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1. Surfactant-enhanced coagulation and flocculation improves the removal of perfluoroalkyl substances from surface water

   https://doi.org/10.1039/D4VA00093E  

   Maroli, Amith Sadananda; Zhang, Yi; Lubiantoro, Jonathan; Venkatesan, Arjun K (November 2024, Environmental Science: Advances)

   Coagulation/flocculation is a widely used water and wastewater treatment process due to its low cost, simplicity, and effectiveness. However, the process is not effective in the treatment of per- and polyfluoroalkyl substances (PFAS), the presence and treatment of which is an ongoing challenge for water providers. Here, we explore cationic surfactant-enhanced coagulation as a process modification to target the removal of PFAS in existing coagulation/flocculation systems. Batch experiments, in jar testing apparatus, were performed to assess the removal of two short-chain and two long-chain PFAS at an initial concentration of 10 µg/L with the addition of cetyltrimethylammoniumg chloride (CTAC) as the coagulant-aid. Our findings suggest that elevated coagulant dose (60 mg/L of alum or 100 mg/L of FeCl3) coupled with the addition of a cationic surfactant (1 mg/L of CTAC) significantly enhanced the removal of both short-chain (perfluorobutane sulfonate: PFBS removal to >40%) and long-chain PFAS (perfluorooctanoic acid: PFOA and perfluorooctane sulfonate: PFOS removal to >80%), with FeCl3 showing better performance than alum. Sulfonates (PFBS, PFOS) were shown to be removed more efficiently compared to carboxylates (PFBA, PFOA), presumably due to their higher hydrophobicity leading to better interactions with the flocs. Furthermore, CTAC in combination with traditionally used additives such as Powdered Activated Carbon (PAC), served as a better aid for PFAS treatment and improved the removal of PFBS, PFOA, and PFOS to >98%. This study highlights that introducing a cost-effective pre-treatment with a cationic surfactant to existing conventional treatment systems can improve the performance efficiency in treating PFAS-contaminated waters. 

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2. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

   https://doi.org/10.1038/s43705-022-00121-8  

   Yeh, Yi-Chun; Fuhrman, Jed A. (April 2022, ISME Communications)

   Abstract Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005–2018), using SSU rRNA gene sequencing from two size fractions (0.2–1 and 1–80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46–93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships. 

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3. Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S

   https://doi.org/10.1111/1462-2920.15553  

   Yeh, Yi‐Chun; McNichol, Jesse; Needham, David_M; Fichot, Erin_B; Berdjeb, Lyria; Fuhrman, Jed_A (May 2021, Environmental Microbiology)

   Summary Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance for all rRNA genes, universal primers are rarely used, due to various concerns including amplicon length variation and its effect on bioinformatic pipelines. We thus developed 16S and 18S rRNA mock communities and a bioinformatic pipeline to validate this approach. Using these mocks, we show that universal primers (515Y/926R) outperformed eukaryote‐specific V4 primers in observed versus expected abundance correlations (slope = 0.88 vs. 0.67–0.79), and mock community members with single mismatches to the primer were strongly underestimated (threefold to eightfold). Using field samples, both primers yielded similar 18S beta‐diversity patterns (Mantel test,p < 0.001) but differences in relative proportions of many rarer taxa. To test for length biases, we mixed mock communities (16S + 18S) before PCR and found a twofold underestimation of 18S sequences due to sequencing bias. Correcting for the twofold underestimation, we estimate that, in Southern California field samples (1.2–80 μm), there were averages of 35% 18S, 28% chloroplast 16S, and 37% prokaryote 16S rRNA genes. These data demonstrate the potential for universal primers to generate comprehensive microbiome profiles. 

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4. Eukaryotic algal community composition in tropical environments from solar salterns to the open sea

   https://doi.org/10.3389/fmars.2023.1131351  

   Eckmann, Charlotte A.; Eberle, Jessica S.; Wittmers, Fabian; Wilken, Susanne; Bergauer, Kristin; Poirier, Camille; Blum, Marguerite; Makareviciute-Fichtner, Kriste; Jimenez, Valeria; Bachy, Charles; et al (June 2023, Frontiers in Marine Science)

