Since 2005, advances in next-generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species-specific DNA barcodes has been a key application of next-generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next-generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis.© 2012 Blackwell Publishing Ltd.

翘嘴鲌具有很高的营养价值、经济价值和生态价值，近年来其野生资源趋于枯竭，因而掌握翘嘴鲌遗传多样性对于科学保护其种质资源具有重要意义。为了解太湖和洪泽湖翘嘴鲌种质资源遗传状况，通过线粒体Cyt b基因序列测定，分析了其群体的遗传多样性和遗传结构。结果显示，翘嘴鲌Cyt b基因全序列长度为1 141 bp，碱基A+T含量明显高于G+C含量。98条Cyt b序列共检测出29个变异位点，共定义29种单倍型，平均单倍型多样性指数（Hd）和核苷酸多样性指数（Pi）分别为0.923和0.002 74，平均核苷酸差异数（K）为3.127。太湖和洪泽湖群体的Hd分别为0.927和0.816，Pi分别为0.002 85和0.002 20，遗传多样性表现出高Hd、低Pi的特点。分子方差分析结果显示，群体内分子变异占比为15.01%，群体间分子变异占比为84.99%，两群体间遗传分化系数（Fst）为0.150 15（P<0.01），表明两群体间有显著性遗传分化。Tajima’s D中性检验结果为不显著性负值，Fu’s Fs中性检验结果为显著性负值，且歧点分布曲线为单峰型，表明翘嘴鲌在进化过程中经历过群体扩张事件。本研究结果为太湖和洪泽湖翘嘴鲌种质资源管理保护提供了数据资料。

为研究上海选育群体（SC）、浙江养殖群体（ZJ）和泰国野生群体（TL）3个罗氏沼虾群体的遗传多样性，实验对3个不同群体的线粒体COⅠ基因序列进行PCR扩增和测定。在长度为458 bp的COⅠ基因序列中，只检测到8个变异位点和4个单倍型；平均A+T含量（54.4%）高于G+C含量（45.7%）。遗传变异参数分析显示，单倍型多样性指数最高为TL群体（Hd=0.733），核苷酸多样性指数最高为ZJ群体（π=0.005）。AMOVA分析表明，来自群体间的遗传变异（74.5%）高于来自群体内的遗传变异（25.5%）。采用NJ法和UPMGA法构建的系统进化树的趋势一致，都显示SC群体和ZJ群体遗传关系最近，首先聚在一起成为一小支，然后再与TL群体聚为另一支。研究结果可为罗氏沼虾种质资源保护和利用提供参考。

Advances in detection of genetic material from species in aquatic ecosystems, including environmental DNA (eDNA), have improved species monitoring and management. eDNA from target species can readily move in streams and rivers and the goal is to measure it, and with that infer where and how abundant species are, adding great value to delimiting species invasions, monitoring and protecting rare species, and estimating biodiversity. To date, we lack an integrated framework that identifies environmental factors that control eDNA movement in realistic, complex, and heterogeneous flowing waters. To this end, using an empirical approach and a simple conceptual model, we propose a framework of how eDNA is transported, retained, and resuspended in stream systems. Such an understanding of eDNA dispersal in streams will be essential for designing optimized sampling protocols and subsequently estimating biomass or organismal abundance. We also discuss guiding principles for more effective use of eDNA methods, highlighting the necessity of understanding these parameters for use in future predictive modeling of eDNA transport.

The contributions of environmental DNA to ecology are reviewed, focusing on diet, trophic interactions, species distributions and biodiversity assessment. Environmental DNA has the potential to dramatically improve quantitative studies in these fields. Achieving this, however, will require large investments of time and money into developing the relevant databases, models, and software.© 2012 Blackwell Publishing Ltd.

