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Protecting plants from new pathogen incursions requires effective surveillance practices. Environmental DNA (eDNA) metabarcoding shows considerable promise for detecting invasive organisms in terrestrial and aquatic ecosystems. Metabarcoding is widely used to characterise plant microbiotas and is beginning to be applied to plant biosecurity. However, diagnostic assays for biosecurity must fit within internationally agreed frameworks. Development of new gene targets to improve taxonomic resolution, improved reference databases and simplified bioinformatics platforms are required before phytopathogenic bacteria and fungi can be routinely detected by metabarcoding. Building biodiversity maps from accumulated metabarcoding data represents an important opportunity to define organism presence/absence in New Zealand and Australia and thus to enhance biosecurity decision making. Advances in sequencing technologies and infrastructure promise the creation of eDNA biosecurity surveillance networks from substrates including soil, trapped spores and insects.

Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.

This study investigated freshwater macroinvertebrate communities in waterways contaminated by active and abandoned mining and industrial activities in order to ascertain any impact on freshwater ecosystems. We compared macroinvertebrate communities at the species, family and order levels of taxonomic resolution. We also collected water samples to compare ionic composition and metal concentrations from waste-affected and reference (non-affected) sites. In addition to assessing ecological impairment, the study also sought to determine whether the degree of sensitivity in detecting any impairment varied according to the taxonomic level of identification used. We calculated the biotic indices of EPT richness and taxonomic richness at the species, family and order levels, and performed multivariate analyses to measure differences in community structure at all three levels. We found significant differences in both biotic indices and macroinvertebrate community structure at each taxonomic level, indicating ecological impairment at waste-affected sites. We also concluded that the most appropriate taxonomic level for evaluating macroinvertebrates depends on the information required. In this study, the family level provided the clearest assessment of ecological impairment at waterways affected by mining and/or industrial wastes, and order-level data provided only a marginally less sensitive measure of this impairment.

Benthic estuarine studies are usually very time-consuming. Therefore, it is critical to optimize procedures ensuring efficiency with low cost. The present study aimed to assess the cost/benefit ratio of different sampling procedures and analyze its effect on the description of spatial pattern of benthic assemblages along an estuarine gradient. Six methodological combinations (sampling gear: van Veen grab or corer; mesh sizes: 0.5, 0.7 or 1.0 mm) were applied at 11 sampling stations. The van Veen grab captured 1,219 individuals and 59 taxa, while the corer captured 967 individuals and 53 taxa. Increasing the mesh size caused a decrease in the number of specimens retained and in the time needed to sort samples. However, no significant differences were observed among the analyzed sampling methods (sampling gear and mesh size). Spearman rank correlation coefficient showed that there was little ‘information loss’ when aggregating data to genus and family taxonomic levels. A cost/benefit index is introduced which reveals that the van Veen grab + 1.0 mm sieve + family level was the best combination to achieve the best balance between cost and precision of the results. However, choice of sampling procedure must consider estuary characteristics, target fauna, and research infrastructure, resources and objectives.

The use of lower taxonomic resolutions and ecological classifications can function as a strategy to minimize difficulties in plankton identification. To assess this issue, we evaluated the concordance of the spatial ordering of lakes in a floodplain using phytoplankton and zooplankton densities scaled at three taxonomic levels (species, genus, and family) and two exclusive ecological classifications for phytoplankton [Reynolds functional groups (RFGs) and morphology-based functional groups]. Furthermore, we evaluated the concordance of environmental variables with each taxonomic resolution/ecological classification. Procrustes and Mantel tests (simple and partial) were used for the concordance analysis. The correlations between species and higher taxonomic levels were found for phytoplankton and zooplankton. For the ecological classifications, significant r values, greater than 0.70, were obtained only for the Mantel test between species and RFGs. The relationship between species and genus and between species and family for phytoplankton can be explained by the environmental structure. For zooplankton, only species were related to environmental variables. These results indicate that it is possible to adopt a lower taxonomic resolution for identification of phytoplankton and zooplankton without a significant loss of information. However, the use of ecological classifications for phytoplankton is not recommended for this purpose.

The human gastrointestinal (GI) microbiota is important to human health and imbalances or shifts in the gut microbial community have been linked to many diseases. Most studies of the GI microbiota only capture snapshots of this dynamic community at one or a few time points. Although this is valuable in terms of providing knowledge of community composition and variability between individuals, it does not provide the foundation for going beyond descriptive studies and toward truly predictive ecological models. In order to achieve this goal, we need longitudinal data of appropriate temporal and taxonomic resolution, so that established time series analysis tools for identifying and quantifying putative interactions among community members can be used. Here, we present new analyses of existing data to illustrate the potential usefulness of this approach. We discuss challenges related to sampling and data processing, as well as analytical approaches and considerations for future studies of the GI microbiota and other complex microbial systems.

