The atmospheric partial pressure of carbon dioxide (p(CO(2))) will almost certainly be double that of pre-industrial levels by 2100 and will be considerably higher than at any time during the past few million years. The oceans are a principal sink for anthropogenic CO(2) where it is estimated to have caused a 30% increase in the concentration of H(+) in ocean surface waters since the early 1900s and may lead to a drop in seawater pH of up to 0.5 units by 2100 (refs 2, 3). Our understanding of how increased ocean acidity may affect marine ecosystems is at present very limited as almost all studies have been in vitro, short-term, rapid perturbation experiments on isolated elements of the ecosystem. Here we show the effects of acidification on benthic ecosystems at shallow coastal sites where volcanic CO(2) vents lower the pH of the water column. Along gradients of normal pH (8.1-8.2) to lowered pH (mean 7.8-7.9, minimum 7.4-7.5), typical rocky shore communities with abundant calcareous organisms shifted to communities lacking scleractinian corals with significant reductions in sea urchin and coralline algal abundance. To our knowledge, this is the first ecosystem-scale validation of predictions that these important groups of organisms are susceptible to elevated amounts of p(CO(2)). Sea-grass production was highest in an area at mean pH 7.6 (1,827 (mu)atm p(CO(2))) where coralline algal biomass was significantly reduced and gastropod shells were dissolving due to periods of carbonate sub-saturation. The species populating the vent sites comprise a suite of organisms that are resilient to naturally high concentrations of p(CO(2)) and indicate that ocean acidification may benefit highly invasive non-native algal species. Our results provide the first in situ insights into how shallow water marine communities might change when susceptible organisms are removed owing to ocean acidification.

Surface ocean pH is likely to decrease by up to 0.4 units by 2100 due to the uptake of anthropogenic CO 2 from the atmosphere. Short-term experiments have revealed that this degree of seawater acidification can alter calcification rates in certain planktonic and benthic organisms, although the effects recorded may be shock responses and the long-term ecological effects are unknown. Here, we show the response of calcareous seagrass epibionts to elevated CO 2 partial pressure in aquaria and at a volcanic vent area where seagrass habitat has been exposed to high CO 2 levels for decades. Coralline algae were the dominant contributors to calcium carbonate mass on seagrass blades at normal pH but were absent from the system at mean pH 7.7 and were dissolved in aquaria enriched with CO 2 . In the field, bryozoans were the only calcifiers present on seagrass blades at mean pH 7.7 where the total mass of epiphytic calcium carbonate was 90 per cent lower than that at pH 8.2. These findings suggest that ocean acidification may have dramatic effects on the diversity of seagrass habitats and lead to a shift in the biogeochemical cycling of both carbon and carbonate in coastal ecosystems dominated by seagrass beds.

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo’orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at ≥ 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a ≥ 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.

SignificanceCoral reef taxa produce a diverse array of molecules, some of which are important pharmaceuticals. To better understand how molecular diversity is generated on coral reefs, tandem mass spectrometry datasets of coral metabolomes were analyzed using a novel approach called meta-mass shift chemical (MeMSChem) profiling. MeMSChem profiling uses the mass differences between molecules in molecular networks to determine how molecules are related. Interestingly, the same molecules gain and lose chemical groups in different ways depending on the taxa it came from, offering a partial explanation for high molecular diversity on coral reefs.

Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While Makiola et al. Questions for Next-Generation Biomonitoring not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current-and outlook-related categories, corresponding to the organization of this paper.

The bacterial communities associated with healthy and diseased colonies of the cold-water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. Significant differences in community structure between healthy and diseased samples were discovered, as were differences in the level of disturbance to these communities at each site; this correlated with depth and sediment load. The majority of cloned sequences from healthy coral tissue affiliated with the Gammaproteobacteria. The stability of the bacterial community and dominance of specific genera found across visibly healthy colonies suggest the presence of a specific microbial community. Affiliations included a high proportion of Endozoicomonas sequences, which were most similar to sequences found in tropical corals. This genus has been found in a number of invertebrates and is suggested to have a role in coral health and in the metabolisation of dimethylsulfoniopropionate (DMSP) produced by zooxanthellae. However, screening of colonies for the presence of zooxanthellae produced a negative result. Diseased colonies showed a decrease in affiliated clones and an increase in clones related to potentially harmful/transient microorganisms but no increase in a particular pathogen. This study demonstrates that a better understanding of these bacterial communities, the factors that affect them and their role in coral health and disease will be of critical importance in predicting future threats to temperate gorgonian communities.

Successful microbial invasions are determined by a species' ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre-invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.