环境DNA宏条形码（eDNA metabarcoding）技术通过提取水体、土壤、空气中的环境DNA,使用引物PCR扩增与高通量测序,进行物种鉴定与生物多样性评估。作为一种新的监测技术,相比于传统监测技术更加快捷、准确以及对自然环境的破坏小,因此在一定程度上改变了我们调查地球生物多样性的方式。本文综述了环境DNA宏条形码技术的发展历程与操作流程;归纳了在水体、土壤、空气环境中的应用现状,并总结了其独特的间接生物多样性监测方法,同时讨论了优势及存在的问题,以期能为后续生物多样性研究与监测研究提供新的思路和启发。

Environmental DNA (eDNA) studies show great promise for non-invasive surveys of aquatic organisms, but should account for imperfect detection and the influences of biotic and abiotic conditions on detection. We evaluated an eDNA protocol for Roanoke logperch (RLP) Percina rex, an endangered fish of the eastern United States occupying habitats ranging from cold, clear creeks to warm, turbid rivers. We assayed water samples from streams presumed likely to be occupied or unoccupied by RLP based on previous fish surveys. Data were analyzed using multi-scale occupancy models that estimated occurrence and detection probability at the scales of sites, replicate water filters, and replicate PCR reactions, and environmental influences on these probabilities. We detected RLP eDNA at 11 of 12 sites in occupied streams and no sites in presumed-unoccupied streams. In best-supported models, detection was positively related to an index of fish density, whereas other environmental factors had no consistent effects. This approach had a higher detection rate and lower sensitivity to sampling conditions than traditional techniques like snorkeling and electrofishing, suggesting it could provide a powerful tool for assessing the distribution of this and other rare fishes that occur across a wide range of fluvial habitats.

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)-based methods have been shown to be highly sensitive and cost-efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA-detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA-based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.© 2019 John Wiley & Sons Ltd.

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.

Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2-0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.© 2015 John Wiley & Sons Ltd.

. Estuaries are biogeochemical hot spots because they receive large inputs of nutrients and organic carbon from land and oceans to support high rates of metabolism and primary production. We synthesize published rates of annual phytoplankton primary production (APPP) in marine ecosystems influenced by connectivity to land – estuaries, bays, lagoons, fjords and inland seas. Review of the scientific literature produced a compilation of 1148 values of APPP derived from monthly incubation assays to measure carbon assimilation or oxygen production. The median value of median APPP measurements in 131 ecosystems is 185 and the mean is 252 g C m−2 yr−1, but the range is large: from −105 (net pelagic production in the Scheldt Estuary) to 1890 g C m−2 yr−1 (net phytoplankton production in Tamagawa Estuary). APPP varies up to 10-fold within ecosystems and 5-fold from year to year (but we only found eight APPP series longer than a decade so our knowledge of decadal-scale variability is limited). We use studies of individual places to build a conceptual model that integrates the mechanisms generating this large variability: nutrient supply, light limitation by turbidity, grazing by consumers, and physical processes (river inflow, ocean exchange, and inputs of heat, light and wind energy). We consider method as another source of variability because the compilation includes values derived from widely differing protocols. A simulation model shows that different methods reported in the literature can yield up to 3-fold variability depending on incubation protocols and methods for integrating measured rates over time and depth. Although attempts have been made to upscale measures of estuarine-coastal APPP, the empirical record is inadequate for yielding reliable global estimates. The record is deficient in three ways. First, it is highly biased by the large number of measurements made in northern Europe (particularly the Baltic region) and North America. Of the 1148 reported values of APPP, 958 come from sites between 30 and 60° N; we found only 36 for sites south of 20° N. Second, of the 131 ecosystems where APPP has been reported, 37% are based on measurements at only one location during 1 year. The accuracy of these values is unknown but probably low, given the large interannual and spatial variability within ecosystems. Finally, global assessments are confounded by measurements that are not intercomparable because they were made with different methods. Phytoplankton primary production along the continental margins is tightly linked to variability of water quality, biogeochemical processes including ocean–atmosphere CO2 exchange, and production at higher trophic levels including species we harvest as food. The empirical record has deficiencies that preclude reliable global assessment of this key Earth system process. We face two grand challenges to resolve these deficiencies: (1) organize and fund an international effort to use a common method and measure APPP regularly across a network of coastal sites that are globally representative and sustained over time, and (2) integrate data into a unifying model to explain the wide range of variability across ecosystems and to project responses of APPP to regional manifestations of global change as it continues to unfold.\n

