Microviruses are single-stranded DNA bacteriophages and members of the highly diverse viral family Microviridae. Microviruses have a seemingly ubiquitous presence across animal gut microbiomes and other global environmental ecosystems. Most of the studies on microvirus diversity so far have been associated with vertebrate gut viromes. In this study, we investigate the less explored invertebrate microviruses in a freshwater ecosystem. We analysed microviruses from invertebrates in the Chironomidae, Gastropoda, Odonata, Sphaeriidae, Unionidae clades, as well as from water and benthic sediment sampled from a lake ecosystem in New Zealand. Using gene-sharing networks and an expanded framework of informal and proposed microvirus subfamilies, the 463 distinct microvirus genomes identified in this study were grouped as follows: 382 genomes in the Gokushovirinae subfamily and 47 in the Pichovirinae subfamily clade, 18 belonging to Group D, 3 belonging to the proposed Alpavirinae subfamily clade, 1 belonging to the proposed Occultatumvirinae/Tainavirinae subfamilies clade and 12 belonging to an undefined viral cluster VC 1. Inverse associations of microviruses were noted between environmental benthic sediment samples and the Odonata group, while ‘defended’ invertebrates in the Gastropoda, Sphaeriidae and Unionidae groups showed correlative associations in the principal coordinate analysis of unique microvirus genomes (each genome sharing <98% genome-wide pairwise identity with each other) across sample types. This study expands the known diversity of microviruses and highlights the diversity of these relatively poorly classified bacteriophages.

The distribution of species in relation to latitude and altitude is of fundamental interest to ecologists and is expected to attain increasing importance as the Earth’s climate continues to change. Species diversity is commonly greater at lower than higher latitudes on a global scale, and the similarity of communities frequently decreases with distance. Nevertheless, reasons for such patterns are not well understood. We investigated species richness and changes in community composition of mayflies (Ephemeroptera) over 13 degrees of latitude at 81 locations throughout New Zealand by light-trapping and the benthic sampling of streams. Mayflies were also sampled along an altitudinal gradient on a prominent inactive volcano in the east of North Island. Sampled streams were predominantly in the native forest, at a wide range of altitudes from sea level to c. 1000 m a. s. l. A total of 47 of the 59 described New Zealand mayflies were recorded during the study, along with five undescribed morphospecies. Species richness declined and the degree of dissimilarity (beta diversity) of mayfly communities increased significantly from north to south but less strongly with increasing altitude. Our results suggest that the southward decline in species richness has historical origins with the north of the country having acted as a major refuge and region of speciation during the Pleistocene. The increasing dissimilarity of the northern and southern communities may reflect an increasingly harsh climate, variable amounts of subsequent southward dispersal of northern species and, in the South Island, the presence of species which may have evolved in the newly uplifted mountains during the Miocene–Pliocene.

Artificial light at night (ALAN), which can confuse and distract insects, has been implicated as a contributor of their decline worldwide. Changes in artificial light technology has led to a widespread conversion of outdoor lighting to light-emitting diode (LED) bulbs, which are more energy efficient than older high-intensity discharge or fluorescent lamps. However, many outdoor LED lights emit a proportion of short-wavelength blue light, to which insects are commonly sensitive. The potential to reduce flying insect attraction to outdoor lights by using LEDs that emit different amounts of blue light, or by placing lights further from insect sources has not been well-studied, particularly for freshwater insects.We tested whether four blue-white LEDs that varied in their emittance of blue light intensity (3000, 4000, 5650, 6500 Kelvin [K] colour temperature) differed in their attractiveness to flying insects, particularly adult caddisflies (Trichoptera) over distances up to 100 m from a river. LEDs were deployed at a lit urban river and a predominantly unimpacted braided river in Canterbury, New Zealand. We expected a greater abundance and species richness of adult caddisflies to be attracted to LEDs that emit more blue light (cooler white LEDs [6500, 5650 K]) than those that emit less (warmer colour temperatures [3000 K, 4000 K]). We also expected the abundance and species richness of adult caddisflies in light traps to decline rapidly with increasing distance from the river, regardless of colour temperature.Moths, flies and a total of 26 caddisfly species were collected from both rivers. Significantly more caddisflies were attracted to higher than lower colour temperature LEDs. For example, a more than 1.6-fold number of caddisflies were caught by the bluer-white 6500 K LEDs than the warmer-white 3000 K LEDs. This trend was consistent across most caddisfly taxa and both rivers. The number of caddisflies attracted to LEDs significantly declined with increasing distance from the river edge for the two most abundant caddisfly families and the four most abundant species; 65% of all caddisflies were caught by 20 m from the river margin.In order to reduce the attraction of caddisflies to outdoor lights such as streetlights, our study highlights the importance of considering a low LED colour temperature (3000 K or 4000 K) or those that emit less blue light and the benefit of positioning lights further back from waterways, where possible.Our results indicate that plans for urban outdoor lighting should consider the ecological implications of different colour temperature LEDs and their spatial position as project design considerations.

