Riparian ecosystems support mosaics of terrestrial and aquatic plant species that enhance regional biodiversity and provide important ecosystem services to humans. Species composition and the distribution of functional traits – traits that define species in terms of their ecological roles – within riparian plant communities are rapidly changing in response to various global change drivers. Here, we present a conceptual framework illustrating how changes in dependent wildlife communities and ecosystem processes can be predicted by examining shifts in riparian plant functional trait diversity and redundancy (overlap). Three widespread examples of altered riparian plant composition are: shifts in the dominance of deciduous and coniferous species; increases in drought‐tolerant species; and the increasing global distribution of plantation and crop species. Changes in the diversity and distribution of critical plant functional traits influence terrestrial and aquatic food webs, organic matter production and processing, nutrient cycling, water quality, and water availability. Effective conservation efforts and riparian ecosystems management require matching of plant functional trait diversity and redundancy with tolerance to environmental changes in all biomes.

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.

Despite widespread implementation of best management practices, sustainable farming is neither practical nor possible in certain locations, where protecting water quality and promoting agricultural production are likely to be incompatible. Some strategic prioritization of land-use options and acceptance of continually degraded waterbodies may be required to ensure optimization of multiple ecosystem services in catchments (also known as watersheds or drainage basins). We examine approaches to prioritization and propose catchment buffering capacity as a concept to manage the pressure-impact relationship between land use and aquatic ecosystems. Catchment buffering capacity can be considered as a continuum of biogeochemical, hydrological, and ecological catchment properties that define this relationship. Here, we outline a conceptual framework to assist prioritization: (1) establish a water-quality target, (2) quantify the gap in compliance to achieve the desired target, (3) assess catchment sensitivity to change, and (4) determine the adaptive capacity of catchment communities to reach the target.

Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host–pathogen dynamics, where the viruses may peak before, during or after the peak in their host’s abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.

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