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1. Temporal and spatial diversity and abundance of cryptophytes in San Diego coastal waters

   https://doi.org/10.1111/jpy.13451  

   Rammel, Tristin; Nagarkar, Maitreyi; Palenik, Brian (June 2024, Journal of Phycology)

   Abstract Cryptophytes (class Cryptophyceae) are bi‐flagellated eukaryotic protists with mixed nutritional modes and cosmopolitan distribution in aquatic environments. Despite their ubiquitous presence, their molecular diversity is understudied in coastal waters. Weekly 18S rRNA gene amplicon sequencing at the Scripps Institution of Oceanography pier (La Jolla, California) in 2016 revealed 16 unique cryptophyte amplicon sequence variants (ASVs), with two dominant “clade 4” ASVs. The diversity of cryptophytes was lower than what is often seen in other phytoplankton taxa. One ASV represented a knownSynechococcusgrazer, while the other one appeared not to have cultured representatives and an unknown potential for mixotrophy. These two dominant ASVs were negatively correlated, suggesting possible niche differentiation. The cryptophyte population in nearby San Diego Bay was surveyed in 2019 and showed the increasing dominance of a different clade 4 ASV toward the back of the bay where conditions are warmer, saltier, and shallower relative to other areas in the bay. An ASV representing a potentially chromatically acclimating cryptophyte species also suggested that San Diego Bay exerts differing ecological selection pressures than nearby coastal waters. Cryptophyte andSynechococcuscell abundance at the SIO Pier from 2011 to 2017 showed that cryptophytes were consistently present and had a significant correlation withSynechococcusabundance, but no detectable seasonality. The demonstrated mixotrophy of some cryptophytes suggests that grazing on these and perhaps other bacteria is important for their ecological success. Using several assumptions, we calculated that cryptophytes could consume up to 44% (average 6%) of theSynechococcuspopulation per day. This implies that cryptophytes could significantly influenceSynechococcusabundance. 

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2. Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific

   https://doi.org/10.1002/lno.70075  

   Tucker, Sarah J; Rii, Yoshimi M; Freel, Kelle C; Kotubetey, Keliʻiahonui; Kawelo, A Hiʻilei; Winter, Kawika B; Rappé, Michael S (May 2025, Limnology and Oceanography)

   Abstract Islands in the tropical Pacific supply elevated nutrients to nearshore waters that enhance phytoplankton biomass and create hotspots of productivity in otherwise nutrient‐poor oceans. Despite the importance of these hotspots in supporting nearshore food webs, the spatial and temporal variability of phytoplankton enhancement and changes in the underlying phytoplankton communities across nearshore to open ocean systems remain poorly understood. In this study, a combination of flow cytometry, pigment analyses, 16S rRNA gene amplicons, and metagenomic sequencing provides a synoptic view of phytoplankton dynamics over a 4‐yr, near‐monthly time series across coastal Kāneʻohe Bay, Hawaiʻi, spanning from an estuarine Indigenous aquaculture system to the adjacent offshore environment. Through comparisons with measurements taken at Station ALOHA located in the oligotrophic North Pacific Subtropical Gyre, we observed a sharp and persistent transition between picocyanobacterial communities, fromSynechococcusclade II abundant in the nearshore toProchlorococcushigh‐light adapted clade II (HLII) proliferating in offshore and open ocean waters. In comparison to immediately adjacent offshore waters and the surrounding open ocean, phytoplankton biomass within Kāneʻohe Bay was dramatically elevated. Members of the phytoplankton community revealed strong seasonal patterns, while nearshore phytoplankton biomass positively correlated with wind speed, rainfall, and wind direction, and not water temperatures. These findings elucidate the spatiotemporal dynamics underlying transitions in ocean biogeochemistry and phytoplankton dynamics across estuarine to open ocean waters in the tropical Pacific and provide a foundation for quantifying deviations from baseline conditions due to ongoing climate change. 