Background: Plankton, including phytoplankton and zooplankton, are the main source of food for organisms in the ocean and form the base of marine food chain. As the fundamental components of marine ecosystems, plankton is very sensitive to environment changes, and the study of plankton abundance and distribution is crucial, in order to understand environment changes and protect marine ecosystems. This study was carried out to develop an extensive applicable plankton classification system with high accuracy for the increasing number of various imaging devices. Literature shows that most plankton image classification systems were limited to only one specific imaging device and a relatively narrow taxonomic scope. The real practical system for automatic plankton classification is even non-existent and this study is partly to fill this gap.Results: Inspired by the analysis of literature and development of technology, we focused on the requirements of practical application and proposed an automatic system for plankton image classification combining multiple view features via multiple kernel learning (MKL). For one thing, in order to describe the biomorphic characteristics of plankton more completely and comprehensively, we combined general features with robust features, especially by adding features like Inner-Distance Shape Context for morphological representation. For another, we divided all the features into different types from multiple views and feed them to multiple classifiers instead of only one by combining different kernel matrices computed from different types of features optimally via multiple kernel learning. Moreover, we also applied feature selection method to choose the optimal feature subsets from redundant features for satisfying different datasets from different imaging devices. We implemented our proposed classification system on three different datasets across more than 20 categories from phytoplankton to zooplankton. The experimental results validated that our system outperforms state-of-the-art plankton image classification systems in terms of accuracy and robustness.Conclusions: This study demonstrated automatic plankton image classification system combining multiple view features using multiple kernel learning. The results indicated that multiple view features combined by NLMKL using three kernel functions (linear, polynomial and Gaussian kernel functions) can describe and use information of features better so that achieve a higher classification accuracy.

为查明长湖浮游植物群落特征及其水环境影响因子, 并确定水体富营养化程度, 于2012年夏季对长湖浮游植物及相关环境因子进行调查检测分析, 运用藻类生物学法和综合营养状态指数法, 对长湖水体营养状态进行综合评定, 同时利用典范对应分析法(CCA)对浮游植物与环境因子的关系进行了分析。结果表明, 2012年夏季长湖浮游植物共有53种(含变种、变型), 隶属于7门41属, 其中以绿藻最多(24种, 占总数量的38.9%), 其次为蓝藻(15种, 占总数量的36.0%)和硅藻(7种, 占总数量的14.1%)。优势种(优势度指数大于0.02)共10种, 其中两栖颤藻(Oscillatoria amphibia)是4个区域的共有优势种, 最高优势度达0.72。浮游植物丰度为12.03 × 10 ⁶- 62.13 × 10 ⁶cell·L ^-1, 平均值为27.71 × 10 ⁶cell·L ^-1。浮游植物丰度的平面分布呈现圆心湖、海子湖、马洪台、庙湖依次降低的特点。浮游植物多样性指数变化范围为0.89-3.24, 均匀度指数变化范围为0.23-0.83。选取叶绿素a、总磷、总氮、透明度和化学需氧量5项参数计算得出综合营养化指数。通过藻类生物学法和综合营养状态指数法进行综合评价发现: 2012年夏季长湖处于中度富营养化到富营养化程度。典范对应分析表明: 浮游植物空间分布主要受总氮、总悬浮物、总磷、溶氧以及亚硝酸氮等环境因子的影响。针状蓝纤维藻(Dactylococcopsis acicularis)、两栖颤藻、席藻属(Phormidium)、鱼腥藻属(Anabeana)等蓝藻对总氮的需求较大。长湖各站点由于在不同程度上受到地形、人为干扰以及水动力条件的影响, 它们与环境因子的典范对应分析表现出明显的区域性。