Rivers suffer from multiple stressors acting simultaneously on their biota, but the consequences are poorly quantified at the global scale. We evaluated the biological condition of rivers globally, including the largest proportion of countries from the Global South published to date. We gathered macroinvertebrate- and fish-based assessments from 72,275 and 37,676 sites, respectively, from 64 study regions across six continents and 45 nations. Because assessments were based on differing methods, different systems were consolidated into a 3-class system: Good, Impaired, or Severely Impaired, following common guidelines. The proportion of sites in each class by study area was calculated and each region was assigned a Köppen-Geiger climate type, Human Footprint score (addressing landscape alterations), Human Development Index (HDI) score (addressing social welfare), % rivers with good ambient water quality, % protected freshwater key biodiversity areas; and % of forest area net change rate. We found that 50% of macroinvertebrate sites and 42% of fish sites were in Good condition, whereas 21% and 29% were Severely Impaired, respectively. The poorest biological conditions occurred in Arid and Equatorial climates and the best conditions occurred in Snow climates. Severely Impaired conditions were associated (Pearson correlation coefficient) with higher HDI scores, poorer physico-chemical water quality, and lower proportions of protected freshwater areas. Good biological conditions were associated with good water quality and increased forested areas. It is essential to implement statutory bioassessment programs in Asian, African, and South American countries, and continue them in Oceania, Europe, and North America. There is a need to invest in assessments based on fish, as there is less information globally and fish were strong indicators of degradation. Our study highlights a need to increase the extent and number of protected river catchments, preserve and restore natural forested areas in the catchments, treat wastewater discharges, and improve river connectivity.

Riparian plants provide an important source of energy for freshwater food webs through inputs of leaf litter. Planting riparian buffers with mixed species could enhance the detrital resource supply for invertebrates through varied leaf breakdown rates. To quantify leaf breakdown rates and invertebrate colonisation, we used leaves from eleven grass, shrub and tree species common along agricultural waterways in New Zealand. Breakdown of leaves immersed in a spring-fed stream differed significantly among species, being fastest for pasture grass (k = 0.0458 day(-1)) followed by broadleaf, pittosporum, willow, toetoe, poplar, gorse, Carex, eucalyptus, flax, and slowest for cabbage tree leaves (k = 0.0099 day(-1)). Invertebrate community composition did not differ between leaf species, but consumers were extremely abundant on some leaves (e.g. 51-83 Potamopyrgus snails g(-1) pasture grass), indicating coarse detrital resources were in high demand for food or habitat. These breakdown rates could inform selection of riparian plant combinations that will enhance food availability for stream communities, especially continuity of supply, thereby contributing to waterway restoration.

