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The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet‐exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta‐carotene and beta‐cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria‐produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water. [ABSTRACT FROM AUTHOR]

Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. [ABSTRACT FROM AUTHOR]

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay. [ABSTRACT FROM AUTHOR]

Submarine groundwater discharge (SGD) can be an important pathway for chemical or biological pollutants from land to the ocean around the world. However, studies on the microbial communities associated with SGD in Southeast Asia, which has been hypothesized as SGD hotspot, remain scarce. In this study, we examined the microbial community composition with 16S rRNA gene sequencing along the hydrological continuum of an SGD site in a tropical urban area of Indonesia. Of the observed parameters in this study, salinity and temperature were the most determinant variables explaining patterns in microbial community composition. The bacterial taxon Burkholderiaceae was predominantly found in low salinity samples, including those from terrestrial groundwater and brackish pore water, while cyanobacteria of the genus Synechococcus sp. CC9902 were indicative of saline SGD and seawater samples. The composition of microbial taxa in each sample pointed to the influence of shallow terrestrial groundwater in the beach pore water, while seawater recirculation dominated the SGD sampling points situated further offshore. We identified taxa containing fecal indicators and potential pathogens at the SGD compartments; however, while a likely explanation, we could not conclude with certainty that SGD was a conduit for these bacteria. Overall, the results from this study show that microbial community analysis can highlight hydrological processes and water quality at the SGD site; thus, they could be useful for environmental policymakers to formulate water management strategies in coastal areas. Unlabelled Image • Microbial community composition can depict hydrological process at SGD site. • Salinity and temperature were the primary variables explaining microbial community composition. • Burkholderiaceae and Synechococcus represent fresh and saline SGD, respectively. • Genera containing fecal indicator and potential pathogens were found at SGD compartments. [ABSTRACT FROM AUTHOR]

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps. Biofilms on upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis was used to characterize 240 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. Bacterial biofilms consisted predominantly of Alpha-, Gamma-, and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia, and Cytophagia, whereas taxa that induce settlement of invertebrate larvae only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous, with on average only ~25% of operational taxonomic units shared between samples. Among the observed environmental parameters, pH was only weakly related to community composition (R2 ~ 1%), and was unrelated to community richness and evenness. In contrast, biofilms strongly differed between upper and lower tile surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms on mature surfaces than changes in seawater pH. [ABSTRACT FROM AUTHOR]

Seagrass meadows are a crucial component of tropical marine reef ecosystems. Seagrass plants are colonized by a multitude of epiphytic organisms that contribute to broadening the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of E nhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next-generation sequencing of 16 S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared with the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased relative sequence abundance of bacterial types associated with coral diseases at the CO2-impacted site ( F usobacteria, T halassomonas), whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E . acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios. [ABSTRACT FROM AUTHOR]

It has been hypothesized that endolithic photo-autotrophs inside the skeleton of cold-water corals may have a mutualistic relationship with the coral host positively affecting coral calcification. This study investigated the effect of endolithic photo-autotrophs on the apical septal extension of the cold-water coral Desmophyllum dianthus at Fjord Comau, southern Chile (42.41°-42.15°S, 72.5°W). The fluorescent staining agent calcein was used to document the linear apical extension of septae for a period of one and a half years between 2006 and 2007. The results showed a severe reduction in extension rates associated with the presence of endolithic photo-autotrophs. Infested individuals grew about half as fast as non-infested polyps with a median value of 1.18 μm day compared to 2.76 μm day. Contrary to the initial hypothesis, these results point toward a parasitic relationship between D. dianthus and its endolithic photo-autotrophs potentially impairing coral fitness. However, further data on physiological parameters and other aspects of the calcification process are necessary to confirm these findings. [ABSTRACT FROM AUTHOR]

Summary: Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO2 sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice‐covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom‐responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia‐Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub‐zero seawater temperatures. A co‐occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. [ABSTRACT FROM AUTHOR]

With the ever increasing demand for food, global aquaculture practices have intensified enormously over the last years. Due to this intensification, (inadequate) management strategies can cause (chronic) stress in cultured fish, hereby affecting fish performance and welfare. In Southeast Asia milkfish (Chanos chanos) is an important aquaculture species. Traditionally, milkfish are cultured in pond systems with extensive culture practices, however, as culture practices intensified, other systems such as marine cages were introduced. Here we aimed to identify potential environmental and/or commercial management related chronic stressors for milkfish kept in marine cage systems using ontogenetic (OG) scale cortisol. We quantified OG scale cortisol as indicator for chronic stress levels in juvenile milkfish (average TL between 20 and 30 cm) from four cage systems (F1-F4; culture time: 2.5–3 months) with different geographic locations and management strategies within the mariculture area (approx. 2.2 × 0.6 km) of the Guiguiwanen Channel in Bolinao (Philippines). The sites were chosen along the mariculture area, with F1 located in the mouth of the channel, F2 at the beginning, F3 mid-way, and F4 at the end of the mariculture area. Each site was sampled twice (I, II) with a time interval of 15 days between both samplings. OG scale cortisol increased significantly between sampling I and II at all four sites, indicating that milkfish at all sites experienced to a certain extent stressful conditions within their cage system. At both samplings OG scale cortisol was highest at F4, where also the highest stocking density was observed. Taking into account the existing culture conditions, OG scale cortisol levels showed that different aspects of typically applied management strategies (e.g. stocking density, feeding strategy) as well as the location might have an effect on the stress level of cultured milkfish and therefore should be considered as potentially severe stressors in milkfish mariculture. To our knowledge this is the first study quantifying OG scale cortisol as indicator for chronic stress in commercial milkfish aquaculture settings, hereby contributing to overall more sustainable aquaculture practices. • First study quantifying chronic stress (scale cortisol) in milkfish mariculture. • Scale cortisol increased significantly within 15 days. • Scale cortisol levels differed between applied culture practices (stocking density). [ABSTRACT FROM AUTHOR]

