zones are highly diverse, which makes them key ecosystems for the development of sea life (both flora and fauna) exposed to drastic environmental change. The 59 visual censuses campaigns were carried out during the full moon of each month from 2015 to 2019. Temperature, salinity and dissolved oxygen were recorded during each visual census and showed variations between years. Temperature showed two distinct seasons, warm and cold. A total of 14,995 organisms were recorded, belonging to 30 species, 28 genera, 15 families, five orders and one class. Ecological indices like species richness (SR), Shannon-Wiener’s diversity (H') and Fisher’s alpha (α-Fisher) showed significant differences between years, 2015 and 2016 recorded as the most diverse years, while the lowest values were recorded in 2019. Therefore, fish communities of tide pools showed to be highly diverse, with 30 species recording similar relative abundances, and according to the BVI, only 11 species were dominant. Spatio-temporal variations of temperature, salinity and dissolved oxygen were highly correlated to changes in fish community structure, and the dominance of certain species, which are of great importance for the structure and dynamic of the tide pool communities. Therefore, the aim of the present study was to determine the fish community structure of tide pools during the low tide in the intertidal zone of a locality known as El Faro, on the west coast of La Paz, B. C. S., Mexico.

Decommissioning of Mature Oil Fields and Artisanal Fisheries： The Case of Todosos Santos Bay, Brazil

Consequences of decommissioning oil fields on artisanal fishing activities are still little known in the literature. This paper is intended to shed some light on a process of dismantling and sinking of oil and gas structures in shallow waters, with severe disturbing impacts on low income artisanal fishing activities. From a socio-economic perspective, the relationship of oil industry with local communities is described, with the main perceived problems pointed out in local fishermen leadership perspective. The notions of ＂damages＂ and ＂mitigation＂ used by the oil industry are discussed in connection to the expansion and dismantling of oil installations during the past 20 yrs. A comparative view of oil fields decommissioning in Europe and Brazil during the late 1990s suggests the need to review transparency and social commitment standards which have been far less prominent in this Brazilian case. The authors believe that the Brazilian oil industry has acquired a social and environmental debt towards the whole society, as far as it has been unable to establish a clear and effective process for decommissioning their oil installations within the artisanal fishing areas of the Todosos Santos Bay. Furthermore, the discussion of fair and specific compensations has been avoided, which otherwise would be instrumental to regain local economic conditions found among fishermen just few decades ago.

Functional Diversity of the Fish Community Associated to Soft-Bottoms in the Lagoon of La Paz B.C.S., México

There has been an increase of community studies that incorporate the use of functional diversity indices. The incorporation of these indices in the analysis of marine communities is recent, however, could contribute with relevant information about the health of those communities. The lagoon of La Paz is a body of water located in La Paz, B.C.S., México. Despite its regional importance, there are not recent studies about its fish communities. Therefore, the aim of the present study was to analyze the temporal and spatial structure of the functional diversity of fish communities associated to soft bottoms, from August 2016 to July 2017, as well as important environmental variables. Functional diversity indices showed significant differences between months. Spatial analysis did not show significant differences perhaps due to low variability of the type of substrate. Temperature showed temporal differences as well. Therefore, temperature may be a limiting environmental variable for many fish species inhabiting coastal lagoons.

Angling of hybrid sunfish from a hatchery pond with potential implications for community fisheries

Hatcheries are frequently called upon to produce catchable-sized fish for stocking community fishing ponds.Desirable attributes of fish selected for stocking into community ponds are that they are easy to produce in a hatchery system to sizes anglers are interested in catching and they provide anglers with high catch rates once stocked.Hybrid sunfish[male Bluegill(Lepomis macrochirus)×female Green Sunfish(L.cyanellus)]have attributes that potentially make them attractive for use in community fishing ponds.We assessed initial angler catch rates of 100 stocked hybrid sunfish in a 0.12-ha hatchery pond and after being subjected to angling(four,1-hr catch-and-release fishing events with five anglers).We also investigated whether catch rates would change following a supplemental stocking of an additional 100 hybrid sunfish(four,1-hr catch-and-release fishing events with five anglers).The anal fin of each fish in the second stocking was hole punched to differentiate them from those of the first stocking and fish caught by anglers were hole punched in the caudal fin each time they were caught before being released back into the pond.Angler catch rates were highest during initial fishing events that followed stocking(9.2 fish/angler hr and 18.0 fish/angler hr)and substantially declined in subsequent events(≤3.4 fish/angler hr).Catches of the newly stocked fish and previously stocked fish contributed to the high catch following the supplemental stocking.Most(80%)of the fish were caught in the first 30 min of each event and 45%were caught during the first 10 min.Anglers were able to catch 88%of the fish from the first stocking and 67%from the second stocking at least once.No mortality occurred during the study as all fish were recovered when the pond was drained.Our results suggest that hybrid sunfish will potentially provide high initial catch rates following stocking into community ponds,but managers should expect reduced catch rates following initial fishing even without harvest.Additional stocking will be needed to provide periodic increases in angler catch rates even without harvest.