Metabarcoding is becoming an increasingly valuable alternative approach to biodiversity assessment, due to the combination of extreme sensitivity and potential for the highest taxonomic resolution in a cost- and time-effective methodology. To evaluate the capacity of metabarcoding for estuarine plankton monitoring, a comparison between the results obtained with this approach were compared with those based on traditional taxonomic analysis (microscopy). Database incompleteness, one of the main limitations of metabarcoding, was somewhat overcome by the addition of DNA sequences for local species, which increased the taxonomic assignment success from 23.7 to 50.5 %. When the communities were studied along with environmental variables, similar spatial and temporal trends of taxonomic diversity were observed for metabarcoding and microscopic studies of zooplankton, but not for phytoplankton. This is most likely attributable to the lack of representative sequences for phytoplankton species in current databases. In addition, there was high correspondence in community composition when comparing abundances estimated from metabarcoding and microscopy, suggesting semiquantitative potential for metabarcoding. Furthermore, metabarcoding allowed the detection and identification of two non-indigenous species (NIS) found in the study area at abundances hardly detectable by microscopy. Overall, our results indicate that metabarcoding is a powerful approach with excellent possibilities for use in plankton monitoring, early detection of NIS and plankton biodiversity shifts.

Due to an unfortunate turn of events, the statistical results for TS1 (F- and p-values) in Table 4 were displayed in reversed order. The correct representation of Table 4 is published here and should be treated as definitive.

Daphnia subfossils from lake sediments are useful for exploring the impacts of environmental stressors on aquatic ecosystems. Unfortunately, taxonomic resolution of Daphnia remains is coarse, as only a small portion of the animal is preserved, and so the identification of daphniid subfossils typically relies upon postabdominal claws. Daphniid claws can be assigned to one of two species complexes: D. longispina or D. pulex. Both complexes contain species with differing environmental optima, and therefore improved taxonomic resolution of subfossil daphniid claws would aid paleolimnological analyses. To identify morphological features that may be used to help differentiate between species within complexes, we used species presence/absence data from net tows to select lakes in central Ontario (Canada) containing only a single species from a particular complex, then used remains preserved in surface sediments of these lakes to isolate four Daphnia species: D. ambigua and D. mendotae from the D. longispina complex, and D. pulicaria and D. catawba from the D. pulex complex. Our analyses demonstrate that, within the D. longispina complex, postabdominal claw length (PCL) and spinule length can be used to distinguish D. mendotae from D. ambigua. In addition, within the D. pulex complex, there are differences between D. pulicaria and D. catawba in the relative lengths of the proximal and middle combs on the postabdominal claw. However, the number of stout spines on the middle comb is an unreliable character for differentiating species. Overall, our data demonstrate that greater resolution within Daphnia species complexes is possible using postabdominal claws; however, the process is arduous, and applicability will likely decrease with the number of taxa present.

The resolution achievable for chironomid identifications has increased in recent years because of significant improvements in taxonomic literature. However, high taxonomic resolution requires more training for analysts. Furthermore, with greater taxonomic resolution, misidentifications and the number of rare, poorly represented taxa in chironomid calibration datasets may increase. We assessed the effects of various levels of taxonomic resolution on the performance of chironomid-based temperature inference models (transfer functions) and temperature reconstruction. A calibration dataset consisting of chironomid assemblage and temperature data from 100 lakes was examined at four levels of taxonomic detail. The coarsest taxonomic resolution primarily represented identifications to genus or suprageneric level. At the highest level of taxonomic resolution, identification to genus level was possible for 37% of taxa, and identification below genus was possible for 60% of taxa. Transfer functions were obtained using Weighted Averaging (WA) and Weighted Averaging-Partial Least Squares (WA-PLS) regression. Cross-validated performance statistics, such as the root mean square error of prediction (RMSEP) and the coefficient of determination (r2) between inferred and observed values improved considerably from the lowest taxonomic resolution level (WA: RMSEP 1.91°C, r2 0.78; WA-PLS: RMSEP 1.59°C, r2 0.86) to the highest taxonomic resolution level (WA: RMSEP 1.66°C, r2 0.84; WA-PLS: RMSEP 1.41°C, r2 0.89). Reconstructed July air temperatures during the Lateglacial period based on fossil chironomid assemblages from Hijkermeer (The Netherlands) were similar for all levels of taxonomic resolution, except the coarsest level. At the coarsest taxonomic level, reconstruction failed to infer one of the known Lateglacial cold episodes in the record. Also, the difference in reconstructed values based on lowest and highest taxonomic resolutions exceeded sample-specific estimated standard errors of prediction in several instances. Our results suggest that chironomid-based transfer functions at the highest taxonomic resolution outperform models based on lower-resolution calibration data. However, transfer functions of intermediate taxonomic resolution produced results very similar to models based on high-resolution taxonomic data. In studies that include analysts with different levels of expertise, inference models based on intermediate taxonomic resolution, therefore, might provide an alternative to transfer functions of maximum taxonomic detail in order to ensure taxonomic consistency between calibration datasets and down-core records produced by different analysts.