   Tropical environments with unique abiotic and biotic factors—such as salt ponds, mangroves, and coral reefs—are often in close proximity. The heterogeneity of these environments is reflected in community shifts over short distances, resulting in high biodiversity. While phytoplankton assemblages physically associated with corals, particularly their symbionts, are well studied, less is known about phytoplankton diversity across tropical aquatic environments. We assess shifts in phytoplankton community composition along inshore to offshore gradients by sequencing and analyzing 16S rRNA gene amplicons using primers targeting the V1-V2 region that capture plastids from eukaryotic phytoplankton and cyanobacteria, as well as heterotrophic bacteria. Microbial alpha diversity computed from 16S V1-V2 amplicon sequence variant (ASV) data from 282 samples collected in and around Curaçao, in the Southern Caribbean Sea, varied more within the dynamic salt ponds, salterns, and mangroves, compared to the seemingly stable above-reef, off-reef, and open sea environments. Among eukaryotic phytoplankton, stramenopiles often exhibited the highest relative abundances in mangrove, above-reef, off-reef, and open sea environments, where cyanobacteria also showed high relative abundances. Within stramenopiles, diatom amplicons dominated in salt ponds and mangroves, while dictyochophytes and pelagophytes prevailed above reefs and offshore. Green algae and cryptophytes were also present, and the former exhibited transitions following the gradient from inland to offshore. Chlorophytes and prasinophyte Class IV dominated in salt ponds, while prasinophyte Class II, including Micromonas commoda and Ostreococcus Clade OII, had the highest relative abundances of green algae in mangroves, above-reef, off-reef, and the open sea. To improve Class II prasinophyte classification, we sequenced 18S rRNA gene amplicons from the V4 region in 41 samples which were used to interrelate plastid-based results with information on uncultured prasinophyte species from prior 18S rRNA gene-based studies. This highlighted the presence of newly described Ostreococcus bengalensis and two Micromonas candidate species. Network analyses identified co-occurrence patterns between individual phytoplankton groups, including cyanobacteria, and heterotrophic bacteria. Our study reveals multiple uncultured and novel lineages within green algae and dictyochophytes in tropical marine habitats. Collectively, the algal diversity patterns and potential co-occurrence relationships observed in connection to physicochemical and spatial influences help provide a baseline against which future change can be assessed. 

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5. Organoclay flocculation as a pathway to export carbon from the sea surface

   https://doi.org/10.1038/s41598-024-79912-z  

   Sharma, Diksha; Menon, Vignesh_Gokuladas; Desai, Manasi; Niu, Danielle; Bates, Eleanor; Kandel, Annie; Zinser, Erik_R; Fields, David_M; O’Toole, George_A; Sharma, Mukul (December 2024, Scientific Reports)

   Abstract Marine microorganisms play a critical role in regulating atmospheric CO₂concentration via the biological carbon pump. Deposition of continental mineral dust on the sea surface increases carbon sequestration but the interaction between minerals and marine microorganisms is not well understood. We discovered that the interaction of clay minerals with dissolved organic matter and a γ-proteobacterium in seawater increases Transparent Exopolymer Particle (TEP) concentration, leading to organoclay floc formation. To explore this observation further, we conducted a microcosm experiment using surface seawater collected from the Spring 2023 phytoplankton bloom in the Gulf of Maine. Unfiltered (natural community) and filtered (200 μm and 3 μm) seawater was sprayed with clay (20 mg L^− 1and 60 mg L^− 1) and incubated. All clay treatments led to a tenfold increase in TEP concentration. 16S rRNA gene amplicon sequence analyses of seawater and settled organoclay flocs showed the dominance of α-proteobacteria, γ-proteobacteria, and Bacteroidota. The initial seawater phytoplankton community was dominated by dinoflagellates followed by a haptophyte (Phaeocystissp.) and diatoms. Following clay addition, dinoflagellate cell abundance declined sharply while diatom cell abundance increased. By analyzing organoclay flocs for 18S rRNA we confirmed that dinoflagellates were removed in the flocs. The clay amendment removed as much as 50% of phytoplankton organic carbon. We then explored the fate of organoclay flocs at the next trophic level by feeding clay and phytoplankton (Rhodomonas salina) toCalanus finmarchicus. The copepod ingestedR. salinaand organoclay flocs and egested denser fecal pellets with 1.8- to 3.6- fold higher sinking velocity compared to controls. Fecal pellet density enhancement could facilitate carbon sequestration through zooplankton diel vertical migration. These findings provide insights into how atmospheric dust-derived clay minerals interact with marine microorganisms to enhance the biological carbon pump, facilitating the burial of organic carbon at depths where it is less likely to exchange with the atmosphere. 

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