Evaluation of cone fishways to facilitate passage of small-bodied fish

Fishways are being provided more regularly than ever before and new designs are needed to provide passage for whole fish communities.Despite recent progress,fishways have frequently performed poorly,especially for small-bodied fish(i.e.10-100 mm long),which can form large aggregations below stream barriers.This was the genesis for the development of the cone fishway design,a new style of technical fishway which consists of a series of pre-fabricated cone-shaped concrete baffles installed laterally within a concrete channel.The cone design arose from the need to install rock ramp fishways at remote sites where rock was unavailable and where maintenance would be infrequent.The objective of the present study was to evaluate the suitability of the new cone fishway design to provide passage for small-bodied diadromous species(i.e.<100 mm long).Cone fishways were evaluated at three low head(e.g.<3 m high)case-study sites in tropical and temperate Australia and in total,45 species and 28,556 fish were collected.There was passage of a broad range of the target size-classes of small-bodied fish and individuals as small as nine mm could ascend.However,further work is needed to quantify the proportion of the small-bodied fish population in the river downstream which find and pass through the cone fishways.The most suitable experimental application of the cone fishway is at sites where there is:(i)a narrow(e.g.<0.4 m)headwater range,and(ii)where passage of small-bodied fish is a major ecological priority.Cone fishways provide a useful and novel option to improve passage of small-bodied fish,at appropriate sites,and contribute to a contemporary vision of restoration of whole fish communities.

Quantifying relations between altered hydrology and fish community responses for streams in Minnesota

Background:Altered hydrology is a stressor on aquatic life,but quantitative relations between specific aspects of streamflow alteration and biological responses have not been developed on a statewide scale in Minnesota.Best sub-sets regression analysis was used to develop linear regression models that quantify relations among five categories of hydrologic metrics(i.e.,duration,frequency,magnitude,rate-of-change,and timing)computed from streamgage records and six categories of biological metrics(i.e.,composition,habitat,life history,reproductive,tolerance,trophic)computed from fish-community samples,as well as fish-based indices of biotic integrity(FIBI)scores and FIBI scores normalized to an impairment threshold of the corresponding stream class(FIBI_BCG4).Relations between hydrology and fish community responses were examined using three hydrologic datasets that represented periods of record,long-term changes,and short-term changes to flow regimes in streams of Minnesota.Results:Regression models demonstrated significant relations between hydrologic explanatory metrics and fish-based biological response metrics,and the five regression models with the strongest linear relations explained over 70%of the variability in the biological metric using three hydrologic metrics as explanatory variables.Tolerance-based biological metrics demonstrated the strongest linear relations to hydrologic metrics.The most commonly used hydrologic metrics were related to bankfull flows and aspects of flow variability.Conclusions:Final regression models represent paired streamgage records and biological samples throughout the State of Minnesota and encompass differences in stream orders,hydrologic landscape units,and watershed sizes.Presented methods can support evaluations of stream fish communities and facilitate targeted efforts to improve the health of fish communities.Methods also can be applied to locations outside of Minnesota with continuous streamgage data and fish-community samples.

Comparative fish community structure among different types of enclosures of estuarine environments

This study explores the differences of fish assemblages in three macrotidal estuaries of Man-gyeong River Estuary(MRE),Geum River Estuary(GRE),and Han River Esturay(HRE)with similar ranges of seasonal water temperature that are diked with different levels of disconnection from freshwater discharge.The distribution of major species in the three estuaries could generally be grouped into three distinctive patterns based on their cumulative distribution with respect to the salinity gradient.The MRE was geographically closer to the GRE than to the HRE,but the fish community of the MRE more closely resembled that of the HRE.Increased freshness of the water inside the dike and the limit of coastal fish to the river may have led to this result.The results provide clues to how enclosure patterns of estuarine waters could affect fish communities over a long-term period.In addition,the information may provide guidance for how a fish community may return once environmental conditions are restored.

Influence of sampling frequency on detectability of fish community and fish species in a fishery-independent survey

Understanding the dynamics and regulation of a particular ecological process requires monitoring of the process at appropriate spatial and temporal scales.Information collected at an inappropriate spatiotemporal scale may be insufficient for capturing spatio-temporal dynamics of fish populations and community.In this study,a Monte Carlo method was developed to evaluate the detectability performances of different sampling frequencies,sampling timings and sampling intensities on fish community indices and fish species.Species richness indices tended to decrease with an increased sampling frequency,while species diversity indices had small changes in response to changes in sampling frequency.The diversity index was more likely to be influenced by the choice of sampling timing compared to the richness index.The total number of species,especially seasonal and rare species present in the simulated sampling,increased with sampling frequency.Although sampling frequency is more important than sampling intensity,sampling intensity is also important for the detectability of fish species.This study showed that sampling frequency and intensity could greatly influence the estimation of fish community.Choices of sampling timing,sampling frequency and intensity may result in different estimates of fish species compositions and community structure.It is very necessary to consider the importance of sufficient sampling frequency and intensity in a survey program.

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.