The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence. [ABSTRACT FROM AUTHOR]

Marine aquaculture is a major industry that supports the economy in many countries, including the Philippines. However, excess feeds and fish waste generated by mariculture activities contribute an immense nutrient load to the environment that can affect the underlying sediment. To better understand these impacts, we compared the physicochemical characteristics and microbial community composition of sediments taken at a fish cage and an off cage site in Bolinao, Philippines. Sediments and pore water at the fish cage site showed evidence of greater organic enrichment relative to the off cage site. Under these conditions, we found lower relative abundance of dissimilatory sulfate reductase and nitrite reductase genes, suggesting shifts in prevalent nutrient cycling processes. This is further supported by 16S rRNA gene sequencing that revealed differences in the community composition between sites. Fish cage sediments favored the growth of taxa that thrive in anaerobic, organic carbon-enriched environments, such as members of class Anaerolineae, which can potentially serve as bioindicators of eutrophication in sediments. This study demonstrates that intensive mariculture activity can cause eutrophic sediment conditions that influence microbial community structure and function. [ABSTRACT FROM AUTHOR]

Fresh submarine groundwater discharge (FSGD) is an important pathway for nutrients andother forms of pollutants from land to the ocean. Microbial communities in SGD may have aneffect on sediments and coastal waters. In this study, we examined microbial communitycomposition along the hydrological continuum of a SGD site in an urban tropical area inIndonesia. Microbial communities in coastal water were clustered according to salinity. The bacterialtaxa Novosphingobium, Flavobacterium and Burkholderiaceae were predominantly found inlow salinity samples, including those from terrestrial groundwater and brackish SGD, whilecyanobacteria of the genus Synechococcus CC9902 were indicative of saline SGD andseawater samples. The microbial community composition of each sample pointed towards amixture of shallow and deep groundwater contribution into the SGD sites, as well as a highinfluence of seawater recirculation. Ammonia oxidation and denitrification likely were thedominant biochemical processes occurring along the SGD pathway based on the taxonomiccomposition of the microbial community. The identification of fecal and potentiallypathogenic bacteria along the land-ocean interface also suggested biological contaminationfrom anthropogenic activities. Results from this study suggest that groundwater and coastal pore water were relatedbased on their microbial community composition and it supports previous findingsregarding the occurrence of fresh SGD in the area. Furthermore, microbial analyses inSGD studies can determine the quality of SGD; thus, it could be a useful tool forenvironmental policy makers in formulating water management strategies in coastal areas. [ABSTRACT FROM AUTHOR]

Among the most successful Lessepsian invaders is the symbiont-bearing benthic foraminifera Amphistegina lobifera. In its newly conquered habitat, this prolific calcifier and ecosystem engineer is exposed to environmental conditions that exceed the range of its native habitat. To disentangle which processes facilitated the invasion success of A. lobifera into the Mediterranean Sea we analyzed a ~ 1400 bp sequence fragment covering the SSU and ITS gene markers to compare the populations from its native regions and along the invasion gradient. The genetic variability was studied at four levels: intra-genomic, population, regional and geographical. We observed that the invasion is not associated with genetic differentiation, but the invasive populations show a distinct suppression of intra-genomic variability among the multiple copies of the rRNA gene. A reduced genetic diversity compared to the Indopacific is observed already in the Red Sea populations and their high dispersal potential into the Mediterranean appears consistent with a bridgehead effect resulting from the postglacial expansion from the Indian Ocean into the Red Sea. We conclude that the genetic structure of the invasive populations reflects two processes: high dispersal ability of the Red Sea source population pre-adapted to Mediterranean conditions and a likely suppression of sexual reproduction in the invader. This discovery provides a new perspective on the cost of invasion in marine protists: The success of the invasive A. lobifera in the Mediterranean Sea comes at the cost of abandonment of sexual reproduction. [ABSTRACT FROM AUTHOR]

Highlighting spatiotemporal changes occurring within mangrove habitats at the finest possible scale could contribute fundamental knowledge and data for local sustainable management. This study presents the current situation of the Pichavaram mangrove area, a coastal region of Southeast India prone to both cyclones and reduced freshwater inflow. Based on the supervised classification and visual inspection of very high spatial resolution (VHSR) satellite images provided with a pixel size of <4 m, we generated time-series maps to analyze the changes that occurred in both the natural and planted mangroves between 2003 and 2019. We achieved a high mapping accuracy (>85%), which confirmed the potential of classification techniques applied to VHSR images in capturing changes in mangroves on a very fine scale. Our diagnosis reveals variable expansion rates in plantations made by the local authorities. We also report an ongoing mangrove dieback and confirm progressive shoreline erosion along the coastline. Despite a lack of field data, VHSR images allowed for the multiscale diagnosis of the ecosystem situation, thus constituting the first fine-scale assessment of the fragile Pichavaram mangrove area upon which the coastal community is dependent. [ABSTRACT FROM AUTHOR]

Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events. [ABSTRACT FROM AUTHOR]