Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea

BACKGROUND

Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS

The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION

Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

Impact of persistently high sea surface temperatures on the rhizobiomes of Zostera marina in a Baltic Sea benthocosms

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass-microorganism interactions is needed to leverage knowledge on host-microbe interactions in seagrasses.

Microbial diversity in shallow-sea sediment from Tsukumo Bay, Japan, determined by 16S rRNA gene amplicon sequencing

Information about the microbiota in marine sediments is important because the microbiota and their activities in sediments affect the surrounding marine environment. To evaluate the microbial diversity, we performed 16S rRNA gene amplicon sequencing on sediment samples from 19 stations in Tsukumo Bay, the northern area of Noto Peninsula, Japan.

Bioindicator responses to extreme conditions: Insights into pH and bioavailable metals under acidic metal environments

Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA>4). Acidiferrobacter and Thermoplasmataceae were found to be pH-tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH-sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu-Zn-Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.

Structurally stable but functionally disrupted marine microbial communities under a future climate change scenario: Potential importance for nitrous oxide emissions

The blue mussel Mytilus edulis is a widespread and abundant bivalve species along the North Sea with high economic and ecological importance as an engineer species. The shell of mussels is intensively colonized by microbial organisms that can produce significant quantities of nitrous oxide (N2O), a potent greenhouse gas. To characterize the impacts of climate change on the composition, structure and functioning of microbial biofilms on the shell surface of M. edulis, we experimentally exposed them to orthogonal combinations of increased seawater temperature (20 vs. 23 °C) and decreased pH (8.0 vs. 7.7) for six weeks. We used amplicon sequencing of the 16S rRNA gene to characterize the alpha and beta diversity of microbial communities on the mussel shell. The functioning of microbial biofilms was assessed by measuring aerobic respiration and nitrogen emission rates. We did not report any significant impacts of climate change treatments on the diversity of mussel microbiomes nor on the structure of these communities. Lowered pH and increased temperature had antagonistic effects on the functioning of microbial communities with decreased aerobic respiration and N2O emission rates of microbial biofilms in acidified seawater compared to increased rates in warmer conditions. An overriding impact of acidification over warming was finally observed on N2O emissions when the two factors were combined. Although acidification and warming in combination significantly reduced N2O biofilm emissions, the promotion of aquaculture activities in coastal waters where shellfish do not normally occur at high biomass and density could nonetheless result in unwanted emissions of this greenhouse gas in a near future.

Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes

Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves.

IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.

Ocean Acidification Induces Changes in Virus-Host Relationships in Mediterranean Benthic Ecosystems

Acidified marine systems represent "natural laboratories", which provide opportunities to investigate the impacts of ocean acidification on different living components, including microbes. Here, we compared the benthic microbial response in four naturally acidified sites within the Southern Tyrrhenian Sea characterized by different acidification sources (i.e., CO₂ emissions at Ischia, mixed gases at Panarea and Basiluzzo and acidified freshwater from karst rocks at Presidiana) and pH values. We investigated prokaryotic abundance, activity and biodiversity, viral abundance and prokaryotic infections, along with the biochemical composition of the sediment organic matter. We found that, despite differences in local environmental dynamics, viral life strategies change in acidified conditions from mainly lytic to temperate lifestyles (e.g., chronic infection), also resulting in a lowered impact on prokaryotic communities, which shift towards (chemo)autotrophic assemblages, with lower organic matter consumption. Taken together, these results suggest that ocean acidification exerts a deep control on microbial benthic assemblages, with important feedbacks on ecosystem functioning.

Influence of Acidification and Warming of Seawater on Biofouling by Bacteria Grown over API 5L Steel

The acidification and warming of seawater have several impacts on marine organisms, including over microorganisms. The influence of acidification and warming of seawater on biofilms grown on API 5L steel surfaces was evaluated by sequencing the 16S ribosomal gene. For this, three microcosms were designed, the first simulating the natural marine environment (MCC), the second with a decrease in pH from 8.1 to 7.9, and an increase in temperature by 2 °C (MMS), and the third with pH in around 7.7 and an increase in temperature of 4 °C (MES). The results showed that MCC was dominated by the Gammaproteobacteria class, mainly members of the Alteromonadales Order. The second most abundant group was Alphaproteobacteria, with a predominance of Rhodobacterales and Oceanospirillales. In the MMS system there was a balance between representatives of the Gammaproteobacteria and Alphaproteobacteria classes. In MES there was an inversion in the representations of the most prevalent classes previously described in MCC. In this condition, there was a predominance of members of the Alphaproteobacteria Class, in contrast to the decrease in the abundance of Gammaproteobacteria members. These results suggest that possible future climate changes may influence the dynamics of the biofouling process in surface metals.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00925-7.

Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs

Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, dynamics, and ecology of eukaryotic heterotrophs. Here, we focus on the Labyrinthulomycetes, a fungus-like protistan group whose biomass can exceed that of the bacterioplankton in coastal waters. We examined their diversity and community structure in a weekly temperate coastal ocean time series. Their seasonal community patterns were related to temperature, insolation, dissolved inorganic carbon, fungal abundance, ammonia, chlorophyll a, pH, and other environmental variables. Similar to the bacterioplankton, annual community patterns of the Labyrinthulomycetes were dominated by a few persistent taxa with summer or winter preferences. However, like the patterns of fungi at this site, the majority of the Labyrinthulomycetes phylotypes occurred mostly as short, reoccurring, season-specific blooms. Furthermore, some specific phylotypes of Labyrinthulomycetes displayed time-lagged correlations or cooccurrences with bacterial, algal, or fungal phylotypes, suggesting their potentially multifaceted involvement in the marine food webs. Overall, this study reports niche partitioning between closely related Labyrinthulomycetes and identifies distinct ecotypes and temporal patterns compared to bacterioplankton and fungi.IMPORTANCE Increasing evidence has shown that heterotrophic microeukaryotes are an important component in global marine ecosystems, while their diversity and ecological functions remain largely unknown. Without appropriately incorporating these organisms into the food web models, our current understanding of marine microbial community ecology is incomplete, which may further hamper broader studies of biogeochemistry and climate change. This study focuses on a major group of unicellular fungus-like protists (Labyrinthulomycetes) and reveals their distinct annual community patterns relative to fungi and bacteria. Results of our observations provide new information on the community structure and ecology of this protistan group and shed light on the intricate ecological roles of unicellular heterotrophic eukaryotes in the coastal oceans.

Acidification decreases microbial community diversity in the Salish Sea, a region with naturally high pCO2

Most literature exploring the biological effects of ocean acidification (OA) has focused on macroscopic organisms and far less is known about how marine microbial communities will respond. Studies of OA and microbial community composition and diversity have examined communities from a limited number of ocean regions where the ambient pH is near or above the global average. At San Juan Island (Salish Sea), a region that experiences naturally low pH (average = 7.8), the picoplankton (cell diameter is 0.2–2μm) community was predicted to show no response to experimental acidification in a three-week mesocosm experiment. Filtered seawater mesocosms were maintained via semicontinuous culturing. Three control mesocosms were maintained at pH 8.05 and three acidified mesocosms were maintained at pH 7.60. Total bacteria was quantified daily with a flow cytometer. Microbial communities were sampled every two days via filtration followed by DNA extraction, 16S rRNA amplification, and MiSeq sequencing. There was no significant difference in total bacteria between pH treatments throughout the experiment. Acidification significantly reduced Shannon’s diversity over time. During the final week of the experiment, acidification resulted in a significant decrease in Shannon’s diversity, Faith’s phylogenetic distance, and Pielous’s Evenness. ANCOM results revealed four bacterial ASVs (amplicon sequence variants), in families Flavobaceriaceae and Hyphomonadaceae that significantly decreased in relative frequency under acidification and two bacterial ASVs, in families Flavobacteriaceae and Alteromonadaceae, that significantly increased under acidification. This is the first OA study on the microbial community of the Salish Sea, a nutrient rich, low pH region, and the first of its kind to report a decrease in both picoplankton richness and evenness with acidification. These findings demonstrate that marine microbial communities that naturally experience acidic conditions are still sensitive to acidification.

Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation

In this study, the shoreline of Lebanon, which extends over 225 km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

Impacts of ocean acidification on intertidal benthic foraminiferal growth and calcification

Foraminifera are expected to be particularly susceptible to future changes in ocean carbonate chemistry as a function of increased atmospheric CO₂. Studies in an experimental recirculating seawater system were performed with a dominant benthic foraminiferal species collected from intertidal mudflats. We investigated the experimental impacts of ocean acidification on survival, growth/calcification, morphology and the biometric features of a calcareous species Elphidium williamsoni. Foraminifera were exposed for 6 weeks to four different pH treatments that replicated future scenarios of a high CO₂ atmosphere resulting in lower seawater pH. Results revealed that declining seawater pH caused a decline in foraminiferal survival rate and growth/calcification (mainly through test weight reduction). Scanning electron microscopy image analysis of live specimens at the end of the experimental period show changes in foraminiferal morphology with clear signs of corrosion and cracking on the test surface, septal bridges, sutures and feeding structures of specimens exposed to the lowest pH conditions. These findings suggest that the morphological changes observed in shell feeding structures may serve to alter: (1) foraminiferal feeding efficiency and their long-term ecological competitiveness, (2) the energy transferred within the benthic food web with a subsequent shift in benthic community structures and (3) carbon cycling and total CaCO₃ production, both highly significant processes in coastal waters. These experimental results open-up the possibility of modelling future impacts of ocean acidification on both calcification and dissolution in benthic foraminifera within mid-latitude intertidal environments, with potential implications for understanding the changing marine carbon cycle.

Effect of Acidic Industrial Effluent Release on Microbial Diversity and Trace Metal Dynamics During Resuspension of Coastal Sediment

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2–3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum Bacteroidetes. Members of the order Saprospirales were enriched from sediment in natural seawater (initial pH > 8), while the family Flavobacteriaceae was favored by acidified seawater (initial pH < 8). Some Flavobacteriaceae members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems.

Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments

Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.

Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency

Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO₂ through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO₂ may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO₂ conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO₂ on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO₂. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food.

In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.