John K. Pearman

Microbial communities underpin nutrient cycling across aquatic ecosystems and are strongly influenced by human disturbance, yet the implication for functional redundancy remains poorly understood. Lake eutrophication is a global threat to freshwater systems, primarily driven by human activities within lakes and surrounding catchments. We hypothesize that eutrophication alters functional redundancy of key metabolic pathways in lake sediments. To test this, we conducted a national scale metagenomic study of surface sediments from 144 New Zealand lakes spanning a broad nutrient gradient. Increasing eutrophication is associated with reduced taxon-based functional redundancy, the potential of multiple species to perform the same function, indicating a narrower taxa pool supporting core functions. In contrast, abundance-based functional redundancy, characterized by the abundance of organisms that can perform the function, showed pathway-specific responses across trophic gradients. For example, nitrification and denitrification have greater abundance-based functional redundancy under higher nutrient conditions, whereas phosphorus transport shows reduced redundancy. By eroding microbial functional redundancy, eutrophication may increase susceptibility of microbial communities to environmental perturbations, potentially compromising their ability to sustain key metabolic processes. As lakes play key roles in biogeochemical cycles, the lower stability of vital biogeochemical pathways in lake sediments is likely to have an impact across ecosystems globally.

The emergence of aquatic diseases poses significant risks to ecological, social, cultural and economic values. Aquatic environments are intricately linked to human and animal health, as water can facilitate the spread and transmission of pathogens and waterborne diseases. We conducted an environmental DNA survey of 287 lakes across Aotearoa New Zealand, spanning a broad gradient of natural and human‐influenced conditions. Using a curated bacterial pathogens database, we detected 412 potentially pathogenic taxa—250 detected only in water and 162 found in both water and sediment; none were exclusive to sediment. Dominant groups included Pseudomonas , Acinetobacter , Clostridium , Afipia and Burkholderiaceae. Putative pathogens were ubiquitous in all lakes, including remote alpine sites with minimal human impact. Pathogen communities were associated with the extent of high‐productivity exotic grassland in the catchment and elevated nutrient levels, although richness was not linked to environmental drivers. Our findings show that eDNA can be a cost‐effective, broad‐spectrum screening tool that complements targeted diagnostics. The widespread occurrence of potential pathogens in lakes underscores the need for improved understanding of their ecological dynamics and the environmental conditions that promote disease outbreaks, supporting freshwater biosecurity, ecosystem management and public and animal health.

The use of Next‐Generation Sequencing (NGS) in environmental DNA (eDNA) research offers increased sensitivity in detecting rare species within vast marine ecosystems. However, conventional NGS methods often fail to accurately capture low‐frequency variants, posing risks of imprecise detections. Inspired by clinical research, innovations like SiMSen‐Seq (simple multiplexed PCR‐based barcoding of DNA for ultrasensitive mutation detection using sequencing) have emerged. SiMSen‐Seq utilizes molecular barcoding to track individual DNA templates, correcting polymerase‐induced errors and quantification biases. In this study, we adapted the SiMSen‐Seq protocol for eDNA analysis, targeting 18S rRNA metabarcoding in seawater samples to enhance marine biodiversity assessment, particularly for identifying rare non‐indigenous species (NIS). Comparative analysis against an Illumina MiSeq protocol (Illumina—DADA2) and the SiMSen‐Seq protocol with DADA2 bioinformatics (SiMSen‐Seq—DADA2) revealed that SiMSen‐Seq detected a higher number (1495) of molecular Operational Taxonomic Units (mOTUs) compared to the other two pipelines (Illumina—DADA2: 585 and SiMSen‐Seq—DADA2: 578). In terms of genera, SiMSen‐Seq detected the lowest number of genera, Illumina—DADA2 the highest number, and 45% of genera were detected across protocols. While all three protocols identified the predominant NIS, they differed in detecting rare taxa: SiMSen‐Seq uniquely detected Arenigobius bifrenatus and Pseudopolydora paucibranchiata but did not detect some others (e.g., Asterias amurensis / A. forbesi ). These findings suggest that for some species (especially Stylea plicata and Ciona savignyi ), SiMSen‐Seq could potentially be useful to detect intraspecific variability for population genetic studies, with uses in more precise ecological monitoring and effective marine conservation.

Eukaryotic microalgae are key organisms in marine environments, contributing to essential nutrient and biogeochemical cycles. Climate change is already causing shifts in the composition and diversity of microalgal assemblages, with coastal ecosystems experiencing increased pressure. Molecular techniques, such as environmental DNA (eDNA) metabarcoding, have allowed eukaryotic microalgal communities (EMCs) to be characterised more rapidly than traditional methods, addressing some data gaps. Many geographic regions still lack comprehensive baseline assessments of entire EMCs, often focusing on specific taxonomic or functional groups. In this study, we used eDNA metabarcoding of the 18S V9 gene region to characterise EMCs across a latitudinal gradient spanning five ecoregions from the South Pacific to the Ross Sea. Temperate sites had the highest alpha diversity and the most distinct EMCs across all ecoregions. Community composition showed clear latitudinal gradients, with a shift from dinoflagellate‐dominant EMCs at lower latitudes to diatom‐dominant EMCs at higher latitudes. The formation of EMCs was influenced by similar habitats/conditions (homogeneous selection) and proximity (homogenising dispersal) within ecoregions, while variable conditions (variable selection) and limited interconnectivity (dispersal limitation) were more prevalent between ecoregions. This snapshot of coastal EMC diversity across five ecoregions highlights distinct latitudinal patterns in community composition, with temperate regions showing higher diversity compared to polar areas. These findings provide a useful baseline for future monitoring and can help guide assessments of potential changes in microalgal communities due to climate change.

Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.

Regional DNA reference libraries are essential to improve the accuracy of molecular‐based biodiversity assessments, species identification and conservation. However, these libraries are often incomplete, limiting the full potential of molecular tools. In this study, we evaluated the completeness of DNA barcode reference data for annelids from the Red Sea, Arabian Gulf and Gulf of Oman and examined its implications for biodiversity assessments. A database of 2291 worldwide annelid species and 3131–4047 Molecular Operational Taxonomic Units (MOTUs) was compiled from the Barcode of Life Data System (BOLD). Two regional checklists ‐OBIS (498 species) and Wehe & Fiege (892 species)—were cross‐referenced against this database to identify coverage gaps and taxonomic inconsistencies. Only 24% and 23% of species in each checklist, respectively, had corresponding barcodes, and just three species were sampled from the region. Additionally, 43% of BOLD's Barcode Index Numbers (BINs) revealed taxonomic ambiguities. To further assess local annelid biodiversity, we analysed a metabarcoding dataset from 135 Autonomous Reef Monitoring Structures (ARMS) deployed on shallow reefs in the region. This yielded 5375 Amplicon Sequence Variants (ASVs), with 55% classified only to class or phylum level. Of the 1350 MOTUs identified, either none to just 14 species‐level identifications were found depending on the taxonomic classification method and database, 10 of which appear to be cryptic species complexes. Based on proposed MOTU/species ratios, we estimate approximately 992 annelid species in the ARMS dataset, highlighting underexplored regional diversity. Manual inspection of clustered ASVs also revealed potential pseudogene artifacts, taxonomic misidentifications up to the class level and underestimation of species matches due to discordant MOTUs. These findings underscore the urgent need to expand regional reference libraries, apply integrative taxonomy and implement refined, user‐defined MOTU clustering algorithms to improve molecular biodiversity assessments in the region.

Molecular-based techniques provide the potential for novel insights into the functioning of ecosystems, especially those that are globally rare such as coastal dune lakes. In the surface sediments of lakes, microbial communities play a vital role in biogeochemical cycling and techniques such as metagenomics can provide information on the roles play in these ecosystems. The current study aimed to investigate the taxonomic and functional composition of six coastal dune lakes on Chatham Island using sediment DNA approaches. The use of metabarcoding (16S rRNA gene) and metagenomics showed that there were distinct differences in the microbial community composition and functional potential amongst the lakes, especially in the lakes with higher salinity. Investigation of metabolic potential with metagenomics showed that the abundance of genes involved in nitrogen cycling were related to the nitrogen:phosphorus ratio while assimilatory sulfate reduction was correlated with sulfur and organic matter concentrations. Analysis showed differences in the carbon fixation strategies amongst the lakes. The lake with the highest salinity levels also had elevated levels of osmoprotectants and related transporters. The sequencing of sediment DNA enables the investigation of the composition and functioning of lake environments providing a basis for the increased understanding of the processes occurring within lakes.

Man‐made environments such as ports and marinas are gateways for many marine non‐indigenous species (mNIS) transported via shipping worldwide. These habitats are often the focus of biosecurity programs for the surveillance of mNIS, but there have been few studies investigating the distribution of biofouling communities in natural habitats and nearby artificial habitats. Here, following a DNA metabarcoding approach, we tested for differences in spatio‐temporal trends of biological pioneer communities established after one‐week colonization between a port, a marina, and coral reefs using two different matrices (PVC panels and water samples) in the central Red Sea. In addition, we aimed to investigate differences in the prevalence of mNIS between man‐made and natural habitats during the summer and winter seasons, and whether the number and patterns of mNIS differed between the port (an active historic port subjected to intense shipping traffic) and the marina (a small recently developed marina utilized by small and medium research vessels). The community structure from samples collected at the two coral reefs showed greater similarity to each other compared to that obtained from the port and the marina. A total of 29 mNIS were detected across all sites, of which 16 were reported in the Red Sea for the first time, with Jeddah port hosting 28 mNIS. By applying standardized methodological approaches, this study provides comparable data regarding the monitoring of introduced and invasive species, particularly within the data‐poor Red Sea, a major shipping corridor. This study serves as the foundation for implementing a robust and rapid baseline monitoring system to assess native biodiversity and facilitate the early detection of NIS.