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3. Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

   https://doi.org/10.1371/journal.pone.0298139  

   Harbeitner, Rachel C; Wittmers, Fabian; Yung, Charmaine_C M; Eckmann, Charlotte A; Hehenberger, Elisabeth; Blum, Marguerite; Needham, David M; Worden, Alexandra Z (April 2024, PLOS ONE)

   Casotti, Raffaella (Ed.)

   Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×10⁶cells ml^-1in the variable photic zone to 1.44 ± 0.25 ×10⁵and 6.71 ± 1.23 ×10⁴cells ml^-1in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a ‘copiotrophic’ module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an ‘oligotrophic’ module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4–10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300–750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed. 

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4. Sphingomonas clade and functional distribution with simulated climate change

   https://doi.org/10.1128/spectrum.00236-24  

   Sorouri, Bahareh; Scales, Nicholas C; Gaut, Brandon S; Allison, Steven D (May 2024, Microbiology Spectrum)

   Steven, Blaire (Ed.)

   ABSTRACT Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response ofSphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplantedSphingomonasclade and functional composition would correspond with site conditions and reflect theSphingomonascomposition of native communities. We extractedSphingomonassequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 majorSphingomonasclades were found at varying relative abundances along the climate gradient, and transplantedSphingomonasclade composition shifted after 18 months. Site had a significant effect (PERMANOVA;P< 0.001) on the distribution of bothSphingomonasfunctional (R²= 0.465) and clade composition (R²= 0.400), suggesting thatSphingomonascomposition depends on climate parameters. Additionally, for bothSphingomonasclade and functional composition, ordinations revealed that the transplanted communities shifted closer to the nativeSphingomonascomposition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determineSphingomonasclade and functional composition.IMPORTANCESphingomonasis the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whetherSphingomonasresponds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. WithinSphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change. 

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5. Ecological Differentiation Among Nitrous Oxide Reducers Enhances Temperature Effects on Riverine N ₂ O Emissions

   https://doi.org/10.1111/gcb.70096  

   Zhang, Sibo; Yang, Meijuan; Xia, Xinghui; Gu, Qinyuan; Gao, Qun; Wang, Junfeng; Liu, Shaoda; Li, Xiaokang; Li, Yingjie; McDowell, William H; et al (February 2025, Global Change Biology)

   ABSTRACT Nitrous oxide (N₂O) reductase, the sole natural microbial sink for N₂O, exists in two microbial clades:nosZI andnosZII. Although previous studies have explored inter‐clade ecological differentiation, the intra‐clade variations and their implications for N₂O dynamics remain understudied. This study investigated both inter‐ and intra‐clade ecological differentiation among N₂O reducers, the drivers influencing these patterns, and their effects on N₂O emissions across continental‐scale river systems. The results showed that bothnosZI andnosZII community turnovers were associated with similar key environmental factors, particularly total phosphorus (TP), but these variables explained a larger proportion of variation in thenosZI community. The influence of mean annual temperature (MAT) on community composition increased for more widespread N₂O‐reducing taxa. We identified distinct ecological clusters within each clade of N₂O reducers and observed identical ecological clustering patterns across both clades. These clusters were primarily characterized by distinct MAT regimes, coarse sediment texture as well as low TP levels, and high abundance of N₂O producers, with MAT‐related clusters constituting predominant proportions. Intra‐clade ecological differentiation was a crucial predictor of N₂O flux and reduction efficiency. Although different ecological clusters showed varying or even contrasting associations with N₂O dynamics, the shared ecological clusters across clades exhibited similar trends. Low‐MAT clusters in both thenosZI andnosZII communities were negatively correlated with denitrification‐normalized N₂O flux and the N₂O:(N₂O + N₂) ratio, whereas high‐MAT clusters showed positive correlations. This contrasting pattern likely stems from low‐MAT clusters being better adapted to eutrophic conditions and their more frequent co‐occurrence with N₂O‐producing genes. These findings advance our understanding of the distribution and ecological functions of N₂O reducers in natural ecosystems, suggesting that warming rivers may have decreased N₂O reduction efficiency and thereby amplify temperature‐driven emissions. 

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