In the drinking water reservoir ecosystem, phytoplankton and bacteria play important roles in shaping freshwater health and function. In this work, the associated bacterial community functional diversity during degradation of phytoplankton was determined using the substrate utilization profiling (BIOLOG) technique, meanwhile, the composition and concentration of phytoplankton were examined using a microscope. The results indicated that Euglena decreased 58.33% from 0 to 38 d, while the smallest degradation of Bacillariophyta was 20.19%. Average well color development (AWCD590nm) increased during the static periods from 0 to 38 d; however, the AWCD590nm of 18 and 38 d had no significant difference (p < 0.05). The Simpson’s index (D) was in accordance with Shannon’s diversity (H) and species richness(S); it was measured to be18 > 38 > 5 > 0 d. There were significant differences in the pattern and level of carbon sources used by the phytoplankton-associated bacteria. In addition, the principle component analyses (PCA) suggested that the first principle component (PC1) and the second principle component (PC2) explained 46.76% and 21.49% of the total variation for bacterial community, respectively. Redundancy analysis (RDA) revealed that cell abundance of phytoplankton was negatively correlated with the AWCD590nm, amino acids and other functional indexes. Therefore, the data suggest that there are differences in the phytoplankton-associated bacterial community functional diversity during different static stages of water samples collected from the drinking water reservoir.

Zooplankton provide a vital source of nutrition to a variety of fish and marine predators. Measuring the total lipid content of zooplankton provides important information about diet quality available to predators, revealing details about trophic dynamics and ecosystem status. We analyze the performance of a microplate assay, utilizing the sulfo-phospho-vanillin (SPV) reaction, to quantify the total lipid content of various large crustacean zooplankton in a rapid and high throughput manner. Pilot experiments were performed by measuring the total lipid content of purchased freeze-dried zooplankton ( and ) by both SPV and gravimetric analysis (low throughput and requires large sample size). The results of the SPV assay were not statistically different from gravimetric analysis for either species (> 0.05). Further, an inter-laboratory comparison study was performed to measure the total lipid content (% of wet mass) of field-collected Arctic and North Pacific zooplankton (copepods ( = 19) and euphausiids ( = 29)) of various species utilizing multiple analysis methods. Results from thin layer chromatography with flame ionization detection (TLC-FID) demonstrated that lipid classes in zooplankton samples varied in composition of steryl/wax esters (3-95%), triacylglycerols (1-52%), free-fatty acids (0.4-25%), sterols (0-4%) and polar lipids (1-42%). Despite this variation in lipid class composition among samples, the results of the SPV assay agreed well with gravimetric analysis. The mean absolute and relative differences between SPV and gravimetric analysis for all zooplankton lipids in this study were 1.0% and 11.6%, respectively. The SPV assay is rapid (<2 hours), high throughput (25 samples processed in parallel), low cost (supplies <$ 0.67 per sample), precise (inter assay CV = 6.9%, intra assay CV = 6.0%), sensitive (limit of detection < 1.7 micrograms of lipid per analysis), and accurate when calibrated with appropriate standards.

Marine zooplankton comprise a phylogenetically and functionally diverse assemblage of protistan and metazoan consumers that occupy multiple trophic levels in pelagic food webs. Within this complex network, carbon flows via alternative zooplankton pathways drive temporal and spatial variability in production-grazing coupling, nutrient cycling, export, and transfer efficiency to higher trophic levels. We explore current knowledge of the processing of zooplankton food ingestion by absorption, egestion, respiration, excretion, and growth (production) processes. On a global scale, carbon fluxes are reasonably constrained by the grazing impact of microzooplankton and the respiratory requirements of mesozooplankton but are sensitive to uncertainties in trophic structure. The relative importance, combined magnitude, and efficiency of export mechanisms (mucous feeding webs, fecal pellets, molts, carcasses, and vertical migrations) likewise reflect regional variability in community structure. Climate change is expected to broadly alter carbon cycling by zooplankton and to have direct impacts on key species.