Studies conducted along the southern Iberian coastline validate macrobenthic community analyses at taxonomic levels higher than that of species. Twelve studies on littoral benthic communities, carried out by the same research team, were selected spanning both a variety of sampling strategies (spatial, temporal, spatiotemporal) and substrate/habitat types (sediment, rock, algae). In order to establish differences between the results obtained at the taxonomic levels of species, family and order, similarities among stations were calculated using Spearman’s coefficient for ranges. A subset of three studies was selected to investigate possible differences in ‘best-explaining’ environmental variables with taxonomic level. The environmental variables selected at species level were the same as those found at levels of family and order. It is concluded that studies at the different levels of taxonomic resolution (species, family, order) lead to similar results both with regard to relative community distributions and the environmental variables associated with these. The importance of this result for monitoring similar benthic communities is discussed.

Several studies in semi-natural coastal lagoons in the Ria Formosa lagoonal system have been carried out. These man-made water reservoirs behave as small lagoons with one opening to the tidal channels, which may be intermittent. Because of their size, these reservoirs are ideal sites for ecological studies. Water quality and macrobenthic fauna were analysed in five water reservoirs. All reservoirs received the same incoming water through a tidal channel, but they differed in water renewal regime. Multidimensional Scaling (MDS) and Discriminant Analysis were used to evaluate the similarity among sites, stations and sampling occasions. Different levels of taxonomic resolution (family, large taxonomic groups and phylum level) were also evaluated. The separation of sites and stations became unclear using high taxonomic levels. Results from the multivariate analyses suggest a slight differentiation of the stations according to sampling occasion but a clear differentiation of the several water reservoirs. Some of the lagoons studied with low water renewal rates showed strong environmental variations. They were characterised by low diversity indexes and abundance of small-sized organisms. Other lagoons, with high water renewal rates, showed low environmental variation and well diversified and structured benthic communities. The main environmental factor that seems to affect the benthic communities was the variation in salinity between neap and spring tides, which is related with the water renewal regime. Coastal lagoons offer a protected shallow habitat, which can be highly productive. Well structured communities, controlled by k-strategists, can develop and settle in leaky lagoons, that is, lagoons with wide entrance channels and tidal currents which guarantee a good water renewal. In these lagoons, biomass can accumulate in large organisms. In contrast, lagoons with a single narrow entrance, that may be closed for long periods, are characterised by persistent physical stress and are dominated by communities of small-sized r-strategists.

Solanum L. sect. Petota Dumort., the potato and its wild relatives, contains 232 species, according to the latest taxonomic interpretation of Hawkes (1990). Section Petota is distributed in the Americas from the southwestern United States to southern Chile. This economically important group has attracted the attention of numerous taxonomists with various taxonomic philosophies. There are 531 validly published basionyms in the group, plus 67 nomina nuda or nomina dubia, and subsequent transfers to other ranks raise the number of names to 664. The taxonomy of sect. Petota has been dominated in recent years by J. G. Hawkes & J. P. Hjerting (co-workers) and C. M. Ochoa. The near simultaneous and independent publication of three recent books by these workers, treating the Bolivian species of sect. Petota, provides a novel opportunity to compare their taxonomic philosophies. Additionally, a recent independent treatment of all of the South American species by L. E. Gorbatenko provides a new interpretation of affiliations of species to series that is compared to the recent treatment of Hawkes and earlier treatments of S. M. Bukasov and D. S. Correll. These treatments differ in the placement of species into series, species boundaries, rank of infraspecific taxa, and hypotheses of hybridization. Our analysis illustrates the wide differences of taxonomic interpretation possible when independent workers treat the same material. The comparison provides insights into unresolved taxonomic questions in sect. Petota and indicates the need for a practical taxonomic resolution that will benefit plant breeders and other researchers on wild potatoes. Reasons for the discrepancies are discussed and suggestions for future research are provided.