Freshwater biota are more comprehensive and direct indicators of biological impacts, and more meaningful to the public than water quality or physical habitat surrogates. Freshwater biotic data and the multiple biological indicators developed from them offer a much richer array of data for assessing the impacts of pollution controls than a limited set of physical or chemical measures. In recent decades, assemblage-based assessments by ecologists, environmental scientists, and water quality agencies have been employed globally for determining the condition of, and threats to, freshwater ecosystems. A key step in this advance has been the development of multimetric indices (MMIs) or indices of biotic integrity (IBIs) based on quantitative assessments of algae, macrophyte, macroinvertebrate, fish or riparian bird assemblages. In Europe, where biological assemblages are mandated for assessing freshwater ecosystem health, many indices are multimetric. However, the proliferation of MMIs globally has not always occurred through the application of rigorous study designs and monitoring protocols, nor have they always effectively incorporated functional metrics, stressor assessments, and statistical analyses. Therefore, in this review, we discuss eleven major concerns with the development and application (including logistical limitations) of multimetric indicators based on freshwater biota to encourage more rigorous and widely applicable (transferable) MMI use and implementation. Specifically, our concerns focus on reference conditions; sampling effort, methods, and season; trophic guild definition; metric comprehensiveness, options, screening and scoring; and MMI validation. MMIs could also benefit from increased attention to ecological mechanisms and metric development, to further improve our understanding of anthropogenic impacts as well as rehabilitation effects on freshwater ecosystems globally. Paying closer attention to study designs, ecological mechanisms and metric development should further improve our understanding of anthropogenic impacts and better facilitate rehabilitation of degraded freshwater ecosystems, as well as aiding in the conservation of healthy freshwater ecosystems globally.

The 2018 conservation status assessment of freshwater invertebrate taxa was the most comprehensive to date. Of the Threatened and At Risk taxa in 2018 (177 taxa), 48 were listed as Nationally Critical, 14 as Nationally Endangered, 16 as Nationally Vulnerable, 10 as Declining, and 89 as Naturally Uncommon. Most taxa were listed as either Not Threatened (315 taxa) or required more information for assessment (Data Deficient; 178 taxa). Analyses of temporal changes in conservation status since 2002 revealed that the majority of changes were due to greater understanding of taxa distributions, rather than gains or losses in population sizes or area of occupancy. Insufficient data on taxa distributions, along with a lack of autecological information, are two of the major knowledge gaps facing freshwater invertebrate conservation in New Zealand. Further impediments to conservation include (i) a lack of systematics research, (ii) a large number of species remain undiscovered and undescribed, and (iii) the status and trend of populations is unknown for most taxa. We also provide an analysis of the habitats that harbour many of the rarer taxa. Finally, we conclude by recommending a number of actions that should, collectively, help fill these knowledge gaps and address these issues.

Globally benthic invertebrate biotic indices are widely used to assess stream health. In New Zealand, the response of biotic indices to high nitrate-nitrogen (hereafter nitrate) concentrations has not been rigorously tested. We conducted a field survey of benthic invertebrates in 41 lowland intensively farmed Canterbury streams representing a wide nitrate gradient (0.4–11.3 mg/l) to determine if biotic indices respond in a predictable manner to increasing nitrate (e.g. show a subsidy stress response). Our results show commonly used biotic indices were not able to detect any effects of high nitrate. We found homogenous and tolerant benthic invertebrate communities dominated and suggest the lack of any detected effects may be because taxa sensitive to nutrients have already been lost from these systems. Therefore, we recommend caution is needed when using biotic indices in lowland agricultural streams where nutrients may be high.