In seasonal climates, dormancy is a common strategy that structures biodiversity and is necessary for the persistence of many species. Climate change will likely alter dormancy dynamics in zooplankton, the basis of aquatic food webs, by altering two important hatching cues: mean temperatures during the ice-free season, and mean day length when lakes become ice free. Theory suggests that these changes could alter diversity, hatchling abundances and phenology within lakes, and that these responses may diverge across latitudes due to differences in optimal hatching cues and strategies. To examine the role of temperature and day length on hatching dynamics, we collected sediment from 25 lakes across a 1800 km latitudinal gradient and exposed sediment samples to a factorial combination of two photoperiods (12 and 16 h) and two temperatures (8 and 12 °C) representative of historical southern (short photoperiod, warm) and northern (long photoperiod, cool) lake conditions. We tested whether sensitivity to these hatching cues varies by latitudinal origin and differs among taxa. Higher temperatures advanced phenology for all taxa, and these advances were greatest for cladocerans followed by copepods and rotifers. Although phenology differed among taxa, the effect of temperature did not vary with latitude. The latitudinal origin of the egg bank influenced egg abundance and hatchling abundance and diversity, with these latter effects varying with taxa, temperature and photoperiod. Copepod hatchling abundances peaked at mid-latitudes in the high temperature and long photoperiod treatments, whereas hatchling abundances of other zooplankton were greatest at low latitudes and high temperature. The overall diversity of crustacean zooplankton (copepods and cladocerans) also reflected distinct responses of each taxa to our treatments, with the greatest diversity occurring at mid-latitudes (~56 °N) in the shorter photoperiod treatment. Our results demonstrate that hatching cues differ for broad taxonomic groups that vary in developmental and life-history strategies. These differences are predicted to drive latitude-specific shifts in zooplankton emergence with climate change and could alter the base of aquatic food webs.© 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

In the present study we performed a microcosm experiment to assess the effects of the insecticide lufenuron on zooplankton communities exposed to increased temperature and drought in (semi-)arid regions. The experiment consisted of 3 environmental scenarios, assessed in 2 parts. Firstly, we assessed how water temperature (20 and 28 °C) affects the sensitivity and resilience of the zooplankton community to lufenuron. Secondly, we investigated the influence of drought on the structure of the zooplankton community at a high water temperature (28 °C) and evaluated its possible interaction with lufenuron. The results show that the community exposed to lufenuron at 28 °C had a faster lufenuron-related response and recovery than the community at 20 °C. The combined effects of lufenuron and temperature resulted in a synergistic effect on some taxa (Daphnia sp., Cyclopoida, and Copepoda nauplii). The tested zooplankton community had a high resilience to drought, although some particular taxa were severely affected after desiccation (Calanoida). Interactions between drought and lufenuron were not statistically significant. However, rewetting after desiccation contributed to lufenuron remobilization from sediments and resulted in a slight Cyclopoida population decline at high exposure concentrations. The study shows how environmental conditions related to global change in (semi-)arid regions may influence chemical fate and the vulnerability of zooplankton communities to chemical stress. Environ Toxicol Chem 2019;38:396-411. © 2018 SETAC.© 2018 SETAC.

Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrialcytochrome c oxidase(COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

Macroinvertebrates are widely used for monitoring freshwater ecosystems. In most monitoring programs, identifications take substantial time and expense. Methods that improve the speed, accuracy and cost-effectiveness of macroinvertebrate identification would benefit such programs. Increasingly, DNA barcodes are being used to provide accurate species-level identifications and have the potential to change how macroinvertebrates are routinely identified. Herein we discuss the need for DNA barcodes of freshwater macroinvertebrates with particular reference to Australia. We examine the use of DNA barcodes for species identification and compare DNA barcoding efforts of macroinvertebrates from Australia with those globally. We consider the role of high-throughput sequencing of DNA barcodes in freshwater bioassessment and its potential use in biosurveillance. Finally, we outline a strategy for developing a comprehensive national DNA barcode database for Australian freshwater macroinvertebrates and present the initial efforts in creating this database.