The biological assessment of rivers i.e., their assessment through use of aquatic assemblages, integrates the effects of multiple-stressors on these systems over time and is essential to evaluate ecosystem condition and establish recovery measures. It has been undertaken in many countries since the 1990s, but not globally. And where national or multi-national monitoring networks have gathered large amounts of data, the poor water body classifications have not necessarily resulted in the rehabilitation of rivers. Thus, here we aimed to identify major gaps in the biological assessment and rehabilitation of rivers worldwide by focusing on the best examples in Asia, Europe, Oceania, and North, Central, and South America. Our study showed that it is not possible so far to draw a world map of the ecological quality of rivers. Biological assessment of rivers and streams is only implemented officially nation-wide and regularly in the European Union, Japan, Republic of Korea, South Africa, and the USA. In Australia, Canada, China, New Zealand, and Singapore it has been implemented officially at the state/province level (in some cases using common protocols) or in major catchments or even only once at the national level to define reference conditions (Australia). In other cases, biological monitoring is driven by a specific problem, impact assessments, water licenses, or the need to rehabilitate a river or a river section (as in Brazil, South Korea, China, Canada, Japan, Australia). In some countries monitoring programs have only been explored by research teams mostly at the catchment or local level (e.g., Brazil, Mexico, Chile, China, India, Malaysia, Thailand, Vietnam) or implemented by citizen science groups (e.g., Southern Africa, Gambia, East Africa, Australia, Brazil, Canada). The existing large-extent assessments show a striking loss of biodiversity in the last 2-3 decades in Japanese and New Zealand rivers (e.g., 42% and 70% of fish species threatened or endangered, respectively). A poor condition (below Good condition) exists in 25% of South Korean rivers, half of the European water bodies, and 44% of USA rivers, while in Australia 30% of the reaches sampled were significantly impaired in 2006. Regarding river rehabilitation, the greatest implementation has occurred in North America, Australia, Northern Europe, Japan, Singapore, and the Republic of Korea. Most rehabilitation measures have been related to improving water quality and river connectivity for fish or the improvement of riparian vegetation. The limited extent of most rehabilitation measures (i.e., not considering the entire catchment) often constrains the improvement of biological condition. Yet, many rehabilitation projects also lack pre-and/or post-monitoring of ecological condition, which prevents assessing the success and shortcomings of the recovery measures. Economic constraints are the most cited limitation for implementing monitoring programs and rehabilitation actions, followed by technical limitations, limited knowledge of the fauna and flora and their life-history traits (especially in Africa, South America and Mexico), and poor awareness by decision-makers. On the other hand, citizen involvement is recognized as key to the success and sustainability of rehabilitation projects. Thus, establishing rehabilitation needs, defining clear goals, tracking progress towards achieving them, and involving local populations and stakeholders are key recommendations for rehabilitation projects (Table 1). Large-extent and long-term monitoring programs are also essential to provide a realistic overview of the condition of rivers worldwide. Soon, the use of DNA biological samples and eDNA to investigate aquatic diversity could contribute to reducing costs and thus increase monitoring efforts and a more complete assessment of biodiversity. Finally, we propose developing transcontinental teams to elaborate and improve technical guidelines for implementing biological monitoring programs and river rehabilitation and establishing common financial and technical frameworks for managing international catchments. We also recommend providing such expert teams through the United Nations Environment Program to aid the extension of biomonitoring, bioassessment, and river rehabilitation knowledge globally.

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

Introduced aquatic macrophytes can dominate small agricultural waterways in summer and autumn becoming a significant management problem. Excessive growth can clog waterways, causing drainage issues and reducing agricultural productivity while in-stream velocities are reduced and sedimentation increased. Consequently, water managers remove them by mechanical clearance, chemical spray and cutting which can be costly and have negative impacts on in-stream habitat and ecological health. We trialled three tools to reduce macrophytes: hand-weeding, weed mat and artificial shading, at a reach-scale (50 m) and larger-scale (200-400 m). Hand-weeding reduced cover in the short-term, however macrophytes recovered to pre-treatment levels within one season. Weed mat along the banks was effective at reducing emergent macrophytes, particularly Erythranthe guttata (monkey musk) and Nasturtium microphyllum (watercress). Weed mat lasted for several growing seasons and continued to be effective. Shading over the waterway using polythene markedly reduced submerged macrophytes indicating that heavy shading by riparian plantings could reduce submerged macrophytes in the longer-term. These results indicate that in the short-term, weed mat could be used to limit sprawling emergent macrophytes. In the longer-term, weed mat used in conjunction with riparian planting could provide shading so that macrophyte cover in these small waterways could be reduced and controlled.

Through the CAREX project, we have tested a series of practical tools, and developed solutions and approaches to address aquatic weed, sediment, and nutrient management issues in agricultural waterways in lowland Canterbury.We have developed a set of steps and toolboxes, underpinned by science, which can be applied by farmers, landowners and stakeholders to facilitate rehabilitation and improve agricultural waterway health.This handout provides examples of the steps taken and tools used to restore two agricultural waterways in lowland Canterbury as part of the CAREX project. Suggested citation: Febria, C.M., Hogsden, K.L., Devlin, H.S., Collins, K.E., Goeller, B.C. Harding, J.S. and A.M. McIntosh. 2018. Restoration in Action, CAREX Toolbox Handout, University of Canterbury, Christchurch.

In Aotearoa New Zealand, agricultural land-use intensification and decline in freshwater ecosystem integrity pose complex challenges for science and society. Despite riparian management programmes across the country, there is frustration over a lack in widespread uptake, upfront financial costs, possible loss in income, obstructive legislation and delays in ecological recovery. Thus, social, economic and institutional barriers exist when implementing and assessing agricultural freshwater restoration. Partnerships are essential to overcome such barriers by identifying and promoting co-benefits that result in amplifying individual efforts among stakeholder groups into coordinated, large-scale change. Here, we describe how initial progress by a sole farming family at the Silverstream in the Canterbury region, South Island, New Zealand, was used as a catalyst for change by the Canterbury Waterway Rehabilitation Experiment, a university-led restoration research project. Partners included farmers, researchers, government, industry, treaty partners (Indigenous rights-holders) and practitioners. Local capacity and capability was strengthened with practitioner groups, schools and the wider community. With partnerships in place, co-benefits included lowered costs involved with large-scale actions (e.g., earth moving), reduced pressure on individual farmers to undertake large-scale change (e.g., increased participation and engagement), while also legitimising the social contracts for farmers, scientists, government and industry to engage in farming and freshwater management. We describe contributions and benefits generated from the project and describe iterative actions that together built trust, leveraged and aligned opportunities. These actions were scaled from a single farm to multiple catchments nationally.

Reducing excessive reactive nitrogen (N) in agricultural waterways is a major challenge for freshwater managers and landowners. Effective solutions require the use of multiple and combined N attenuation tools, targeted along small ditches and streams. We present a visual framework to guide novel applications of ‘tool stacking’ that include edge-of-field and waterway-based options targeting N delivery pathways, timing, and impacts in the receiving environment (i.e., changes in concentration or load). Implementing tools at multiple locations and scales using a ‘toolbox’ approach will better leverage key hydrological and biogeochemical processes for N attenuation (e.g., water retention, infiltration and filtering, contact with organic soils and microbes, and denitrification), in addition to enhancing ecological benefits to waterways. Our framework applies primarily to temperate or warmer climates, since cold temperatures and freeze–thaw-related processes limit biologically mediated N attenuation in cold climates. Moreover, we encourage scientists and managers to codevelop N attenuation toolboxes with farmers, since implementation will require tailored fits to local hydrological, social, and productive landscapes. Generating further knowledge around N attenuation tool stacking in different climates and landscape contexts will advance management actions to attenuate agricultural catchment N. Understanding how different tools can be best combined to target key contaminant transport pathways and create activated zones of attenuation along and within small agricultural waterways will be essential.

Understanding what makes food webs stable has long been a goal of ecologists. Topological structure and the distribution and magnitude of interaction strengths in food webs have been shown to confer important stabilizing properties. However, our understanding of how variable species interactions affect food-web structure and stability is still in its infancy. Anthropogenic stress, such as acid mine drainage, is likely to place severe limitations on the food-web structures availabe, due to changes in community composition and body mass distributions. Here, we used mechanistic models to infer food-web structure and quantify stability in streams across a gradient of acid mine drainage. Multiple food webs were iterated for each community based on species pairwise interaction probabilities, in order to incorporate the variability of realistic food-web structure. We found that food-web structure was altered systematically with a 32-fold decrease in the number of links and a twofold increase in connectance across the gradient. Stability generally increased sixfold with increasing acid mine drainage stress, regardless of how interaction strengths were estimated. However, the distribution of the stability measure, s, for some impacted communities separated into clusters of higher and lower magnitude depending on how interaction strengths were estimated. Management and restoration of impacted sites needs to consider their increased stability, as this may have important implications for the recolonization of desirable species. Furthermore, active species introductions may be required to overcome the internal ecological inertia of affected communities.

Food webs are a powerful way to represent the diversity, structure, and function of ecological systems. However, the accurate description of food webs requires significant effort in time and resources, limiting their widespread use in ecological studies. Newly published methods allow for the inference of feeding interactions using proxy variables. Here, we compare the accuracy of two recently described methods, as well as describe a composite model of the two, for the inference of feeding interactions using a large, well‐described dataset. Both niche and neutral processes are involved in determining whether or not two species will form a feeding link in communities. Three different models for determining niche constraints of feeding interactions are compared, and all three models are extended by incorporating neutral processes, based on relative abundances. The three models compared here infer niche processes through (a) phylogenetic relationships, (b) local species trait distributions (e.g., body size), and (c) a composite of phylogeny and local traits. We show that all three methods perform well at predicting individual species interactions, and that these individual predictions scale up to the network level, resulting in food web structure of inferred networks being similar to their empirical counterparts. Our results indicate that inferring food web structure using phylogenies can be an efficient way of getting summary webs with minimal data, and offers a conservative test of changes in food web structure, particularly when there is low species turnover between sites. Inferences made using traits require more data, but allows for greater understanding of the mechanisms underlying trophic interactions. A composite model of the two methods provides a framework for investigating the importance of how phylogeny, trait distributions, and relative abundances, affect species interactions, and network structure.

Nitrate pollution is a global issue threatening the health and function of many lowland freshwater ecosystems. Quantifying nitrate loads and instream attenuation associated with land use is a critical requirement for improving freshwater management. One often overlooked nitrate source in catchments is invasive N-fixing trees such as Ulex europaeus (European gorse). This study compared nitrate concentrations in conjunction with stable isotope analyses (nitrate δ 15 N and δ 18 O) to investigate the effects of catchment gorse cover on stream nitrate export relative to three other land uses. These were regenerating native forest, low-intensity (dry-stock) and high-intensity (dairying) agriculture. We tested two hypotheses: (1) gorse is a regionally significant nitrate source; (2) instream nitrate attenuation is land-use dependent. The study was conducted in 24 reaches across six small, mixed land-use coastal catchments located on Banks Peninsula, New Zealand. Our results demonstrated that gorse-dominated stream reaches had significantly higher nitrate concentrations than all other land uses. Within the gorse-dominated reaches, nitrate concentration was significantly correlated with upstream catchment gorse cover. Furthermore, nitrate oxygen and nitrogen stable isotope compositions demonstrated that elevated nitrate concentrations in gorse streams were associated with decomposition of dead gorse foliage. The isotope data revealed sub-catchment-scale land-use-specific patterns of nitrate attenuation within streams. All three anthropogenic land uses (gorse, dry stock and dairy) showed distinctly different N -cycling from native-forested reaches where nitrate was efficiently cycled with evidence for highly localised nitrification. Stable isotope data demonstrated that overall nitrate attenuation became less efficient with higher nitrate loads. Our research demonstrates the significant impact N-fixing plants have on nitrate concentrations and instream attenuation. Quantifying the effects of N-fixing plants on water quality is an important step in achieving globally significant goals of sustaining ecosystem health and (sub)catchment-scale nutrient management.